Structure of PDB 4neh Chain B Binding Site BS01

Receptor Information
>4neh Chain B (length=668) 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
VIRALGFTDIVTVQVLPQCECRCRDRSLCHGKGFLECGICRCDTGYIGKN
CECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIY
GQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCERTTE
GCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAE
CLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQD
GMDRYLIYVDESRECCGG
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 chain4neh Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4neh An internal ligand-bound, metastable state of a leukocyte integrin, alpha X beta 2.
Resolution2.7505 Å
Binding residue
(original residue number in PDB)		D151 N207 D209 P211 E212
Binding residue
(residue number reindexed from 1)		D147 N203 D205 P207 E208
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4neh, PDBe:4neh, PDBj:4neh
PDBsum4neh
PubMed24385486
UniProtP05107|ITB2_HUMAN Integrin beta-2 (Gene Name=ITGB2)

[Back to BioLiP]