Biochemical Functions

Proteins are organic compounds made of amino acids arranged in a linear chain and
joined together by peptide bonds between the carboxyl and amino groups of adjacent
amino acid residues. The sequence of amino acids in a protein is defined by the sequence
of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20
standard amino acids, however in certain organisms the genetic code can include
selenocysteine - and in certain archaea - pyrrolysine. The residues in a protein are often
observed to be chemically modified by post-translational modification, which can happen
either before the protein is used in the cell, or as part of control mechanisms. Proteins can
also work together to achieve a particular function, and they often associate to form
stable complexes.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins
are essential parts of organisms and participate in every process within cells. Many
proteins are enzymes that catalyze biochemical reactions and are vital to metabolism.
Proteins also have structural or mechanical functions, such as actin and myosin in muscle
and the proteins in the cytoskeleton, which form a system of scaffolding that maintains
cell shape. Other proteins are important in cell signaling, immune responses, cell
adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals
cannot synthesize all the amino acids they need and must obtain essential amino acids
from food. Through the process of digestion, animals break down ingested protein into
free amino acids that are then used in metabolism

Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and
the larger eukaryotic genomes are predicted to be completely sequenced within the next
decade. In all genomes sequenced to date, a large portion of these organisms’ predicted
protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or
cellular functions. Three-dimensional structures of these proteins may suggest
biochemical or biophysical functions. Here we report the crystal structure of one such
protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii , at 1.7-Å
resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an
ATP-mediated molecular switch, which we confirm by biochemical experiments.
Furthermore, the structure reveals different ATP binding motifs that are shared among
many homologous hypothetical proteins in this family. This result indicates that
structure-based assignment of molecular function is a viable approach for the large-scale
biochemical assignment of proteins and for discovering new motifs, a basic premise of
structural genomics.

• Glycolysis

• Χιτριχ αχιδ χψχλε

 • Ελεχτρον τρανσπορτ

• Πηοτοσψντηεσισ

• Βιοσψντηεσισ οφ χαρβοηψδρατε ανδ γλυχονεογενεσισ

• Μεταβολισµ οφ οτηερ χαρβοηψδρατε

• Λιπιδ βιοσψντηεσισ ανδ µεταβολισµ

• Πηοσπηορψλατιον

• Βιοσψντηεσισ ανδ µεταβολισµ οφ αµινο αχιδ, νυχλειχ αχιδ, ανδ ρελατεδ

µολεχυλεσ

• Χοντρολ οφ ηορµονεσ

• Γενε ανδ χηροµοσοµε

• ∆ΝΑ µεταβολισµ

• ΡΝΑ µεταβολισµ

• Προτειν µεταβολισµ

• Χοντρολ οφ γενε εξπρεσσιον

• Γλοβιν προτειν

Οτηερσ

Glycolysis
• Alcohol dehydrogenase class IV sigma chain [Homo sapiens (human)]:
PDB:1D1S

• Triosephosphate isomerase [Gallus gallus (chicken)]: PDB:1TPH

• Pyruvate dehydrogenase complex [Geobacillus stearothermophilus

(bacteria,thermophile)]: PDB:1W85

Citric acid cycle

• ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17

• ATP synthase (F1 portion) [Bos taurus]: PDB:1E79

• Flavoenzyme Ero1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RP4

Electron transport
• Aldehyde ferredoxin oxidoreductase (AOR) [Pyrococcus furiosus (thermophile,
archaea)]: PDB:1AOR

• ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17

• ATP synthase (F1 portion) [Bos taurus]: PDB:1E79

• Cytochrome C oxidase (before oxidized, with carbon monoxide) [Bos taurus]:

PDB:1OCO

• Flavoenzyme Ero1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RP4

• Cytochrome C oxidase (after oxidized, with peroxide ion) [Bos taurus]:

PDB:2OCC

Cell signaling and ligand binding

A mouse antibody against cholera that binds a carbohydrate antigen.
Many proteins are involved in the process of cell signaling and signal transduction. Some
proteins, such as insulin, are extracellular proteins that transmit a signal from the cell in
which they were synthesized to other cells in distant tissues. Others are membrane
proteins that act as receptors whose main function is to bind a signaling molecule and
induce a biochemical response in the cell. Many receptors have a binding site exposed on
the cell surface and an effector domain within the cell, which may have enzymatic
activity or may undergo a conformational change detected by other proteins within the
cell.
Antibodies are protein components of adaptive immune system whose main function is to
bind antigens, or foreign substances in the body, and target them for destruction.
Antibodies can be secreted into the extracellular environment or anchored in the
membranes of specialized B cells known as plasma cells. Whereas enzymes are limited in
their binding affinity for their substrates by the necessity of conducting their reaction,
antibodies have no such constraints. An antibody's binding affinity to its target is
extraordinarily high.
Many ligand transport proteins bind particular small biomolecules and transport them to
other locations in the body of a multicellular organism. These proteins must have a high
binding affinity when their ligand is present in high concentrations, but must also release
the ligand when it is present at low concentrations in the target tissues. The canonical
example of a ligand-binding protein is haemoglobin, which transports oxygen from the
lungs to other organs and tissues in all vertebrates and has close homologs in every
biological kingdom. Lectins are sugar-binding proteins which are highly specific for their
sugar moieties. Lectins typically play a role in biological recognition phenomena
involving cells and proteins. Receptors and hormones are highly specific binding
proteins.
Transmembrane proteins can also serve as ligand transport proteins that alter the
permeability of the cell membrane to small molecules and ions. The membrane alone has
a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane
proteins contain internal channels that allow such molecules to enter and exit the cell.
Many ion channel proteins are specialized to select for only a particular ion; for example,
potassium and sodium channels often discriminate for only one of the two ions.

