BioLiP

Structure of PDB 1d9i Chain A

Receptor sequence

>1d9iA (length=279) Species: 9606 (Homo sapiens) [Search protein sequence]

ADCGLRPLFEKKSLEDKTERELLESYIDIVEGSDAEIGMSPWQVMLFRKS
PQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYE
RNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPD
RETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRI
RITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGE
GCDRDGKYGFYTHVFRLKKWIQKVIDQFG

3D structure

PDB

1d9i Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1.

Chain

Resolution

2.3 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1)	H71 D127 E223 G224 D225 S226 G227
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	F34 K36 Q38 L65 R67 R73 T74 R75 Y76 K81 I82	F47 K49 Q52 L88 R90 R96 T97 R98 Y99 K105 I106
BS02	00P	A	H57 Y60A W60D I174 C191 E192 S214 W215 G216 E217 G219	H71 Y75 W78 I200 C222 E223 S247 W248 G249 E250 G251	MOAD: Ki=0.78nM PDBbind-CN: -logKd/Ki=9.11,Ki=0.78nM

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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Molecular Function

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Biological Process

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Cellular Component

PDB	RCSB:1d9i, PDBe:1d9i, PDBj:1d9i
PDBsum	1d9i
PubMed	10713516
UniProt	P00734\|THRB_HUMAN Prothrombin (Gene Name=F2)