Structure of PDB 4dy7 Chain F Binding Site BS01

Receptor Information
>4dy7 Chain F (length=378) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HFNPLSLEELGSNTGIQVFNQIVKSRPHDNIVISPHGIASVLGMLQLGAD
GRTKKQLAMVMRYGVNGVGKILKKINKAIVSKKNKDIVTVANAVFVKNAS
EIEVPFVTRNKDVFQCEVRNVNFEDPASACDSINAWVKNETRDMIDNLLS
PDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQVPML
AQLSVFRCGSTSAPNDLWYNFIELPYHGESISMLIALPTESSTPLSAIIP
HISTKTIDSWMSIMVPKRVQVILPKFTAVAQTDLKEPLKVLGITDMFDSS
KANFAKITTGSENLHVSHILQKAKIEVSEDGTKASAATTAILIARSSPPW
FIVDRPFLFFIRHNPTGAVLFMGQINKP
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 chain4dy7 Chain F Residue 401 [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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PDB4dy7 Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		T309 T310 G311
Binding residue
(residue number reindexed from 1)		T308 T309 G310
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004867 serine-type endopeptidase inhibitor activity
GO:0005102 signaling receptor binding
GO:0005515 protein binding
GO:0005539 glycosaminoglycan binding
GO:0008201 heparin binding
Biological Process
GO:0007399 nervous system development
GO:0007596 blood coagulation
GO:0008285 negative regulation of cell population proliferation
GO:0009611 response to wounding
GO:0010466 negative regulation of peptidase activity
GO:0010544 negative regulation of platelet activation
GO:0010757 negative regulation of plasminogen activation
GO:0010766 negative regulation of sodium ion transport
GO:0010955 negative regulation of protein processing
GO:0021683 cerebellar granular layer morphogenesis
GO:0030154 cell differentiation
GO:0030163 protein catabolic process
GO:0030168 platelet activation
GO:0030195 negative regulation of blood coagulation
GO:0030308 negative regulation of cell growth
GO:0030334 regulation of cell migration
GO:0032940 secretion by cell
GO:0033363 secretory granule organization
GO:0042177 negative regulation of protein catabolic process
GO:0042628 mating plug formation
GO:0045861 negative regulation of proteolysis
GO:0045879 negative regulation of smoothened signaling pathway
GO:0048505 regulation of timing of cell differentiation
GO:0048711 positive regulation of astrocyte differentiation
GO:0050974 detection of mechanical stimulus involved in sensory perception
GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051966 regulation of synaptic transmission, glutamatergic
GO:0060291 long-term synaptic potentiation
GO:0060384 innervation
GO:0061108 seminal vesicle epithelium development
GO:0090331 negative regulation of platelet aggregation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005829 cytosol
GO:0031091 platelet alpha granule
GO:0031594 neuromuscular junction
GO:0062023 collagen-containing extracellular matrix
GO:1903561 extracellular vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4dy7, PDBe:4dy7, PDBj:4dy7
PDBsum4dy7
PubMed22618708
UniProtP07093|GDN_HUMAN Glia-derived nexin (Gene Name=SERPINE2)

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