Photosynthesis
• ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17

• ATP synthase (F1 portion) [Bos taurus]: PDB:1E79

• Photosystem II [Synechococcus elongatus (cyanobacteria)]: PDB:1FE1

• Photosystem I P700 chlorophyll a apoprotein A1 [Synechococcus elongatus

(cyanobacteria)]: PDB:1JB0

• Light harvesting protein B-800/850 [Rhodopseudomonas acidophila (phototrophic

bacteria)]: PDB:1KZU

• Photosynthetic Reaction Center [Rhodopseudomonas viridis (phototrophic

bacteria)]: PDB:1PRC

• light-harvesting complex of phtotosystem II (LHC-II) [Spinacia oleracea

(Spinach) ]: PDB:1RWT

• Cyanobacterial phtosystem II [Thermosynechococcus elongatus (cyanobacteria)]:

PDB:1S5L

• Cytochrome b6f complex [Mastigocladus laminosus (cyanobacteria)]: PDB:1VF5

Biosynthesis of carbohydrate and gluconeogenesis

Metabolism of other carbohydrate
• Cellulase CelC [Clostridium thermocellum (bacteria, thermophile)]: PDB:1CEO

• Alpha-amylase [Homo sapiens (human)]: PDB:1SMD

• Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT

• Peptideglycan L,D-transpeptidase [Enterococcus faecium]: PDB:1ZAT

• Ca2+/calmodulin-dependent protein kinase-II (CaMKII) [Caenorhabditis elegans

(nematode)]: PDB:2BDW
Lipid biosynthesis and metabolism
• Lipase [Homo sapiens (human)]: PDB:1HLG

• Phospholipase A2 [Homo sapiens (human)]: PDB:1POD

• Lanosterol synthase [Homo sapiens (human)]: PDB:1W6J

• Acetyl-coenzyme A carboxylase [Saccharomyces cerevisiae (Baker's yeast)]:

PDB:1W93

• 3-ketoacyl-coA thiolase 2 [Arabidopsis thaliana (mouse-ear cress)]: PDB:2C7Y

• Cholesterol ester transfer protein [Human]: PDB:2OBD

• β2 adrenergic receptor [Human]: PDB:2RH1

The best-known role of proteins in the cell is as enzymes, which catalyze chemical
reactions. Enzymes are usually highly specific and accelerate only one or a few chemical
reactions. Enzymes carry out most of the reactions involved in metabolism, as well as
manipulating DNA in processes such as DNA replication, DNA repair, and transcription.
Some enzymes act on other proteins to add or remove chemical groups in a process
known as post-translational modification. About 4,000 reactions are known to be
catalyzed by enzymes. The rate acceleration conferred by enzymatic catalysis is often
enormous - as much as 1017-fold increase in rate over the uncatalyzed reaction in the case
of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the
enzyme).
The molecules bound and acted upon by enzymes are called substrates. Although
enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the
residues that come in contact with the substrate, and an even smaller fraction - 3-4
residues on average - that are directly involved in catalysis.The region of the enzyme that
binds the substrate and contains the catalytic residues is known as the active site

Phosphorylation
• Protein kinase CheY/CheA complex (bacteria chemotaxis) [Escherichia coli
(bacteria)]: PDB:1A0O

• DBL homology domain from beta-PIX [Homo sapiens (human)]: PDB:1BY1

• Mitogen-activated protein kinase 1 [Rattus norvegicus (rat)]: PDB:1ERK

• Cyclin A/cyclin-dependent kinase 2(CDK-2) complex [Homo sapiens (human)]:

PDB:1FIN

• Cdc42 / Cdc42GAP complex [Homo sapiens (human)]: PDB:1GRN

 • Peutz-Jeghers cancer syndrome (PSJ) related protein Mo25 Alpha in Complex
with the C-Terminus of the Pseudo Kinase STE-20 Related Adaptor [Homo
sapiens (human)]: PDB:1UPK

• SR (serine/arginine rich) protein kinase SRPK1 / peptide complex [Homo sapiens

(human)]: PDB:1WBP

• SWIRM domain of chromosomal DNA binding protein ADA2α [Human]:

PDB:2AQE

• Ca2+/calmodulin-dependent protein kinase-II (CaMKII) [Caenorhabditis elegans

(nematode)]: PDB:2BDW

• Epac, Guanine-nucleotide-exchange factor for GTP-binding protein Rap [Mus

musculus (house mouse)]: PDB:2BYV

• Lipoate protein ligase A (LplA) [Thermoplasma acidophilum

(archaea,thermophile)]: PDB:2C8M

• Protein phosphatase 2A (heterotrimeric holoenzyme) [Homo sapiens (human) ]:

PDB:2IAE

• Protein Phosphatase 2A [Homo sapiens (human)]: PDB:2NPP

• Protein Phosphatase 2A with C-terminus truncated catalytic subunit [Homo

sapiens (human)]: PDB:2NYM

• TGF-β3 - TGF-β receptor complex [Human]: PDB:2PJY

• Protein kinase A [Mouse]: PDB:2QCS

• Tyrosine-protein kinase c-Src/AMP-PNP complex [Homo sapiens (human)]:

