6ZRN | pdb_00006zrn

Crystal structure of the RLIP76 Ral binding domain mutant (E427S/L429M/Q433L/K440R) in complex with RalB-GMPPNP

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	d6zrna_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6zrnb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	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	8057486	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057486	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	e6zrnA1	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)
B	Ras	e6zrnB1	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)
C	KOG4370	e6zrnC1	A: alpha bundles	X: Long alpha-hairpin	H: Ral binding domain of RLIP76 (From Topology)	T: Ral binding domain of RLIP76	F: KOG4370	ECOD (1.6)
D	KOG4370	e6zrnD1	A: alpha bundles	X: Long alpha-hairpin	H: Ral binding domain of RLIP76 (From Topology)	T: Ral binding domain of RLIP76	F: KOG4370	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 (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, motili ...	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
C, D	PF20924	RLIP76, Ral binding domain (RLIP76_Ral-bd)	RLIP76, Ral binding domain	This domain is found in RLIP76 (also known as RalA-binding protein 1, RalBP1), a multifunctional protein that interacts with multiple small G protein families and endocytosis proteins. The Ral binding domain is a coiled-coil. The orientation of its a ...	This domain is found in RLIP76 (also known as RalA-binding protein 1, RalBP1), a multifunctional protein that interacts with multiple small G protein families and endocytosis proteins. The Ral binding domain is a coiled-coil. The orientation of its alpha-helices and the loop between them slightly changes upon binding to RalB. This interaction appears to be related to the cellular localization of the complex [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ras-related protein Ral-B	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding ATPase binding	regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cell division apoptotic process cell death programmed cell death cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA response to stimulus cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of biological process regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation regulation of localization exocyst localization macromolecule localization regulation of exocyst localization protein-containing complex localization regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization regulation of exocyst assembly exocyst assembly membrane docking cellular component biogenesis cellular component organization organelle localization by membrane tethering regulation of protein-containing complex assembly cellular component assembly secretion by cell organelle localization protein-containing complex assembly cellular component organization or biogenesis vesicle docking involved in exocytosis protein-containing complex organization secretion export from cell regulation of cellular component biogenesis exocytosis vesicle docking exocytic process regulation of vesicle docking positive regulation of organelle organization catabolic process positive regulation of cellular component organization macroautophagy positive regulation of vacuole organization autophagy autophagosome organization regulation of autophagy positive regulation of autophagosome assembly positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis regulation of autophagosome assembly regulation of catabolic process regulation of vacuole organization regulation of organelle organization positive regulation of catabolic process organelle organization regulation of macroautophagy regulation of organelle assembly positive regulation of organelle assembly positive regulation of protein binding positive regulation of binding	midbody cellular anatomical structure extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane
C, D	RalA-binding protein 1	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity xenobiotic transmembrane transporter activity ABC-type transporter activity small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity xenobiotic transmembrane transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type xenobiotic transporter activity transporter activity transmembrane transporter activity ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding sulfur compound transmembrane transporter activity ABC-type glutathione S-conjugate transporter activity	doxorubicin transport localization glycoside transport nitrogen compound transport transport organic hydroxy compound transport carbohydrate derivative transport establishment of localization organic cation transport cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process small GTPase-mediated signal transduction doxorubicin transport localization glycoside transport nitrogen compound transport transport organic hydroxy compound transport carbohydrate derivative transport establishment of localization organic cation transport cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction biological regulation regulation of signal transduction regulation of Cdc42 protein signal transduction regulation of Rho protein signal transduction intracellular signal transduction Rho protein signal transduction Cdc42 protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity transmembrane transport chemotaxis taxis response to chemical response to external stimulus locomotion positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process positive regulation of biological process cellular component organization positive regulation of developmental process anatomical structure development cellular component organization or biogenesis positive regulation of cellular process regulation of anatomical structure morphogenesis mitochondrion organization developmental process organelle fission mitochondrial fission regulation of organelle organization anatomical structure morphogenesis organelle organization regulation of mitochondrial fission regulation of mitochondrion organization positive regulation of mitochondrial fission positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoskeleton spindle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoskeleton spindle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane cytosol cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR020849	Small GTPase, Ras-type	Family
A, B	IPR001806	Small GTPase	Family
C, D	IPR049041	RalA-binding protein 1-like, Ral binding domain	Domain
C, D	IPR008936	Rho GTPase activation protein	Homologous Superfamily
C, D	IPR000198	Rho GTPase-activating protein domain	Domain
C, D	IPR039767	RalA-binding protein 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P11234	astrocytic tumor malignant ependymoma osteosarcoma breast carcinoma malignant mesothelioma psoriasis large cell medulloblastoma medulloblastoma rheumatoid arthritis
C, D	Pharos: Q15311	hypertensive disorder prostate cancer astrocytic tumor interstitial cystitis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Prostatic Neoplasms coronary artery disease myocardial ischemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma subependymal giant cell astrocytoma

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.