Structure of PDB 3da9 Chain B

Receptor sequence
>3da9B (length=251) Species: 9606 (Homo sapiens) [Search protein sequence]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G
3D structure
PDB3da9 Compounds binding to the S2-S3 pockets of thrombin.
ChainB
Resolution1.8 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) H43 D99 E195 G196 D197 S198 G199
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 B E44 G46 M47 P49 W50 D149 H152 P153 C155 Y170 K171 R173 N194 M241 K242 N247 R248 W249 E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02 peptide B F55 R98 R104 T105 R106 Y107 K113 I114 F19 R62 R68 T69 R70 Y71 K77 I78
BS03 44U B Y83 N131 L132 I209 C231 S235 S256 W257 G258 E259 Y47 N95 L96 I172 C194 S198 S219 W220 G221 E222 MOAD: Kd=3.1uM
PDBbind-CN: -logKd/Ki=5.51,Kd=3.1uM
BindingDB: Kd=3100nM,IC50=18000nM
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

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Molecular Function
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Biological Process
External links
PDB RCSB:3da9, PDBe:3da9, PDBj:3da9
PDBsum3da9
PubMed19371038
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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