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Protein Data bank

http://www.rcsb.org/pdb/ http://www.pdb.org The Research Collaboratory for Structural Informatics Protein Data Bank (PDB) <http://www.rcsb.org/pdb/> is the single international source for 3D structure files, not only for proteins, but also for nucleic acids and macromolecular complexes. Many of the molecular graphic images in Lehninger Principles of Biochemistry, fourth edition by Nelson and Cox are derived from information provided by the Protein Data Bank. In such cases, a four character PDB ID is included in the figure caption (the full citation appears in the illustration credits appendix). For your convenience, these IDs are collected below and arranged by figure number and chapter (to see the full citation of the original article, see pages C-1 through C-8 of the text). To view the complete information for a given molecule, simply copy the four character ID, click on the link above, and paste the ID into the search field in the center of the PDB home page. The data from the PDB files provide only a series of coordinates detailing the location of atoms and their connectivity. However, dynamic images of the molecule can be viewed by using graphics programs such as RasMol and Chime, which convert the coordinates into an image and allow the viewer to manipulate the structure in three dimensions. For detailed information on Chime, please see the Tips on Using Chime section of the Lehninger Principles of Biochemistry web site. You can download the RasMol plug-in at the following two sites: http://www.bernstein-plus-sons.com/software/rasmol/ http://www.openrasmol.org/

Chapter 4
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

4-1 4-4 4-5 4-12 4-16 4-18 4-18 Box 4-4, Figure 1d Box 4-4, Figure 3b Box 4-4, Figure 3c 4-19 4-20d 4-20d 4-21 4-22 4-22 4-22 4-22 4-22 4-22 4-22 4-22 4-22 4-22 4-22

p. 117 Chymotrypsin PDB ID6GCH p. 121 Troponin C ( helix) PDB ID 4TNC p. 121 Troponin C ( helix) PDB ID 4TNC p. 128 Collagen PDB ID 1CGD p. 135 Cytochrome c PDB ID 1CCR p. 135 Lysozyme PDB ID 3LYM p. 135 Ribonuclease A PDB ID 3RN3 p. 137 Myoglobin PDB ID 2MBW p. 139 Globin PDB ID 1VRF p. 139 Globin PDB ID 1VRE p. 140 Troponin C PDB ID 4TNC p. 140 -hemolysin PDB ID 7AHL p. 140 DNA photolyase PDB ID 1DNP p. 141 Pyruvate kinase PDB ID 1PKN p. 142 Serum albumin PDB ID 1AO6 p. 142 Bacterioferritin (cytochrome b1) PDB ID 1BCF p. 142 Glucoamylase PDB ID 1GAI p. 142 engrailed Homeodomain PDB ID 1ENH p. 142 -Amylase inhibitor tendamistatPDB ID 1HOE p. 142 UDP N-acetylglucosamine acyltransferase 1LXA p. 142 Collagenase-3 (MMP-13), carboxyl-terminal domain 1PEX p. 142 Lectin (agglutinin) PDB ID 1JPC p. 142 CD8 PDB ID 1CD8 p. 143 Alcohol dehydrogenase PDB ID 1DEH p. 143 Enoyl-CoA hydratase (crotonase) 1DUB

4-22 4-22 4-22 4-22 4-22 4-23 4-25a 4-25b 4-31

p. 143 p. 143 p. 143 p. 143 p. 143 p. 145 p. 146 p. 146 p. 152


PAGE NUMBER

ATP-dependent phosphofructokinase 1PFK Pilin PDB ID 2PIL Thymidylate synthase PDB ID 1SYN Green fluorescent protein, GFP 1EMA Ubiquitin-conjugating enzyme, UBC 1U9A Deoxyhemoglobin PDB ID 2HHB Poliovirus PDB ID 2PLV Tobacco Mosaic Virus PDB ID 1VTM GroEL/GroES complex PDB ID 1AON
TITLE/COMPOUND PDB ID

