Download PDB Files

PDB files listed in the figure legends found in the book can be downloaded from
this site. The coordinates of each molecule will download and when ‘clicked’
should, if your browser is set up to handle pdb files correctly, cause a new
window to open with the structure displayed.
Alternatively readers can obtain the coordinate files from many of the databases
described in the book such as www.rcsb.org
Chapter 2.
Individual coordinate files for each amino acid are available by downloading the
relevant coordinate files.
Ala Asn Asp Arg Cys Gln Glu Gly His Ile
Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
And unusual amino acids such as: D-Alanine L-Alanine Citrulline
Chapter 3.
Chymotrypsin PDB:2CGA
Bovine pancreatic trypsin inhibitor PDB:5PTI
λ repressor protein PDB:1LMB
Cytochrome b-562 PDB:b562
Human thioredoxin PDB:1ERU
Plastocyanin PDB: 1AG6
Human cis-trans proline isomerase PDB:1VBS
Human γ-crystallin: PDB:2GCR
Cytochrome b5 PDB:3B5C
Sulfite oxidase PDB:1SOX
Neuraminidase PDB:1F8D
Tailspike protein of bacteriophage P22 PDB:1TSP
Lactate dehydrogenase PDB:1LDG incorrectly written in the book
Cro repressor from phage 434 PDB:4CRO
Fab region of IgG PDB:7FAB
Monoclonal antibody fragment Fab and lysozyme PDB:1FDL
bacteriocin AS-48 PDB:1E68
microcin J25 PDB:1HG6 now viewed as obsolete entry
MCoTI-II PDB: 1HA9, 1IB9
RTD-1 PDB:1HVZ
kalataB1 PDB:1KAL
SFTI-1 PDB: 1SFI, 1JBL
Chapter 4.
Leucine zipper DNA binding protein GCN4 PDB:1YSA
c-jun c-fos proto-oncogene dimer plus DNA PDB:1FOS
gp41 core domain of SIV PDB:2SIV
Silk polymers PDB:2SLK
Collagen PDB:1BKV
EGF domains from fibrillin-1 PDB:1EMN
Chapter 5.
Bacteriorhodopsin PDB:1C3W
G subunit of transducin PDB:1TND
Reaction centre from Rh.viridis PDB:1PRC
OmpF PDB: 2OMF mistakenly omitted from legends
-hemolysin PDB: 7AHL
bovine cytochrome bc1 complex PDB: 1BE3
Bovine cytochrome oxidase PDB:1OCC, 2OCC
 subunit of ATPase PDB:1BMF
c ring monomer of Fo ATPase PDB:1A91
SR Ca-ATPase PDB:1EUL
Chapter 6.
Tuna cytochrome c PDB:3CYT
Yeast iso-1 cytochrome c PDB:1YCC
P. denitrificans cytochrome c550 PDB:155C
R. rubrum cytochrome c2 PDB:1C2R
Horse cytochrome c PDB:1CRC
Chymotrypsin PDB:2CGA
Elastase PDB:1QNJ
Trypsin PDB:1TGN
Chapter 7.
RNase A PDB: 1FS3
Lysozyme PDB: 1HEW
B.stearothermophilus tyrosyl tRNA synthetase plus tyrosyl adenylate PDB: 3TS1
note the PDB file name is written incorrectly in legend of figure.
Gln-tRNA synthetase in complex of tRNA and ATP PDB: 1GSG
note the PDB file name is
written incorrectly in legend.
Binary complex formed between trypsin and BPTI PDB: 2PTC
Cyclo-oxygenase PDB: 1PRH
Phosphofructokinase PDB: 1PFK
Aspartate transcarbamoylase PDB: 1AT1 note the PDB file name is written incorrectly in legend.
Chapter 8.
Cdk2 PDB: 1HCK
Cdk2 +cyclin binary complex mistakenly omitted from legends PDB: 1FIN
T7 RNA polymerase PDB: 1CEZ
Mouse transcription factor Zif268 in a complex with DNA PDB: 1A1H
note the PDB file
name is written incorrectly in legend.
GCN4 transcription factor complexed with DNA PDB: 1YSA, 2ZTA
is written incorrectly in legend.
Max transcription factor plus DNA PDB: 1AN2
note the PDB file name
Ubx homeobox PDB: 1B8I
Phenylalanyl tRNA PDB: 6TNA
C terminal domain of E. coli ribosomal subunit L7/L12 PDB: 1CTF
L30 domain of the large ribosomal subunit of T. thermophilus PDB: 1BXY
N-terminal domain of the spliceosome RNA binding protein U1A PDB: 1FHT
EF-Tu in a complex with Phe-tRNA PDB: 1TTT
EF-G PDB: 2EFG
FfH subunit from T. aquaticus PDB: 2FFH
Mouse importin- PDB: 1EJL incorrectly described in legend
20S proteasome T. acidophilum PDB: 1PMA
Chapter 10.
Tendamistat PDB : 2AIT, 1HOE
Interleukin-1β PDB: 7I1B
Thioredoxin PDB: 1TRU
β tubulin dimer PDB: 1TUB
Green fluorescent protein PDB: 1EMA
Chapter 11.
GroEL monomer PDB: 1GRL
GroES PDB: 1G31
Thermosome PDB: 1RYP not AG6 as written in legend
Complex of transthyretin and retinol binding protein PDB: 1RLB
Transthyretin PDB: 1BMZ
SH3 domain PDB: 1PNJ
Mouse PrPc protein PDB: 1AG2
Chapter 12.
gp120 core in a complex with a neutralizing antibody and a two domain fragment
of CD4 PDB: 1G9N
HA1/HA2 ‘monomer’ PDB: 2HMG
Neuraminidase PDB: 2BAT
Neuraminidase showing substrate bound to active site PDB: 1MWE
β secretase PDB: 1M4H
p53-DNA complex PDB: 1TUP
α1-antitrypsin PDB: 2PSI, 7API (note 2PSI is now replaced 1QLP).