Structure of PDB 5gim Chain B

Receptor sequence
>5gimB (length=252) Species: 9606 (Homo sapiens) [Search protein sequence]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETKGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
FG
3D structure
PDB5gim Avathrin: a novel thrombin inhibitor derived from a multicopy precursor in the salivary glands of the ixodid tick, Amblyomma variegatum.
ChainB
Resolution2.09 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) H43 D99 E196 G197 D198 S199 G200
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 H57 Y60A E97A N98 I174 D189 A190 S195 W216 G217 H43 Y47 E94 N95 I173 D193 A194 S199 W221 G222
BS02 peptide B F34 R73 T74 R75 Y76 M84 F19 R68 T69 R70 Y71 M80
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:5gim, PDBe:5gim, PDBj:5gim
PDBsum5gim
PubMed28363953
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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