PDB:2SRC

Biosynthesis and metabolism of amino acid, nucleic

acid, and related molecules
• D-amino acid aminotransferase [Thermophilic bacterium PS3]: PDB:1DAA

• Ribonuclease A / ribonuclease inhibitor (RI) complex [Bos taurus]: PDB:1DFJ

• Catalytic antibody 1F7 (chorismate mutase activity) [Mus musculus (house

mouse)]: PDB:1FIG

• Arginases I and nor-NOHA complex [Rattus norvegicus (rat)]: PDB:1HQH

• 3-isopropylmalate dehydrogenase [Thermus thermophilus (bacteria,thermophile)]:

PDB:1IPD
 • Ribonucleoside-diphosphate reductase 1 [Escherichia coli (bacteria)]:
PDB:1MXR

• Amidohydrolase Tm0936 [Thermotoga maritima]: PDB:1P1M

• Acetolactate synthase [Arabidopsis thaliana (thale cress, or mouse-ear cress)]:

PDB:1YBH

• mRNA decapping enzyme Dcp2p [Schizosaccharomyces pombe]: PDB:2A6T

• Epac, Guanine-nucleotide-exchange factor for GTP-binding protein Rap [Mus

musculus (house mouse)]: PDB:2BYV

• Cbf5-Nop10-Gar1 complex (part of the pseudouridylation enzyme) [Pyrococcus

furiosus (thermophile, archaea)]: PDB:2EY4

• B subunit of UvrABC (DNA repair system) complexed with a DNA strand

[Bacillus caldotenax (bacteria)]: PDB:2FDC

• Nicotinamide phosphoribosyl transferase (NMPRTase) [Human]: PDB:2GVG

• Nicotinamide phosphoribosyl transferase (NMPRTase): Complex with FK866

[Human]: PDB:2GVJ

• Glutamate decarboxylase 1(GAD) / cofactor PLP complexed [human]:

PDB:2OKJ

• Nitrogenase molybdenum iron protein [Azotobacter vinelandii (aerobic nitrogen-

fixing bacteria)]: PDB:3MIN

Control of hormones
• Androgen receptor [Homo sapiens (human)]:

• Interleukin-1 beta [Homo sapiens (human)]: PDB:1I1B

• Interleukin-1beta converting enzyme(ICE)/inhibitor peptide complex [Homo

sapiens (human)]: PDB:1IBC

• Interleukin-18 [Homo sapiens (human)]: PDB:1J0S

• Acetylcholine Receptor [Torpedo californica]: PDB:1OED

• Molting hormone receptor (EcR/USP) / steroidal ligand ponA complex [Heliothis

virescens (noctuid moth)]: PDB:1R1K

• Lanosterol synthase [Homo sapiens (human)]: PDB:1W6J

• Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT

 • Human Placental Lactogen [Homo sapiens (human)]: PDB:1Z7C

• insulin-degrading enzyme in complex with insulin B chain [Homo sapiens

(human)]: PDB:2G54

• Ancestral corticoid receptor / aldosterone complex [unidentified]: PDB:2Q1H

• Growth hormon complexed with its receptor [Homo sapiens (human)]:

PDB:3HHR

• Insulin [Sus scrofa (pig)]: PDB:4INS

Gene and chromosome

• deoxyribonucleic acid (DNA) [N/A (synthetic)]: PDB:1BNA

• Human Telomeric DNA (monomer with 22 bases) [Homo sapiens (human)]:

PDB:1KF1

• Ribonucleoside-diphosphate reductase 1 [Escherichia coli (bacteria)]:

PDB:1MXR

• SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 [Danio rerio

(zebra fish)]: PDB:1Z3I

• Nucleosome (nucleosome core / DNA complex) [Xenopus laevis (African clawed

frog)]: PDB:1ZBB

• BPTF PHD finger-linker-bromodomain bound to H3K4me3 [Homo sapiens

(human)]: PDB:2F6J

• Histon modification protein WRD5 / histon subunit H3 complex [Human]:

PDB:2H13

• CIA-histone H3-H4 complex [Homo sapiens (human)]: PDB:2IO5

• Ftsk(C-domain) hexmer [Bacteria(Pseudomonas-aeruginosa)]: PDB:2IUU

DNA metabolism
• Restriction endonuclease BamHI/DNA complex [Bacillus amyloliquefaciens
(bacteria)]: PDB:1BHM

• deoxyribonucleic acid (DNA) [N/A (synthetic)]: PDB:1BNA

• Intein PI-SceI homing endonuclease [Saccharomyces cerevisiae (Baker's yeast)]:

PDB:1DFA
• human 8-oxoguanine glycosylase (hOGG1) bound to DNA [Homo sapiens
(human)]: PDB:1EBM

• Replication terminator protein(Tus)/DNA complex [Escherichia coli]: PDB:1ECR

• DNA repair enzyme [Homo sapiens (human)]: PDB:1EWN

• Gamma delta resolvase / DNA complex [Escherichia coli]: PDB:1GDT

• Human Telomeric DNA (monomer with 22 bases) [Homo sapiens (human)]:

PDB:1KF1

• Intein PI-SceI homing endonuclease / DNA complex [Saccharomyces cerevisiae

(Baker's yeast)]: PDB:1LWS

• Bifunctional DNA primase-polymerase [Sulfolobus islandicus (archaea)]:

