Structure of PDB 2bdy Chain A

Receptor sequence
>2bdyA (length=276) Species: 9606 (Homo sapiens) [Search protein sequence]
ADCGLRPLFEKKSLEDKTERELLESYIIVEGSDAEIGMSPWQVMLFRKSP
QELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYER
NIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDR
ETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEG
CDRDGKYGFYTHVFRLKKWIQKVIDQ
3D structure
PDB2bdy Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.
ChainA
Resolution1.61 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
Catalytic site (residue number reindexed from 1) H70 D126 E222 G223 D224 S225 G226
Enzyme Commision number 3.4.21.5: thrombin.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 peptide A L62 L96 R98 R104 T105 R106 Y107 K113 I114 L53 L87 R89 R95 T96 R97 Y98 K104 I105
BS02 UNB A H79 Y83 W86 E130 L132 I209 D229 A230 C231 S235 V255 S256 W257 G258 G260 H70 Y74 W77 E121 L123 I199 D219 A220 C221 S225 V245 S246 W247 G248 G250 MOAD: ic50=0.017uM
PDBbind-CN: -logKd/Ki=7.77,IC50=17nM
BindingDB: IC50=17nM
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation
Cellular Component
GO:0005576 extracellular region

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Cellular Component
External links
PDB RCSB:2bdy, PDBe:2bdy, PDBj:2bdy
PDBsum2bdy
PubMed16290930
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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