1N6P

Crystal Structure of Human Rab5a A30E mutant complex with GppNHp

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	d1n6pa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	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	Ras-like P-loop GTPases	8054292	3002022	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	Ras	e1n6pA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ras-related protein Rab-5A	pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding G protein activity molecular function regulator activity	cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size localization import into cell receptor internalization transport receptor-mediated endocytosis cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway phagocytosis catabolic process regulation of cellular component organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component assembly process utilizing autophagic mechanism autophagosome assembly organelle assembly vacuole organization regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly metabolic process regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of localization cellular localization regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse regulation of regulated secretory pathway regulation of secretion by cell secretion by cell signal release establishment of localization in cell neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis export from cell neurotransmitter transport regulation of vesicle-mediated transport regulation of secretion signal release from synapse exocytosis regulation of neurotransmitter secretion regulation of exocytosis synaptic vesicle recycling positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis positive regulation of secretion positive regulation of cellular process positive regulation of transport modulation by host of viral process biological process involved in interspecies interaction between organisms modulation by host of symbiont process biological process involved in interaction with symbiont biological process involved in symbiotic interaction protein localization establishment of protein localization nitrogen compound transport intracellular transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport multicellular organismal process amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis filopodium assembly plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection endosome membrane cytoplasmic side of membrane early endosome early endosome membrane endomembrane system cytoplasmic side of endosome membrane cytoplasmic side of early endosome membrane endosome side of membrane phagocytic vesicle phagocytic vesicle membrane postsynaptic early endosome synapse postsynaptic endosome postsynapse cell junction ruffle cell leading edge cell body neuronal cell body transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle axon pigment granule melanosome axon terminus distal axon terminal bouton neuron projection terminus cell periphery plasma membrane membrane microdomain membrane raft early phagosome nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding domain	Domain
A	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P20339	adenoma large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma coronary artery disease myocardial ischemia pilocytic astrocytoma Gaucher disease osteosarcoma psoriasis

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.