PDB:1RNI

• MutY adenine DNA glycosylase/DNA lesion in A*oxoG pair complex [Bacillus

stearothermophilus (bacteria)]: PDB:1RRQ

• Restriction enzyme EcoRV/DNA complex (before DNA cleave, without Mg2+

ion) [Escherichia coli (bacteria)]: PDB:1RVA

• Restriction enzyme EcoRV / DNA Complex (after DNA cleaved, with Mg2+ ion)
[Escherichia coli (bacteria)]: PDB:1RVC

• SV40 large tumor antigen [Simian virus 40 (virus)]: PDB:1SVM

• clamp loader (RFC) bound to the DNA sliding clamp (PCNA) [Saccharomyces
cerevisiae (Baker's yeast)]: PDB:1SXJ

• TAQ polymerase (DNA synthesizer)/DNA complex [Thermus aquaticus

(bacteria)]: PDB:1TAU

• Deoxyribodipyrimidine photolyase/DNA complex [Synechococcus sp. PCC 6301

(cyanobacteria)]: PDB:1TEZ

• DNA repairing complex RecBCD [Escherichia coli (bacteria)]: PDB:1W36

• SUMO1-conjugated thymine DNA glycosylase [Homo sapiens (human)]:

PDB:1WYW

• Type I restriction-modification enzyme, specificity subunit [Methanococcus

jannaschii (archaea)]: PDB:1YF2

• SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 [Danio rerio

(zebra fish)]: PDB:1Z3I
 • Telomere repeat-binding protein [Arabidopsis thaliana (thale cress)]: PDB:2AJE

• Pentapeptide repeat protein for resistance against quinolones, MfpA

[Mycobacterium tuberculosis (bacteria)]: PDB:2BM4

• Transcription-repair coupling factor [Escherichia coli]: PDB:2EYQ

• Restriction enzyme Ecl18kI-DNA complex [Enterobacter cloaceae]: PDB:2FQZ

• Papillomavirus E1 hexameric helicase [Bovine papillomavirus type I]:

PDB:2GXA

• E. coli DNA polymerase III, beta-subunit [Escherichia coli (bacteria)]:

PDB:2POL

• Reverse transcriptase [Human Immunodeficiency Virus type 1]: PDB:3HVT

RNA metabolism
• Sex-lethal (Sxl) protein/RNA complex [Drosophila melanogaster (fruit fly)]:
PDB:1B7F

• Catabolite gene activator protein complex with DNA [Escherichia coli (bacteria)]:
PDB:1CGP

• Ribosome recycling factor (RRF) [Thermotoga maritima (thermophile, bacteria)]:

PDB:1DD5

• Mammalian Poly(A) Polymerase [Bos taurus (bovine)]: PDB:1F5A

• Transcription factor c-Fos-c-Jun / DNA complex [Homo sapiens (Human)]:

PDB:1FOS

• DNA-DIRECTED RNA POLYMERASE II [Saccharomyces cerevisiae (Baker's

yeast)]: PDB:1I6H

• Hypothetical RNA 2'-O-ribose methyltransferase (RrmA) [Thermus thermophilus

(bacteria)]: PDB:1IPA

• 5-methyluridine methyltransferase TrmA [Escherichia coli]: PDB:3BT7

• RNA hammerhead ribozyme [Mus musculus (house mouse)]: PDB:1MME

• mRNA decapping enzyme Dcp1p [Saccharomyces cerevisiae (Baker's yeast)]:

PDB:1Q67

• Transcription factor IIB / RNA polymerase II complex [Saccharomyces cerevisiae

(Baker's yeast)]: PDB:1R5U
• RNA polymerase II-transcribing complex in the post-translocation state
[Saccharomyces cerevisiae (Baker's yeast)]: PDB:1SFO

• Argonaute (RNA interference protein) [Pyrococcus furiosus DSM 3638 (archaea,

thermophile)]: PDB:1U04

• Group I self-splicing intron in complex with its exons [Homo sapiens (Human)]:
PDB:1U6B

• CCA-adding enzyme [Archaeoglobus fulgidus (Archaea)]: PDB:1UET

• Fungal galectin CGL2 [Coprinopsis cinerea (Inky cap fungus)]: PDB:1UL9

• Tryptophanyl-tRNA synthetase [Homo sapiens (human)]: PDB:1ULH

• Phage twort group I ribozyme (self-splicing intron) complexed with it's product
[Bacteriophage Twort (virus)]: PDB:1Y0Q

• Transcriptional activator GCN4/DNA complex [Saccharomyces cerevisiae

(Baker's yeast)]: PDB:1YSA

• Human Argonaute2 to form minimal RISC [Pyrococcus furiosus (archaea)]:

PDB:1Z25

• The zinc finger (DNA binding site) of transcription factor Zif268/DNA complex
[Mus musculus (house mouse)]: PDB:1ZAA

• Archaeal Rrp4 Exosomes [Archaeoglobus fulgidus (archaea)]: PDB:2BA0

• A Piwi domain (part of RNAi protein argonaut)/siRNA-like duplex complex

[Archaeoglobus fulgidus]: PDB:2BGG

• RNase III (D44N) complexed with double-stranded RNA [Aquifex aeolicus

(bacteria,thermophile)]: PDB:2EZ6

• Dicer [Giardia intestinalis (flagellate)]: PDB:2FFL

• RNase Z / tRNA(Thr) complex [Bacillus subtilis]: PDB:2FK6

• Transcription regulating factor CSL-Notch-Mastermind/DNA complex

[Caenorhabditis elegans (nematode)]: PDB:2FO1

• Mitochondorial RNA binding protein (MRP1/MRP2) - guideRNA complex

[Trypanosoma brucei (Africa sleeping sickness parasitic protozoa)]: PDB:2GJE

• RNA ligase Rnl2 complexed with AMP [Bacteriophage T4 (virus)]: PDB:2HVQ

• H/ACA box RNP [Pyrococcus furiosus (archaea,thermophile)]: PDB:2HVY

 • Retinoic acid receptor-gamma / retinoic acid complex [Homo sapiens (human)]:
PDB:2LBD

