Protein Data Bank http://www.pdb.org

The Research Collaboratory for Structural Informatics Protein Data Bank (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, Sixth Edition by David Nelson and Michael 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. You can download the RasMol plug-in at the below two sites.

• http://www.bernstein-plus-sons.com/software/rasmol/ • http://www.openrasmol.org/

1

Chapter 4

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 4-1 p. 115 Chymotrypsin 6GCH 4-4 p. 120 Troponin C (α helix) 4TNC 4-12 p. 127 Collagen 1CGD 4-16 p. 132 Myoglobin 1MBO Box 4-5, Figure 1d p. 135 Myoglobin 2MBW Box 4-5, Figure 3b p. 136 Globin 1VRF Box 4-5, Figure 3b p. 136 Globin 1VRE 4-18b p. 137 α-hemolysin 7AHL 4-19 p. 137 Troponin C 4TNC 4-20c p. 138 DNA photolyase 1DNP 4-21 p. 138 Pyruvate kinase 1PKN 4-22 part 1 p. 139 Serum albumin 1AO6 4-22 part 1 p. 139 Bacterioferritin (cytochrome b1) 1BCF 4-22 part 1 p. 139 Glucoamylase 1GAI 4-22 part 2 p. 139 UDP N-acetylglucosamine acyltransferase 1LXA 4-22 part 2 p. 139 Collagenase-3 (MMP-13), carboxyl-terminal 1PEX domain 4-22 part 2 p. 139 CD8 1CD8 4-22 part 3 p. 139 Alcohol dehydrogenase 1DEH 4-22 part 3 p. 139 Enoyl-CoA hydratase (crotonase) 1DUB 4-22 part 3 p. 139 ATP-dependent phosphofructokinase 1PFK 4-22 part 4 p. 140 Pilin 2PIL 4-22 part 4 p. 140 Thymidylate synthase 1SYN 4-22 part 4 p. 140 Green fluorescent protein, GFP 1EMA 4-24a p. 142 Histone-lysine N-methyltransferase, H3 1XQH lysine-4 specific 4-24b p. 142 Cyclin A 1H26 4-24b p. 142 Sirtuin 1MA3 4-24b p. 142 CBP bromo domain 1JSP 4-24b p. 142 s100B( 1DT7 4-30 p. 147 Hsp70 homolog SSE1 2QXL 4-30 p. 147 Hsp70 ββ) 2KHO 4-30 p. 147 Substrate Binding Domain of DnaK 1DKZ 4-31 p.148 GROEL 1AON Box 4-6, Figure 2 p. 151 Human Prion Protein 1QLX

2

Chapter 5

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 5-1b,c p. 158 Cytochrome c (heme) 1CCR 5-3 p. 159 Myoglobin 1MBO 5-5 p. 162 Myoglobin (heme) 1MBO 5-6 p. 163 Myoglobin 1MBO 5-6 p. 163 Hemoglobin (T-State, Deoxygenated) 1HGA 5-8 p. 164 Hemoglobin (T-State, Deoxygenated) 1HGA 5-9a 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) 1B86 5-18b p. 172 Hemoglobin (R-State, Deoxygenated) 1BBB 5-21 p. 176 Immunoglobulin G 2A intact antibody- 1IGT Mab231 5-25a p. 177 Immunoglobulin G 2A fab fragment 1GGC 5-25b p. 177 Immunoglobulin G 2A fab fragment (50.1) 1GGI complex with 16-residue peptide

Chapter 6

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 6-1 p. 192 Chymotrypsin 7GCH 6-4 p. 195 Dihydrofolate reductase 1RA2 6-19 p. 214 Chymotrypsin 7GCH 6-25a p. 220 Hexokinase 2YHX 6-25b p. 220 Hexokinase 1HKG 6-25b p. 220 Glucokinase 1GLK 6-26b p. 221 Enolase 1ONE 6-27a p. 222 Lysozyme 1LZE 6-28b p. 223 Lysozyme c IH6M 6-33a p. 227 Aspartate transcarbamoylase (T state) 1RAB 6-33b p. 227 Aspartate transcarbamoylase (R state) 1F1B

