5D3X | pdb_00005d3x

Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5d3xa1	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5d3xa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5d3xb1	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5d3xb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PH domain-like	8086342	3000134	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PH domain-like	8086342	3000134	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5d3xA1	A: Inserted helical domain in fatty acid synthase subunit beta	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: Tubulin_C	F:	ECOD (20:10:01)
B		e5d3xB1	A: Inserted helical domain in fatty acid synthase subunit beta	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: Tubulin_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF22697	SOS1/NGEF-like PH domain (SOS1_NGEF_PH)	SOS1/NGEF-like PH domain	This is a PH domain found in a diverse group of animal proteins such as Ephexin-1, SOS1 from human and related RhoGEFs [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding phospholipid binding lipid binding guanyl-nucleotide exchange factor activity protein kinase inhibitor activity molecular function inhibitor activity enzyme inhibitor activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding phospholipid binding lipid binding guanyl-nucleotide exchange factor activity protein kinase inhibitor activity molecular function inhibitor activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity protein binding enzyme binding	superoxide metabolic process reactive oxygen species metabolic process metabolic process cellular process neutrophil activation multicellular organismal process immune system process cell activation myeloid leukocyte activation granulocyte activation leukocyte activation cell chemotaxis cellular response to stimulus chemotaxis superoxide metabolic process reactive oxygen species metabolic process metabolic process cellular process neutrophil activation multicellular organismal process immune system process cell activation myeloid leukocyte activation granulocyte activation leukocyte activation cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion protein polymerization actin polymerization or depolymerization actin filament polymerization actin cytoskeleton organization protein-containing complex organization actin filament organization cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization regulation of neuron projection development regulation of cellular component organization regulation of cellular process regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development system development developmental process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation nervous system development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading positive regulation of cellular process hemopoiesis mononuclear cell differentiation lymphocyte activation lymphocyte differentiation T cell activation T cell differentiation leukocyte differentiation negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction intracellular signaling cassette G protein-coupled receptor signaling pathway regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly regulation of actin filament polymerization regulation of biological quality regulation of actin filament organization regulation of actin polymerization or depolymerization regulation of cellular component biogenesis regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization regulation of anatomical structure size	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth somatodendritic compartment dendrite dendritic tree dendritic shaft perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001849	Pleckstrin homology domain	Domain
A, B	IPR000591	DEP domain	Domain
A, B	IPR000219	Dbl homology domain	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR001331	Guanine-nucleotide dissociation stimulator, CDC24, conserved site	Conserved Site
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR035899	Dbl homology (DH) domain superfamily	Homologous Superfamily
A, B	IPR051832	Regulators of mTOR signaling and Rac activation	Family
A, B	IPR001478	PDZ domain	Domain
A, B	IPR055251	SOS1/NGEF-like, PH domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8TCU6	ulcerative colitis atypical teratoid rhabdoid tumor breast fibroadenoma endogenous depression invasive ductal breast carcinoma lung carcinoma osteosarcoma plasma cell myeloma breast cancer colorectal adenoma heart disease large cell medulloblastoma medulloblastoma ovarian cancer subependymal giant cell astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor breast fibroadenoma endogenous depression invasive ductal breast carcinoma lung carcinoma osteosarcoma plasma cell myeloma breast cancer colorectal adenoma heart disease large cell medulloblastoma medulloblastoma ovarian cancer subependymal giant cell astrocytoma breast carcinoma colorectal cancer interstitial cystitis lung adenocarcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.