Protein metabolism
• Hepatitis C virus NS3 protease [Hepatitis C virus(HCV)]: PDB:1A1R

• Chaperonin (GroEL-GroES) / ADP complex [Escherichia coli (bacteria)]:

PDB:1AON

• Ubiquitin ligase(E6AP)/ubiquitin-conjugating enzyme(UbcH7) complex [Homo

sapiens (human)]: PDB:1C4Z

• Ribosome recycling factor (RRF) [Thermotoga maritima (thermophile, bacteria)]:

PDB:1DD5

• Eukaryotic protein Release Factor eRF1 [Homo sapiens (human)]: PDB:1DT9

• Thiol:disulfide interchange protein DsbC [Escherichia coli (bacteria)]: PDB:1EEJ

• tRNA (phenylalanine) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1EHZ

• Complex of (Arginyl-tRNA synthetase/tRNA/Arginine) [Saccharomyces

cerevisiae (Baker's yeast)]: PDB:1F7U

• Heat shock protein HSP33 [Escherichia coli (bacteria)]: PDB:1HW7

• Ubiquitin ligase complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1LDD

• 20S proteasome [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RYP

• Trypsin [Homo sapiens (human)]: PDB:1TRN

• SARS coronavirus main proteinase [Severe acute respiratory syndrome

coronavirus(SARS-CoV)]: PDB:1UJ1

• Tryptophanyl-tRNA synthetase [Homo sapiens (human)]: PDB:1ULH

• Ribosomal chaperon trigger factor complexed with 50S ribosome [Escherichia

coli (bacteria)]: PDB:1W26

• Simian virus 5 V protien complexed with human DDB1 [Simian virus 5 / Homo
sapiens (human)]: PDB:2B5L

• CmcI, cephamycin biosynthesis-related enzyme [Streptomyces clavuligerus]:

PDB:2BR4

• Lipase (LipA) / lipase chaperon (Lif) complex [Burkholderia glumae (bacteria)]:

PDB:2ES4
 • beta-secretase 2 (BACE2) [Homo sapiens (human)]: PDB:2EWY

• insulin-degrading enzyme in complex with insulin B chain [Homo sapiens

(human)]: PDB:2G54

• Thiamine pyrophosphate-specific riboswitch [Escherichia coli (bacteria)]:

PDB:2GDI

• NS2-3 protease [Hepatitis C virus(HCV)]: PDB:2HD0

• Trapped UBL activation complex [Human]: PDB:2NVU

• Gamma-B crystallin (eye lens componets protein) [Bos taurus (Bovine)]:

PDB:4GCR

• Alpha-thrombin/hirudin complex [Homo sapiens (human)/Hirudo medicinalis

(leech)]: PDB:4HTC

• HIV-1 PROTEASE [Human Immunodeficiency Virus type 1]: PDB:7HVP

• Papain [Carica papaya (Papaya)]: PDB:9PAP

Control of gene expression

• Trp RNA-Binding Attenuation Protein/RNA complex [Bacillus
stearothermophilus (bacteria)]: PDB:1C9S

• Catabolite gene activator protein complex with DNA [Escherichia coli (bacteria)]:
PDB:1CGP

• Met repressor-operator complex [Escherichia coli (bacteria)]: PDB:1CMA

• Ribonuclease A / ribonuclease inhibitor (RI) complex [Bos taurus]: PDB:1DFJ

• Androgen receptor [Homo sapiens (human)]: PDB:1E3G

• Bleomycin hydrolase Gal6 [Saccharomyces cerevisiae (Baker's yeast)]:

PDB:1GCB

• Oct4/Sox2/DNA complex [Mouse, Human]: PDB:1GT0

• lac repressor [Escherichia coli (bacteria)]: PDB:1LBI

• YibK methyltransferase (knot protein) complexed with an inhibitor (AdoHcy)

[Haemophilus influenzae (bacteria)]: PDB:1MXI

• Transcription factor IIB / RNA polymerase II complex [Saccharomyces cerevisiae

(Baker's yeast)]: PDB:1R5U
• Tryptophan operon repressor/operator complex [Escherichia coli (bacteria)]:
PDB:1TRO

• Argonaute (RNA interference protein) [Pyrococcus furiosus DSM 3638 (archaea,

thermophile)]: PDB:1U04

• Trp RNA-Binding Attenuation Protein in Complex with L-Tryptophan [Bacillus

subtilis]: PDB:1WAP

• Murine CAR nuclear receptor/inverse agonist androstenol complex [Mus

musculus (house mouse)]: PDB:1XNX

• Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT

• Ligand-binding domain of human nuclear receptor liver receptor homolog 1

(hLRH-1) in complex with the NR box 1 motif of human SHP [Homo sapiens
(human)]: PDB:1YUC

