Structure of PDB 4m8n Chain E Binding Site BS01

Receptor Information
>4m8n Chain E (length=168) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQ
CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQI
LRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKS
KINVNEIFYDLVRQINSG
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 chain4m8n Chain E Residue 200 [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]
PDB4m8n Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.
Resolution3.294 Å
Binding residue
(original residue number in PDB)		S17 T35
Binding residue
(residue number reindexed from 1)		S17 T35
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0044877 protein-containing complex binding
Biological Process
GO:0007165 signal transduction
GO:0007264 small GTPase-mediated signal transduction
GO:0008283 cell population proliferation
GO:0017156 calcium-ion regulated exocytosis
GO:0030033 microvillus assembly
GO:0032486 Rap protein signal transduction
GO:0033625 positive regulation of integrin activation
GO:0045955 negative regulation of calcium ion-dependent exocytosis
GO:0051649 establishment of localization in cell
GO:0061028 establishment of endothelial barrier
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071320 cellular response to cAMP
GO:0099010 modification of postsynaptic structure
GO:1901888 regulation of cell junction assembly
GO:2000114 regulation of establishment of cell polarity
GO:2000301 negative regulation of synaptic vesicle exocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0035577 azurophil granule membrane
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0070161 anchoring junction
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4m8n, PDBe:4m8n, PDBj:4m8n
PDBsum4m8n
PubMed24137545
UniProtP61224|RAP1B_HUMAN Ras-related protein Rap-1b (Gene Name=RAP1B)

[Back to BioLiP]