3

Chapter 7

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 7-22 p. 261 Heparin 1HPN 7-23 p. 262 Fibroblast growth factor 1E0O 7-33b p. 271 Influenza neuraminidase 2BAT 7-33c p. 271 H5N1 Avian influenza neuraminidase 2HU4 7-33d p. 271 Oseltamivir-resistant influenza virus 3CL0 neuraminidase 7-35 p. 272 Carbon-dependent mannose 6-phosphate 1M6P receptor

Chapter 8

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 8-20b p. 293 DNA triplex 1BCE 8-23b p. 295 P4-P6 RNA ribozyme domain 1GID 8-25a p. 296 Transfer Ribo-Nucleic Acid (Yeast, Phe) 1TRA 8-25b p. 296 RNA (Hammerhead ribozyme) 1MME 8-25c p. 296 Lsu R-RNA group I intron 1GRZ

Chapter 9

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 9-16a p. 334 Green fluorescent protein 1GFL

4

Chapter 11

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 11-10 p. 391 Bacteriorhodopsin 2AT9 11-11a p. 392 Aquaporin 2B60 11-11b p. 392 ATPase from Enterococcus hirae 2BL2 11-13 p. 393 K+ channel protein 1BL8 11-13 p. 393 Maltoporin 1AF6 11-13 p. 393 Outer membrane phospholipase A 1QD5 11-13 p. 393 Urokinase-type plasminogen activator (OmpX) 1QJ9 11-13 p. 393 Phosphoporin E 1PHO 11-14 p. 393 Ferric enterobactin receptor (FepA) 1FEP 11-14 p. 393 Outer membrane phospholipase A 1QD5 11-14 p. 393 Maltoporin 1MAL 11-36b p. 411 Ca2+ ATPase (SERCA pump) 1T5S 11-36c p. 411 Na+K+ ATPase 2KDP 11-36c p. 411 H+ATPase 3B8C 11-36c p. 411 H+K+ ATPase 3IXZ 11-40a p. 414 MDR1 (P glycoprotein) 3G60 11-40b p. 414 Vitamin B12 importer BtuCD 1L7V 11-42a p. 417 Lactose permease (lactose transporter) 1PV7 11-42b p. 417 Lactose permease (lactose transporter) 2CFQ 11-45a p. 420 Aquaporin SoPIP2;1 2B5F 11-45b p. 420 Aquaporin 1, AQP-1 1J4N 11-47 p. 422 K+ channel protein 1BL8 11-48 p. 423 Voltage-gated potassium channel beta-2 2A79 subunit

5

Chapter 12

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 12-6b p. 440 cAMP-dependent protein kinase catalytic 1U7E subunit Box 12-2, Figure 2 p. 441 Ras protein 5P21 Box 12-3, Figure 2 p. 448 Green fluorescent protein (GFP) 1GFL 12-11a p. 451 Calmodulin 1CLL 12-11b p. 451 Calmodulin and calmodulin-dependent protein 1CDL kinase II

12-13a p. 453 Guanine nucleotide-binding protein Gs 3SN6 12-13b p. 453 μ opioid receptor 4DKL 12-13c p. 453 Doxepin 3RZE 12-13d p. 453 A2A adenosine receptor 3EML 12-13d p. 453 β1-adrenergic receptor 2VT4 12-13d p. 453 β2-adrenergic receptor 2RH1 12-13d p. 453 Rhodopsin 2Z73 12-13d p. 453 Rhodopsin 1U19 12-14b p. 454 Insulin receptor ectodomain 2DTG 12-14b p. 454 Insulin 2CEU 12-14c p. 454 Inactive (unphosphorylated) Tyr kinase 1IRK domain (insulin receptor) 12-14d p. 454 Active (triply phosphorylated) Tyr kinase 1IR3 domain (insulin receptor) 12-21 p. 461 SHC (SH2 domain) 1SHC 12-27b p. 467 Ion transport protein 3RW0 12-28c p. 469 Acetylcholine-binding protein 1UV6 12-38 p. 478 Bacteriorhodopsin (rhodopsin and G protein 1BAC transducin) 12-42b p. 485 Cyclin-dependent kinase 2 1FIN 12-42c p. 485 Cyclin-dependent kinase 1JST 12-45a p. 485 Cyclin-dependent kinase 2 1HCK Box 12-5, Figure 2 p. 490 Kinase 1S9I Box 12-5, Figure 3a p. 491 Abl oncogene kinase 1IEP Box 12-5, Figure 3b p. 491 1M17 Box 12-5, Figure 3c p. 491 Cyclin-dependent kinase 2 1S9I Box 12-5, Figure 3d p. 491 Cyclin-dependent kinase 2 2A4L