• DNA binding domain of human liver receptor homologue(hLRH-1 DBD) in

Complex with dsDNA [Homo sapiens (human)]: PDB:2A66

• mRNA decapping enzyme Dcp2p [Schizosaccharomyces pombe]: PDB:2A6T

• DNA-dependent RNA polymerase / tagetitoxin complex [Thermus thermophilus

(thermophile, bacteria)]: PDB:2BE5

• A Piwi domain (part of RNAi protein argonaut)/siRNA-like duplex complex

[Archaeoglobus fulgidus]: PDB:2BGG

• Ribonuclease inhibitor (RI) [Sus scrofa (pig)]: PDB:2BNH

• Lipoate protein ligase A (LplA) [Thermoplasma acidophilum

(archaea,thermophile)]: PDB:2C8M

• Cbf5-Nop10-Gar1 complex (part of the pseudouridylation enzyme) [Pyrococcus

furiosus (thermophile, archaea)]: PDB:2EY4

• RNase III (D44N) complexed with double-stranded RNA [Aquifex aeolicus

(bacteria,thermophile)]: PDB:2EZ6

• BPTF PHD finger-linker-bromodomain bound to H3K4me3 [Homo sapiens

(human)]: PDB:2F6J

• Dicer [Giardia intestinalis (flagellate)]: PDB:2FFL

• Transcription regulating factor CSL-Notch-Mastermind/DNA complex

[Caenorhabditis elegans (nematode)]: PDB:2FO1

• Thiamine pyrophosphate-specific riboswitch [Escherichia coli (bacteria)]:

 PDB:2GDI

• S-adenosylmethionine riboswitch [Thermoanaerobacter tengcongensis]:

PDB:2GIS

• Lysine-Specific Demethylase-1 [Homo sapiens (human)]: PDB:2H94

• CIA-histone H3-H4 complex [Homo sapiens (human)]: PDB:2IO5

• Exon Junction Complex [Human]: PDB:2J0S

• Retinoic acid receptor-gamma / retinoic acid complex [Homo sapiens (human)]:

PDB:2LBD

• Trapped UBL activation complex [Human]: PDB:2NVU

• Inositol-requiring protein-1 [Yeast]: PDB:2RIO

Globin protein
• Myoglobin [Sperm whale]: PDB:1MBN

• Oxidized alpha haemoglobin bound to alpha-haemoglobin-stabilizing protein

(AHSP) [Homo sapiens (human)]: PDB:1Z8U

Others
• Immunoglobulin M rheumatoid factor Fab complexed with IgG4 Fc [Homo
sapiens (human)]: PDB:1ADQ

• Complex between T-cell receptor, viral peptide and HLA-A2 [Homo sapiens
(human)]: PDB:1AO7

• Actin/DNase I complex [Oryctolagus cuniculus (European rabbit)]: PDB:1ATN

• Myosin heavy chain [Argopecten irradians (bay scallop)]: PDB:1B7T

• Clathrin heavy chain [Bos taurus (bovine)]: PDB:1B89

• FOOT-AND-MOUTH DISEASE VIRUS [foot-and-mouth disease virus

(FMDV)]: PDB:1BBT

• COAGULATION FACTOR IX-BINDING PROTEIN A [Trimeresurus

flavoviridis(habu snake)]: PDB:1BJ3

• Collagen like model peptide (T3-785 peptide) [Synthetic peptide (containing

human type III collagen sequence)]: PDB:1BKV

• KcsA Potassium channel [Streptomyces lividans (bacteria)]: PDB:1BL8

• Verotoxin-1 [Escherichia coli (bacteria)]: PDB:1BOV

• Retinol binding protein [Homo sapiens (human)]: PDB:1BRP

• Dethiobiotin synthase [Escherichia coli (bacteria)]: PDB:1BYI

• Collagen-like peptide [Homo sapiens (human)?]: PDB:1CAG

• SCAFFOLDING PROTEIN GPD [bacteriophage phiX174]: PDB:1CD3

• TATA binding protein (TBP)/DNA complex [Homo sapiens (human)]:

PDB:1CDW

• Calmodulin [Homo sapiens (human)]: PDB:1CLL

• Prostaglandin H2 synthase-1 complex with flurbiprofen [Ovis aries (sheep)]:

PDB:1CQE

• Crambin [Crambe abyssinica (Abyssinian cabbage)]: PDB:1CRN

• Axonin-1 (N-terminal domain) [Gallus gallus (chicken)]: PDB:1CS6

• Transferrin (iron transport protein) receptor (TfR) protein [Homo sapiens

(human)]: PDB:1CX8

• Apoptosis-inducing ligand 2 (Apo2L,TRAIL)/death receptor 5 (DR5) complex

[Homo sapiens (human)]: PDB:1D0G

• Coagulation factor VIII precursor [Homo sapiens (human)]: PDB:1D7P

• Major prion protein 1 precursor [Bos taurus (bovine)]: PDB:1DX0

• E-cadherin [Mus musculus (house mouse)]: PDB:1EDH

• Green fluorescent protein [Aequorea victoria (jellyfish)]: PDB:1EMA

• Botulinum neurotoxin type B [Clostridium botulinum (bacteria)]: PDB:1EPW

• Bone morphogenic protein 2 (BMP2)/BRIA ectodomain complex [Homo sapiens

(human)]: PDB:1ES7

• Botulinum neurotoxin type B complex with sialyllactose [Clostridium botulinum

(bacteria)]: PDB:1F31

• Rhodopsin [Bos taurus (Bovine)]: PDB:1F88

• ImmunoglobulinG1-kappa Fab D1.3 (light chain) [Mus musculus (house mouse)]:

