Structure of PDB 5edk Chain A Binding Site BS01

Receptor Information
>5edk Chain A (length=528) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRD
KLAACLEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHP
GADLQENFCRNPDSSTMGPWCYTTDPTVRRQECSIPVCGQEQCVPDRGQQ
YQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEE
GVWCYVAGKPGDFGYCDLNYCEEAVEETSEYQTFFNPRTFGSGEADCGLR
PLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQEL
LCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIE
KISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETA
ASLLQAGYKGRVTGWGNLKETWTAQPSVLQVVNLPIVERPVCKDSTRIRI
TDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGC
DRDGKYGFYTHVFRLKKWIQKVIDQFGE
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5edk Chain A Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5edk How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin.
Resolution3.214 Å
Binding residue
(original residue number in PDB)		E16 E26
Binding residue
(residue number reindexed from 1)		E11 E21
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H341 D397 E500 G501 D502 S503 G504
Catalytic site (residue number reindexed from 1) H317 D373 E471 G472 D473 S474 G475
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:5edk, PDBe:5edk, PDBj:5edk
PDBsum5edk
PubMed26763231
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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