Chapter 13

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 13-25b p. 534 Lactate dehydrogenase 3LDH

6

Chapter 15

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 15-16a p. 604 ATP-dependent phosphofructokinase 1PFK 15-20a p. 607 Phosphoprotein phosphatase 2A (PP2A) 2NPP 15-34 p. 619 Glycogenin 1LL2

Chapter 16

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 16-8a p. 640 Citrate synthase (open form) 5CSC 16-8b p. 640 Citrate synthase (closed form) with bound 5CTS oxaloacetate and carboxymethyl-CoA Box 16-1, Figure 2a p. 643 Cytosolic aconitase (closed form) 2B3Y Box 16-1, Figure 2b p. 643 IRP1 (open form) 2IPY 16-13b p. 645 Succinyl-CoA synthetase 1SCU

Chapter 18

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 18-5e p. 700 Aspartate aminotransferase and Pyridoxal 1AJS phosphate (PLP)

7

Chapter 19

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 19-5d p. 736 Heterocyst ferredoxin 1FRD 19-9 p. 739 Ubiquinone oxidoreductase (Complex I) 3M9S 19-10 p. 740 Succinate dehydrogenase (Complex II) 1ZOY 19-11 p. 741 Cytochrome bc1 complex (Complex III) 1BGY 19-13 p. 742 Cytochrome oxidase (Complex IV) 1OCC 19-16 p. 744 Ubiquinone oxidoreductase (Complex I) 3M9S 19-16 p. 744 Succinate dehydrogenase (Complex II) 1ZOY 19-16 p. 744 Cytochrome bc1 complex (Complex III) 1BGY 19-16 p. 744 Cytochrome c 1HRC 19-16 p. 744 Cytochrome oxidase (Complex IV) 1OCC 19-23b p. 751 Bovine mitochondrial F1-ATP Synthase 1BMF 19-25b p. 753 Bovine mitochondrial F1-ATP Synthase 1BMF 19-25b p. 753 Bovine mitochondrial F1-ATP Synthase 1JNV 19-25c p. 753 Bovine mitochondrial F1-ATP Synthase 1BMF 19-25c p. 753 Bovine mitochondrial F1-ATP Synthase 1JNV 19-25c p. 753 Bovine mitochondrial F1-ATP Synthase 2A7U 19-25c p. 753 Bovine mitochondrial Fo-ATP Synthase 2CLY 19-25c p. 753 Bovine mitochondrial Fo-ATP Synthase 1B9U 19-25c p. 753 Bovine mitochondrial Fo-ATP Synthase 1YCE 19-33 p. 760 Bovine mitochondrial F1–ATPase with IF1 1OHH 19-51 p. 773 LHCII 2BHW 19-57 p. 778 Photosynthetic reaction center 1PRC 19-60b p. 781 C-phycocyanin 1JBO 19-61a p. 782 Cytochrome b6f complex. 1FV5 19-61a p. 782 Plastocyanin 2Q5B 19-62a p. 784 Photosystem II 2AXT 19-62a p. 784 Cytochrome b6f complex 2E74 19-62a p. 784 Plastocyanin 1AG6 19-62a p. 784 Photosystem I 1QZV 19-62a p. 784 Ferredoxin 1A70 16-62a p. 784 Ferredoxin: NADP reductase 1QG0 19-64b p. 785 Photosystem II core light harvesting protein 3ARC 19-69a p. 791 Bacteriorhodopsin α helices 1C8R