PDB:1FDL
• Ferritin (iron transport protein) H-chain mutant (LYS 86 replaced by GLN)
[Homo sapiens (human)]: PDB:1FHA

• Immunosuppressant drug (FK506) binding protein [Homo sapiens (human)]:

PDB:1FKF

• Botulinum neurotoxin type B complex with zinc ion and inhibitor (bis(5-amidino-
2-benzimidazolyl)methane) [Clostridium botulinum (bacteria)]: PDB:1G9B

• ENVELOPE PROTEIN GP120 [Human Immunodeficiency Virus type 1]:

PDB:1GC1

• NAD(P)H:quinone oxidoreductase 1 [Homo sapiens (human)]: PDB:1GG5

• Crustacyanin [Homarus gammarus (European lobster)]: PDB:1GKA

• Iron transport protein Serotransferrin (serum transferrin) [Sus scrofa (pig)]:

PDB:1H76

• Biphenyl-2,3-diol 1,2-dioxygenase [Burkholderia cepacia (bacteria)]: PDB:1HAN

• Human leukocyte antigen B27 [Homo sapiens (human)]: PDB:1HSA

• Immunoglobulin IgG2A [Mus musculus (house mouse)]: PDB:1IGT

• COAGULATION FACTOR X BINDING PROTEIN [Homo sapiens (human)]:

PDB:1IOD

• INFLUENZA A SUBTYPE N2 NEURAMINIDASE [influenza virus]:

PDB:1IVD

• Multidrug efflux transporter AcrB [Escherichia coli (bacteria)]: PDB:1IWG

• Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 [Oryctolagus cuniculus

(rabbit)]: PDB:1IWO

• human cardiac troponin in the Ca2+-saturated form [Homo sapiens (human)]

• Complex of ADP-ribosylation factor 1 and ADP-ribosylation factor binding

protein GGA1 [Mus musculus (house mouse)

• Aquaporin 1 water channel [Bos taurus (bovine)]

• anthrax leathal factor [Bacillus anthracis(anthrax)]

• Trp-cage designed protein TC5b [N/A (synthetic)]

• Luciferase [Photinus pyralis (north american firefly)]

• Ca-activated K+ channel [Methanothermobacter thermautotrophicus (archaea)]

• LDL receptor-binding domain of Apolipoprotein E3 [Homo sapiens (human)]

• Complex of acetylcholinesterase and fasciculin 2 [Mus musculus (house mouse) /

Dendroaspis angusticeps (eastern green mamba)]

• Apoptosis inhibitor BCL-XL [Homo sapiens (human)]

• Camel single-domain VH antibody complexed with lysozyme [Camelus

dromedarius (camel)]

• Human LDL receptor (extracellular domain) [Homo sapiens (human)]

• Lysyl oxidase [Pichia pastoris]

• Neural-cadherin (N-cadherin) [Mus musculus (house mouse)]

• Nucleoside diphosphate (NDP) kinase [Dictyostelium discoideum (slime mold)

P105G mutant]

• Hemeoxygenase domain of cytokine-inducible nitric oxide syntase [Mouse]

• KvAP, a voltage-dependent K+ channel [Aeropyrum pernix (archaea)]

• B-cell-activating factor (BAFF)/BAFF recepter (BAFF-R) complex [Homo

sapiens (human)]

• Inward rectifier potassium channel KirBac1.1 [Burkholderia pseudomallei

(bacteria)]

• Phosphoporin [Escherichia coli (bacteria)]

• Penicillin acylase [Escherichia coli (bacteria)]

• C-H-RAS P21 protein catalytic domain (wild type) [Homo sapiens (human)]

• Major prion protein precursor [Homo sapiens (human)]

• Interferon alpha 2B [Homo sapiens (human)]

• Protein conducting channel secY/secG/secE complex [Methanococcus jannaschii

(archaea)]

• SRP/SRP receptor complex [Thermus aquaticus (bacteria)]

• Sialyltransferase CstII/CMP-NeuAc complex [Campylobacter jejuni (bacteria)]

• Nerve growth factor in complex with its receptor, p75 [Homo sapiens (human)]
• Periplasmic chaperone Skp [Escherichia coli (bacteria)]

• VP4 spike-like protein of rotavirus [Rotavirus]

• Water channel aquaporin-0 [Ovis aries (sheep)]

• Superoxide dismutase [Homo sapiens (human)]

• Long-chain fatty acid transporter (FadL) [Escherichia coli (bacteria)]

• Rab5 complex with Rabaptin5 C-terminal Domain [Homo sapiens (human)]

• Integrin/cacodylate ion complex [Homo sapiens (human)]

• ESCRT-II complex [Saccharomyces cerevisiae (Baker's yeast)]

• Phosphodiesterase 5 [Homo sapiens (human)]

• Serum albumin precursor [Homo sapiens (human)]

• Amphiphysin BAR domain [Drosophila melanogaster (fruit fly)]

• Mycobacterial membrane protein, main porin (MspA) [Mycobacterium

smegmatis (bacteria)]

• Artificial nucleotide-binding protein (ANBP) in a complex with bound ADP [N/A

(synthetic)]

• Polysialic acid-degrading endosialidase [Bacteriophage K1F]

• Calcium Pump with a bound ATP analogue [Oryctolagus cuniculus (rabbit)]

• Vanadium-containing chloroperoxidase (CPO) [Curvularia inaequalis]

• RNA packing motor protain [Pseudomonas phage PHI12]