Chapter 5
FIGURE NUMBER

5-1 p. 159 Cytochrome c (heme) PDB ID 1CCR 5-3 p. 160 Myoglobin PDB ID 1MBO 5-5 p. 162 Myoglobin (heme) PDB ID 1MBO 5-6 p. 163 Myoglobin PDB ID 1MBO 5-6 p. 163 Hemoglobin (T-State, Deoxygenated) 1HGA 5-8 p. 164 Hemoglobin (T-State, Deoxygenated) 1HGA 5-9 p. 164 Hemoglobin (T-State, Deoxygenated) 1HGA 5-10 p. 165 Hemoglobin (T-State, Deoxygenated) 1HGA 5-10 p. 165 Hemoglobin (R-State, Deoxygenated) 1BBB 5-11 p. 165 Hemoglobin (T-State, Deoxygenated) 1HGA 5-11 p. 165 Hemoglobin (R-State, Deoxygenated) 1BBB 5-18a p. 172 Hemoglobin (T-State, Deoxygenated) 1HGA 5-18b p. 172 Hemoglobin (R-State, Deoxygenated) 1BBB 5-22 p. 177 MHC Protein PDB ID 1DDH 5-23 p. 178 Immunoglobulin G 2A intact antibody-Mab231 1IGT 5-27a p. 180 Immunoglobulin G 2A fab fragment 1GGC 5-27b p. 180 Immunoglobulin G 2A fab fragment (50.1) complex with 16-residue peptide PDB ID 1GGI

Chapter 6
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

6-1 6-4 6-18 6-22a 6-22b 6-22b 6-23b 6-24a 6-25b 6-27

p. 193 p. 197 p. 214 p. 218 p. 218 p. 218 p. 219 p. 223 p. 224 p. 226
PAGE NUMBER

Chymotrypsin Dihydrofolate reductase Chymotrypsin Hexokinase Hexokinase Glucokinase Enolase Lysozyme Lysozyme c Aspartate transcarbamoylase
TITLE/COMPOUND

PDB ID 7GCH PDB ID 1RA2 PDB ID 7GCH PDB ID 2YHX PDB ID 1HKG PDB ID 1GLK PDB ID 1ONE PDB ID 1LZE PDB ID IH6M PDB ID 2AT2
PDB ID

Chapter 7
FIGURE NUMBER

7-25 7-35a 7-35c

p. 254 Fibroblast growth factor PDB ID 1E0O p. 265 Sialoadhesin PDB ID 1QFO p. 265 Carbon-dependent mannose 6-phosphate receptor 1M6P

Chapter 8
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

8-22b 8-22d 8-28a 8-28b 8-28c

p. 286 DNA triplex PDB ID 1BCE p. 286 DNA quadruplex structure PDB ID 1QDG p. 290 Transfer Ribo-Nucleic Acid (Yeast, Phe) PDB ID 1TRA p. 290 RNA (Hammerhead ribozyme) PDB ID 1MME p. 290 Lsu R-RNA group I intron PDB ID 1GRZ
PAGE NUMBER TITLE/COMPOUND PDB ID

Chapter 9
FIGURE NUMBER

9-2a

p. 309

Dimeric EcoRV endonuclease

PDB ID 1RVC

Chapter 11
FIGURE NUMBER 11-9 11-10 11-12 11-12 11-12 11-12 11-12 11-13 11-13 11-13 11-13 11-13 11-38 11-41a 11-41b 11-43a 11-46 11-48 11-49 PAGE NUMBER TITLE/COMPOUND PDB ID p. 376 Bacteriorhodopsin PDB ID 2AT9 p. 376 Photosynthetic reaction center 1PRC p. 377 K+ channel protein PDB ID 1BL8 p. 377 Maltoporin PDB ID 1AF6 p. 377 Outer membrane phospholipase A PDB ID 1QD5 p. 377 Urokinase-type plasminogen activator (OmpX) PDB ID 1QJ9 p. 377 Phosphoporin E PDB ID 1PHO p. 378 Ferric enterobactin receptor (FepA) PDB ID 1FEP p. 378 Outer membrane phospholipase A PDB ID 1QD5 p. 378 Maltoporin PDB ID 1MAL p. 378 Outer membrane protein TolC PDB ID 1EK9 p. 378 -hemolysin PDB ID 7AHL p. 400 Calcium-transporting ATPase sarcoplasmic reticulum 1EUL p. 402 Lipid A flippase MsbA PDB ID 1JSQ p. 402 Vitamin B12 importer BtuCD PDB ID 1L7V p. 405 Lactose permease (lactose transporter) PDB ID 1PV7 p. 407 Aquaporin 1, AQP-1 PDB ID 1J4N p. 410 K+ channel protein PDB ID 1BL8 p. 411 Voltage-gated K+ channel PDB ID 1J95
PAGE NUMBER TITLE/COMPOUND PDB ID

