Structure of PDB 4nen Chain B Binding Site BS02

Receptor Information
>4nen Chain B (length=665) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRG
CAADDIMDPTSLAETQEDQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYP
IDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTV
LPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTDNSNQFQTEVGKQLI
SGNLDAPEGGLDAMMQVAACPEEIGWRKVTRLLVFATDDGFHFAGDGKLG
AILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRM
VKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPD
TLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSF
VIRALGFTDIVTVQVLPQCECRCRLCHGKGFLECGICRCDTGYIGKNCEC
QTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQY
CECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCERTTEGCL
NPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAECLK
FEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGMD
RYLIYVDESRECCGG
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 chain4nen Chain B Residue 706 [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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PDB4nen An internal ligand-bound, metastable state of a leukocyte integrin, alpha X beta 2.
Resolution2.9012 Å
Binding residue
(original residue number in PDB)		S116 D242
Binding residue
(residue number reindexed from 1)		S112 D238
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001540 amyloid-beta binding
GO:0001851 complement component C3b binding
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0030369 ICAM-3 receptor activity
GO:0031072 heat shock protein binding
GO:0038024 cargo receptor activity
GO:0046872 metal ion binding
GO:0050839 cell adhesion molecule binding
Biological Process
GO:0001774 microglial cell activation
GO:0006898 receptor-mediated endocytosis
GO:0006909 phagocytosis
GO:0006911 phagocytosis, engulfment
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0007155 cell adhesion
GO:0007159 leukocyte cell-cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0007267 cell-cell signaling
GO:0008360 regulation of cell shape
GO:0030593 neutrophil chemotaxis
GO:0031623 receptor internalization
GO:0032930 positive regulation of superoxide anion generation
GO:0034113 heterotypic cell-cell adhesion
GO:0035987 endodermal cell differentiation
GO:0043113 receptor clustering
GO:0043315 positive regulation of neutrophil degranulation
GO:0045963 negative regulation of dopamine metabolic process
GO:0050730 regulation of peptidyl-tyrosine phosphorylation
GO:0071404 cellular response to low-density lipoprotein particle stimulus
GO:0090314 positive regulation of protein targeting to membrane
GO:0097242 amyloid-beta clearance
GO:0098609 cell-cell adhesion
GO:0098742 cell-cell adhesion via plasma-membrane adhesion molecules
GO:1904996 positive regulation of leukocyte adhesion to vascular endothelial cell
GO:1990266 neutrophil migration
GO:2000363 positive regulation of prostaglandin-E synthase activity
Cellular Component
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0008305 integrin complex
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0034687 integrin alphaL-beta2 complex
GO:0034688 integrin alphaM-beta2 complex
GO:0034689 integrin alphaX-beta2 complex
GO:0035579 specific granule membrane
GO:0043235 receptor complex
GO:0044853 plasma membrane raft
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane
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:4nen, PDBe:4nen, PDBj:4nen
PDBsum4nen
PubMed24385486
UniProtP05107|ITB2_HUMAN Integrin beta-2 (Gene Name=ITGB2)

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