Chapter 20

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 20-5b p. 755 Ribulose 1,5-bisphosphate carboxylase 9RUB (rubsico) complexed with CO2, Mg2+, and substrate ribulose 1,5-bisphosphate 20-5a p. 802 Ribulose 1,5-bisphosphate carboxylase 8RUC (rubsico) 20-6 p. 803 Ribulose bisphosphate carboxylase/oxygenase 1RXO

8

Chapter 21

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 21-3 p. 835 Fatty acid synthase type I (mammalian) 2CF2 21-3 p. 835 Fatty acid synthase type I (fungal) 2UV9 21-3 p. 835 Fatty acid synthase type I (fungal) 2UVA 21-3 p. 835 Fatty acid synthase type I (fungal) 2UVB 21-3 p. 835 Fatty acid synthase type I (fungal) 2UVC

Chapter 22

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 22-3 p. 886 Nitrogenase complex 1FP6 22-3 p. 886 Nitrogenase complex 1M1N 22-7 p. 889 Glutamine synthetase 2GLS 22-20b p. 901 Tryptophan synthase 1KFJ 22-39 p. 916 Carbamoyl phosphate synthetase 1M6V 22-42b p. 917 Ribonucleotide reductase 3UUS 22-45 p. 919 Ribonucleotide reductase 3UUS

Chapter 24

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 24-28 p. 997 Histone H3 (nucleosome core) 1AOI

Chapter 25

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 25-5c p. 1014 DNA polymerase I 4KTQ 25-9b p. 1018 DNA Polymerase III (β-subunit) 2POL 25-31a p. 1040 RecBCD enzyme 1W36 25-32c p. 1041 RecA filament 3CMX 25-37b p. 1047 Cre Recombinase 3CRX

9

Chapter 26

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 26-4 p. 1060 RNA polymerase holoenzyme 1HQM 26-9b p. 1066 Human Tata binding protein (TBP) 1TGH 26-10b p. 1069 DNA with Actinomycin D 1DSC 26-28b p. 1082 RNA (Hammerhead ribozyme) 1MME 26-29b p. 1083 rNA intron (P4-P6 domain) 1GID 26-29c p. 1083 rNA intron 1U6B Box 26-3, Figure 3 p. 1095 RNA Aptamer bound to AMP 1RAW

Chapter 27

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 27-14a p. 1116 Bacterial ribosome (70s) 2OW8 27-14a p. 1116 Bacterial ribosome (70s) 1VSA 27-14b p. 1116 Yeast ribosome 3O58 27-14b p. 1116 Yeast ribosome 3O2Z Box 27-2, Figure 1 p. 1117 50S ribosomal subunit 1Q7Y 27-18b p. 1119 tRNAPhe (yeast) 4TRA 27-21b p. 1122 tRNA 1EHZ 27-22a p. 1123 Glutaminyl-tRNA synthetase from E.coli 1QRT 27-22b p. 1123 Aspartyl-tRNA synthetase from yeast 1ASZ 27-31b p. 1133 EF-Tu complexed with tRNA 1B23 27-31b p. 1133 EF-G complexed with GDP 1DAR 27-48a p. 1148 26S proteasome 3L5Q

Chapter 28

FIGURE NUMBER PAGE NUMBER TITLE/COMPOUND PDB ID 28-8c p. 1160 Lac repressor 2PE5 28-11 p. 1162 Lac repressor 2PE5 28-12 p. 1163 Zif268 1ZAA 28-13 p. 1163 Pax regulatory protein 1FJL 28-14b p. 1164 GCN4 (basic region, leucine zipper) 1YSA 28-15 p. 1164 Transcription factor Max 1HLO 28-16 p. 1166 CRP homodimer 1RUN 28-20 p. 1169 Trp repressor complex with operator 1TRO 28-28c p. 1178 HMG-D 1QRV

10