Structure of PDB 4o03 Chain A Binding Site BS03

Receptor Information
>4o03 Chain A (length=539) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANTFLEEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETA
RTPRDKLAACLEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEIN
STTHPGADLQENFCRNPDSSTTGPWCYTTDPTVRRQECSIPVCGQEQCVP
DRGQQYQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNP
DGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEEETSEYQTFFNPRTFGSGE
ADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFR
KSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTR
YERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVER
PVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWY
QMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain4o03 Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4o03 The linker connecting the two kringles plays a key role in prothrombin activation.
Resolution3.38 Å
Binding residue
(original residue number in PDB)		A1 N2 E6 E7 E16 E26
Binding residue
(residue number reindexed from 1)		A1 N2 E6 E7 E16 E26
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H363 D419 E522 G523 D524 S525 G526
Catalytic site (residue number reindexed from 1) H323 D379 E482 G483 D484 S485 G486
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0004175 endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005102 signaling receptor binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0008201 heparin binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
GO:0048018 receptor ligand activity
GO:0070053 thrombospondin receptor activity
Biological Process
GO:0001934 positive regulation of protein phosphorylation
GO:0006508 proteolysis
GO:0006953 acute-phase response
GO:0007166 cell surface receptor signaling pathway
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007596 blood coagulation
GO:0008284 positive regulation of cell population proliferation
GO:0008360 regulation of cell shape
GO:0009611 response to wounding
GO:0010468 regulation of gene expression
GO:0010544 negative regulation of platelet activation
GO:0030168 platelet activation
GO:0030193 regulation of blood coagulation
GO:0030194 positive regulation of blood coagulation
GO:0030195 negative regulation of blood coagulation
GO:0030307 positive regulation of cell growth
GO:0032024 positive regulation of insulin secretion
GO:0032967 positive regulation of collagen biosynthetic process
GO:0042730 fibrinolysis
GO:0045861 negative regulation of proteolysis
GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT
GO:0048712 negative regulation of astrocyte differentiation
GO:0051281 positive regulation of release of sequestered calcium ion into cytosol
GO:0051480 regulation of cytosolic calcium ion concentration
GO:0051838 cytolysis by host of symbiont cells
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051918 negative regulation of fibrinolysis
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0070945 neutrophil-mediated killing of gram-negative bacterium
GO:0090218 positive regulation of lipid kinase activity
GO:1900016 negative regulation of cytokine production involved in inflammatory response
GO:1900182 positive regulation of protein localization to nucleus
GO:1900738 positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway
GO:1990806 ligand-gated ion channel signaling pathway
GO:2000379 positive regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005788 endoplasmic reticulum lumen
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome
GO:0072562 blood microparticle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4o03, PDBe:4o03, PDBj:4o03
PDBsum4o03
PubMed24821807
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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