Structure of PDB 2j5x Chain A Binding Site BS01

Receptor Information

>2j5x Chain A (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFN
VWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDR
EMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGD
GLYEGLTWLTSNYK

Ligand information

Ligand ID

GSP

InChI

InChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

XOFLBQFBSOEHOG-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04	S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O

Formula

C10 H16 N5 O13 P3 S

Name

5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

PDB chain

2j5x Chain A Residue 190 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2j5x The Structural Gdp-GTP Cycle of Human Arf6.
Resolution	2.8 Å
Binding residue (original residue number in PDB)	D22 A23 G25 K26 T27 T28 T41 P43 T44 G66 K123 D125 L126 A156 T157
Binding residue (residue number reindexed from 1)	D12 A13 G15 K16 T17 T18 T31 P33 T34 G56 K113 D115 L116 A146 T147
Annotation score	3

Enzymatic activity

Catalytic site (original residue number in PDB)	Q67
Catalytic site (residue number reindexed from 1)	Q57
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:0031996	thioesterase binding
GO:0035591	signaling adaptor activity

	Biological Process
GO:0001889	liver development
GO:0006886	intracellular protein transport
GO:0007155	cell adhesion
GO:0007399	nervous system development
GO:0010975	regulation of neuron projection development
GO:0010976	positive regulation of neuron projection development
GO:0015031	protein transport
GO:0016192	vesicle-mediated transport
GO:0030154	cell differentiation
GO:0030838	positive regulation of actin filament polymerization
GO:0030866	cortical actin cytoskeleton organization
GO:0032456	endocytic recycling
GO:0034394	protein localization to cell surface
GO:0035020	regulation of Rac protein signal transduction
GO:0036010	protein localization to endosome
GO:0048261	negative regulation of receptor-mediated endocytosis
GO:0048488	synaptic vesicle endocytosis
GO:0050714	positive regulation of protein secretion
GO:0051301	cell division
GO:0051489	regulation of filopodium assembly
GO:0051549	positive regulation of keratinocyte migration
GO:0060998	regulation of dendritic spine development
GO:0072659	protein localization to plasma membrane
GO:0090162	establishment of epithelial cell polarity
GO:0097178	ruffle assembly
GO:0097284	hepatocyte apoptotic process
GO:0099562	maintenance of postsynaptic density structure
GO:0120183	positive regulation of focal adhesion disassembly
GO:1902217	erythrocyte apoptotic process
GO:1903078	positive regulation of protein localization to plasma membrane
GO:1903438	positive regulation of mitotic cytokinetic process
GO:1905345	protein localization to cleavage furrow
GO:1905606	regulation of presynapse assembly
GO:1990090	cellular response to nerve growth factor stimulus
GO:2000009	negative regulation of protein localization to cell surface
GO:2000171	negative regulation of dendrite development

	Cellular Component
GO:0001726	ruffle
GO:0005737	cytoplasm
GO:0005768	endosome
GO:0005769	early endosome
GO:0005794	Golgi apparatus
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0005925	focal adhesion
GO:0005938	cell cortex
GO:0016020	membrane
GO:0030139	endocytic vesicle
GO:0030496	midbody
GO:0031527	filopodium membrane
GO:0031901	early endosome membrane
GO:0032154	cleavage furrow
GO:0042995	cell projection
GO:0055037	recycling endosome
GO:0055038	recycling endosome membrane
GO:0070062	extracellular exosome
GO:0090543	Flemming body
GO:0098793	presynapse
GO:0098794	postsynapse
GO:0098978	glutamatergic synapse

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:2j5x, PDBe:2j5x, PDBj:2j5x
PDBsum	2j5x
PubMed	11266366
UniProt	P62330\|ARF6_HUMAN ADP-ribosylation factor 6 (Gene Name=ARF6)

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