Chapter 12
FIGURE NUMBER

12-7a p. 431 Inactive (unphosphorylated) Tyr kinase domain (insulin receptor) 1IRK 12-7b p. 431 Active (triply phosphorylated) Tyr kinase domain (insulin receptor) P1IR3 12-13 p. 437 Gs and Adenylyl cyclase PDB ID 1AZS 12-15b p. 438 cAMP-dependent protein kinase, PKA; -catalytic subunit 1JBP 12-21a p. 445 Calmodulin PDB ID 1CLL 12-21b p. 445 Calmodulin and calmodulin-dependent protein kinase II PDB ID 1CDL Box 12-2, Figure 2 p. 446 Green fluorescent protein (GFP) PDN ID 1GFL 12-22 p. 449 SHC (SH2 domain) PDB ID 1SHC 12-33 p. 458 Bacteriorhodopsin (rhodopsin and G protein transducin) 1BAC 12-42a p. 467 Cyclin-dependent kinase 2 PDB ID 1HCK 12-42b p. 467 Cyclin-dependent kinase 2 PDB ID 1FIN 12-42c p. 467 Cyclin-dependent kinase PDB ID 1JST

Chapter 13
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

13-16

p. 514
PAGE NUMBER

Lactate dehydrogenase
TITLE/COMPOUND

PDB ID 3LDH
PDB ID

Chapter 15
FIGURE NUMBER

15-10 15-18a

p. 569 p. 579

Glycogenin ATP-dependent phosphofructokinase

PDB ID 1772 PDB ID 1PFK

Chapter 16
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 16-8a p. 608 Citrate synthase (open form) PDB ID 5CSC 16-8b p. 608 Citrate synthase (closed form) with bound oxaloacetate and carboxymethyl-CoA PDB ID 5CTS 16-12b p. 611 Succinyl-CoA synthetase PDB ID 1SCU

Chapter 18
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND 18-5 p. 661 Aspartate aminotransferase and Pyridoxal phosphate (PLP) PDB ID PDB ID 1AJS
PDB ID

Chapter 19
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND

19-5d 19-10 19-11a 19-13 19-21b 19-23b 19-23d 19-29 19-48 19-51b-c 19-54a 19-59a

p. 695 Heterocyst ferredoxin p. 699 Succinate dehydrogenase (Complex II) p. 700 Cytochrome bc1 complex (Complex III) p. 702 Cytochrome c oxidase (Complex IV) p. 708 Bovine mitochondrial F1-ATP Synthase p. 710 Bovine mitochondrial F1-ATP Synthase p. 711 ATP synthase chain (FoF1) p. 717 Bovine mitochondrial F1ATPase with IF1 p. 732 Photosynthetic reaction center p. 735 C-phycocyanin p. 737 Cytochrome b6f complex p. 744 Bacteriorhodopsin
PAGE NUMBER TITLE/COMPOUND

PDB ID 1FRD PDB ID 1NEK PDB ID 1BGY PDB ID 1OCC PDB ID 1BMF PDB ID 1BMF PDB ID 1QO1 PDB ID 1OHH PDB ID 1PRC PDB ID 1JBO PDB ID 1UM3 PDB ID 1C8R
PDB ID

Chapter 20
FIGURE NUMBER

20-5a p. 755 Ribulose 1,5-bisphosphate carboxylase (rubsico) 8RUC 20-5b p. 755 Ribulose 1,5-bisphosphate carboxylase (rubsico) complexed with CO2, Mg2+, and substrate ribulose 1,5-bisphosphate PDB ID 9RUB 20-6 p. 755 Ribulose bisphosphate carboxylase/oxygenase
PAGE NUMBER TITLE/COMPOUND