• Glycolipid transfer protein GLTP [Bos taurus (bovine)]

• Adenylyl Cyclase in complex with alpha,beta-methylene-ATP [Spirulina platensis

(cyanobacteria)]

• Bet3 in Golgi localization of tethering factor TRAPP [Mus musculus (house

mouse)]

• Antimicrobial peptide, nisin, comoplexed with lipid II [Lactococcus lactis (lactic

acid bacteria)]

• Antifreeze protein isoform hplc6 [Pseudopleuronectes americanus (winter

flounder)]
• Archaeal toxin-antitoxin RelB-RelE complex [Pyrococcus horikoshii (archaea,
thermophile)]

• Glutamate transporter homolog [Pyrococcus horikoshii OT3 (archaea)]

• Bacterial sensory rhodopsin [Anabaena sp. (cyanobacteria)]

• N-terminal Domain of Nucleoporin Nup159 [Saccharomyces cerevisiae (Baker's

yeast)]

• Cholera toxin [Vibrio cholerae]

• Bni1p Formin Homology 2 (FH2) Domain complexed with ATP-actin

[Saccharomyces cerevisiae (Baker's yeast)]

• Peptide segment GNNQQNY from Sup35 forming amyloid-like fibrils

[Saccharomyces cerevisiae (Baker's yeast)]

• gamma-delta T cell receptor in complex with MHC T22 [Mus musculus (house
mouse)]

• Apoptotic protease-activating factor 1 with ADP [Homo sapiens (human)]

• Aromatic prenyltransferase Orf2 [Streptomyces sp. strain CL190 (bacteria)]

• Na(+)/H(+) antiporter [Escherichia coli (bacteria)]

• Hepatitis C virus replicase NS5A [Hepatitis C virus(HCV) ]

• Toll-like receptor 3 (TLR3) extracellular domain (ECD) [Homo sapiens (human)]

• Potassium-channel KcsA [Streptomyces lividans (actinobacteria)]

• Integron integrase-attC sequence complex [Vibria cholelae]

• Bacterial homolog of Na+/Cl- dependent neurotransmitter transporters [Aquifex

aeolicus (thermophile, bacteria) VF5]

• NaK channel [Bacillus cereus]

• quorum-sensing protein SdiA [bacteria (E.coli)]

• CorA Mg2+ transporter [Thermotoga maritima (bacteria, thermophile)]

• Filamin A complexed with integrin beta 7 tail fragment [Homo sapiens (human)]:

• Rabex-5/ubiquitin complex [Homo sapiens (human)]

• ZEBRA protein complexed with double strand DNA [Epstein-Barr virus (EBV,
 Human herpesvirus 4 (HHV-4))]

• SARS coronavirus ORF-9b protein [Human severe acute respiratory syndrome

(SARS) virus]

• Cytochrome c peroxidase [Saccharomyces cerevisiae (Baker's yeast)]

• Myosin V complexed with calmodulins [Gallus gallus (chicken)]

• Periplasmic binding protein [Bordetella pertussis Tohama I (bacteria)]

• Beta-2-microglobulin [Homo sapiens (human)]

• Urokinase plasminogen activator (uPA) complexed with it's soluble receptor

(suPAR) and the antibody against the receptor (ATN615) [uPA,suPAR：Homo
sapiens (human) / ATN615：Mus musculus (mouse)]

• Ta0583, an archaeal actin homolog [Thermoplasma acidophilum

(archaea,thermophile)]

• Mitochondrial import receptor TOM70 [Saccharomyces cerevisiae (yeast)]

• Tie2 receptor ecodomain complexed with Ang2 [Human]

• Rab11/FIP2(RBD domain) complex [Human]

• Complex of integrin B-subunit cytoplasmic domain and talin F3 domain [Gallus

gallus domesticus(chicken)]

• ABC transporters Sav1866 [S. aureus]

• Apoptosis regulator, Bcl-2 homologous antagonist/killer(BAK) [Human]

• Lysozyme [Gallus gallus (chicken)]

• HIV-1 enverope protein gp120/b12 complex [Human]

• Mechanosensitive ion channel [Mycobacterium tuberculosis (bacteria)]

• Outer membrane porin D2 (OprD) [Pseudomonas aeruginos]

• ABC transporter ModBC in complex with its binding protein ModA

[Archaeoglobus fulgidus (archaea, thermophile)]

• Transport vesicle coat protein, Sec13/31 complex [Yeast]

• C-H-RAS P21 protein catalytic domain (oncogenic G12V) [Homo sapiens

(human)]
• Acid sensing ion channel, ASIC1 [Chicken]

• Salmonella effector protein SopA [Salmonella bacterium]

• Paddle-chimaera K+ channel [Rat]

• Outer membrane component of bacteria drug efflux pump, TolC [E.coli]

• IS608 transposase TnpA / DNA complex [Helicobacter pylori]

• Toll-like receptor1 (TLR1)/TLR2/lipopeptide complex [Homo sapiens (human)]

• Sarcoplasmic reticulum calcium pump [Oryctolagus cuniculus (rabbit)]

• E. coli DNA polymerase III, beta-subunit / DNA complex [Escherichia coli]

• Sec13-Nup145C hetero-octamer [human (Sec13), yeast (Nup145C)]

• Beta-lactamase [Bacillus licheniformis (bacteria)]

• Human rhinovirus 14 coat protein [Human rhinovirus 14 (human common cold

virus)]

• Cisplatin/DNA complex [N/A]