PDB ID 1RXO
PDB ID

Chapter 21
FIGURE NUMBER

Box 21-2, Figure 1a Box 21-2, Figure 1b Box 21-2, Figure 1b

p. 803 Cyclooxygenase-2 (COX-2) with flurbiprofen p. 803 Cyclooxygenase-1 (COX-1) with ibuprofen p. 803 Cyclooxygenase-2 (COX-2) with Sc-558

PDB ID 3PGH PDB ID 1EQG PDB ID 6COX

Chapter 22
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

22-3 22-5 22-37 22-40

p. 836 p. 838 p. 868 p. 870

Nitrogenase molybdenum-iron protein 1N2C Glutamine synthetase PDB ID 2GLS Carbamoyl phosphate synthetase PDB ID 1M6V R2 of ribonucleotide reductase PDB ID 1PFR
TITLE/COMPOUND PDB ID

Chapter 24
FIGURE NUMBER PAGE NUMBER

24-27a

p. 940
PAGE NUMBER

Histone H3 (nucleosome core) PDB ID 1AOI


TITLE/COMPOUND PDB ID

Chapter 25
FIGURE NUMBER

25-8 25-10b 25-34b 25-38b

p. 957 p. 958 p. 98 p. 986

DNA polymerase I (Klenow fragment) DNA Polymerase III (-subunit) 3 RecA Cre Recombinase
TITLE/COMPOUND

PDB ID 3BDP PDB ID 2POL PDB ID 2REB PDB ID 3CRX


PDB ID

Chapter 26
FIGURE NUMBER PAGE NUMBER

26-4 26-9b 26-10b 26-25b Box 26-3, Figure 3

p. 999 p. 1004 p. 1006 p. 1018 p. 1030

RNA polymerase holoenzyme Human Tata binding protein (TBP) DNA with Actinomycin D RNA (Hammerhead ribozyme) RNA Aptamer bound to AMP
TITLE/COMPOUND

PDB ID 1IW7 PDB ID 1TGH PDB ID 1DSC PDB ID 1MME PDB ID 1RAW
PDB ID

Chapter 27
FIGURE NUMBER PAGE NUMBER

27-9a 27-9a 27-9b and 1GIY 27-9c Box 27-3, Figure 1 27-13b 27-17a 27-17b 27-25b 27-25b 27-42a

p. 1046 50S ribosomal subunit PDB ID 1JJ2 and 1GIY p. 1046 30S ribosomal subunit PDB ID 1J5E and 1JGO p. 1046 Complete active bacterial ribosome (50S and 30S subunits) PDB ID 1J5E, 1JJ2, 1JGO, p. 1047 p. 1048 p. 1050 p. 1054 p. 1054 p. 1060 p. 1060 p. 1076 50S ribosomal subunit PDB ID 1Q7Y 50S ribosomal subunit PDB ID 1NKW tRNAPhe (yeast) PDB ID 4TRA Glutaminyl-tRNA synthetase from E.coli 1QRT Aspartyl-tRNA synthetase from yeast 1ASZ EF-Tu complexed with tRNA PDB ID 1B23 EF-G complexed with GDP PDB ID 1DAR 20S proteasome PDB ID 1IRU

Chapter 28
FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID

28-7c 28-7d 28-11a 28-11b

p. 1086 p. 1086 p. 1089 p. 1089

Lac operon repressor bound to DNA PDB ID 1LBG Lac operon repressor PDB ID 1LBH and 1LBG Lac repressor PDB ID 1LCC Lac operon repressor PDB ID 1LBG

28-12 28-13 28-14b 28-15 28-16 28-20

p. 1090 p. 1090 p. 1091 p. 1092 p. 1093 p. 1095

Zif268 zinc finger peptide Homeodomain of ultrabithorax GCN4 (basic region, leucine zipper) Transcription factor Max CRP homodimer Trp repressor complex with operator

PDB ID 1A1L PDB ID 1B8I PDB ID 1YSA PDB ID 1HLO PDB ID 1RUN PDB ID 1TRO