1K5D | pdb_00001k5d

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex

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)
L	d1k5dl_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	RNI-like	Rna1p (RanGAP1), N-terminal domain	Rna1p (RanGAP1), N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
I	d1k5di_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	RNI-like	Rna1p (RanGAP1), N-terminal domain	Rna1p (RanGAP1), N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
F	d1k5df_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	RNI-like	Rna1p (RanGAP1), N-terminal domain	Rna1p (RanGAP1), N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
C	d1k5dc_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	RNI-like	Rna1p (RanGAP1), N-terminal domain	Rna1p (RanGAP1), N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
K	d1k5dk_	All beta proteins	PH domain-like barrel	PH domain-like	Ran-binding domain	Ran-binding protein 1, Ranbp1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1k5dh_	All beta proteins	PH domain-like barrel	PH domain-like	Ran-binding domain	Ran-binding protein 1, Ranbp1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1k5de_	All beta proteins	PH domain-like barrel	PH domain-like	Ran-binding domain	Ran-binding protein 1, Ranbp1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1k5db_	All beta proteins	PH domain-like barrel	PH domain-like	Ran-binding domain	Ran-binding protein 1, Ranbp1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d1k5dj_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1k5dg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1k5dd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1k5da_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	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)
L	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
B	SCOP2 Family	Ran-binding domain	8025441	4002438	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PH domain-like	8037820	3000134	SCOP2 (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	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)
L		e1k5dL1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F:	ECOD (develop294)
I		e1k5dI1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F:	ECOD (develop294)
F		e1k5dF1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F:	ECOD (develop294)
C		e1k5dC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F:	ECOD (develop294)
K	Rieske	e1k5dK1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rieske	ECOD (develop294)
H	Rieske	e1k5dH1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rieske	ECOD (develop294)
E	Rieske	e1k5dE1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rieske	ECOD (develop294)
B	Ran_BP1	e1k5dB1	A: beta barrels	X: PH domain-like	H: PH domain-like	T: PH domain-like	F: Ran_BP1	ECOD (develop294)
J	ERG4_ERG24	e1k5dJ2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)
G	ERG4_ERG24	e1k5dG2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)
D	ERG4_ERG24	e1k5dD2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)
A	ERG4_ERG24	e1k5dA2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
I	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
F	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
K	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
H	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
E	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)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
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
B, E, H, K	PF00638	RanBP1 domain (Ran_BP1)	RanBP1 domain		Domain
A, D, G, J	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	Ran GTPase activating 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	localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process nuclear export establishment of localization establishment of protein localization protein export from nucleus protein transport macromolecule localization localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process nuclear export establishment of localization establishment of protein localization protein export from nucleus protein transport macromolecule localization intracellular protein localization intracellular protein transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen
B, E, H, K	Ran-specific GTPase-activating protein	small GTPase binding protein binding binding enzyme binding GTPase binding cell adhesion molecule binding cadherin binding GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity small GTPase binding protein binding binding enzyme binding GTPase binding cell adhesion molecule binding cadherin binding GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication centrosome separation microtubule cytoskeleton organization positive regulation of biological process mitotic cell cycle mitotic centrosome separation cellular component organization centrosome cycle positive regulation of cell cycle process cell cycle cellular component organization or biogenesis regulation of cell cycle positive regulation of cellular process cell cycle process mitotic nuclear division microtubule organizing center organization regulation of cell cycle process organelle fission positive regulation of cell cycle regulation of mitotic centrosome separation organelle organization nuclear division mitotic cell cycle process positive regulation of mitotic centrosome separation microtubule-based process cytoskeleton organization	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system centrosome microtubule organizing center cytoskeleton membraneless organelle membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol protein-containing complex nuclear protein-containing complex nuclear pore
A, D, G, J	GTP-binding nuclear protein RAN	cell adhesion molecule binding cadherin binding protein binding binding protein-containing complex binding dynein intermediate chain 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 protein domain specific binding cell adhesion molecule binding cadherin binding protein binding binding protein-containing complex binding dynein intermediate chain 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 protein domain specific binding chromatin binding protein heterodimerization activity protein dimerization activity RNA binding nucleic acid 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 cation binding magnesium ion binding metal ion binding GDP binding G protein activity molecular function regulator activity importin-alpha family protein binding	cellular localization establishment of protein localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization cellular localization establishment of protein localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization nuclear export intracellular protein transport viral process cell division protein-containing complex localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein localization to organelle protein import into nucleus cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization regulation of localization regulation of cellular process regulation of protein localization positive regulation of nucleocytoplasmic transport positive regulation of biological process positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport regulation of protein import into nucleus positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of transport positive regulation of protein localization to nucleus biological regulation regulation of establishment of protein localization positive regulation of protein import into nucleus regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development germ cell development nucleobase-containing compound metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process GTP metabolic process carbohydrate derivative metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process cellular response to stimulus cellular response to mineralocorticoid stimulus response to lipid response to stimulus response to endogenous stimulus response to mineralocorticoid cellular response to corticosteroid stimulus cellular response to endogenous stimulus response to corticosteroid cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus cell cycle mitotic cell cycle multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development telencephalon development hippocampus development limbic system development system development nitrogen compound transport negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of cellular process RNA localization nucleobase-containing compound transport negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA transport negative regulation of metabolic process nucleic acid transport pre-miRNA export from nucleus regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing RNA export from nucleus regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression establishment of RNA localization biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process regulation of metabolic process establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus cellular component biogenesis ribosome biogenesis ribosomal small subunit export from nucleus organelle localization ribosome localization ribosomal large subunit export from nucleus mitotic nuclear division organelle fission chromosome organization sister chromatid segregation nuclear division mitotic cell cycle process mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cell cycle process protein localization to nucleolus microtubule cytoskeleton organization mitotic spindle organization microtubule-based process microtubule cytoskeleton organization involved in mitosis spindle organization RNA import into nucleus snRNA import into nucleus snRNA transport	cellular anatomical structure membrane protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cellular anatomical structure membrane protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection nuclear protein-containing complex nuclear pore membraneless organelle intracellular membraneless organelle chromatin chromosome endosome intracellular vesicle recycling endosome cytoplasmic vesicle male germ cell nucleus germ cell nucleus midbody membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen pigment granule melanosome microtubule organizing center cytoskeleton centriole microtubule cytoskeleton nucleoplasm manchette

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C, F, I, L	IPR027038	Ran GTPase-activating protein	Family
B, E, H, K	IPR011993	PH-like domain superfamily	Homologous Superfamily
B, E, H, K	IPR000156	Ran binding domain	Domain
B, E, H, K	IPR045256	Ran-specific GTPase-activating protein 1, Ran-binding domain	Domain
B, E, H, K	IPR045255	Ran binding protein RanBP1-like	Family
A, D, G, J	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, D, G, J	IPR002041	Ran GTPase	Family
A, D, G, J	IPR005225	Small GTP-binding domain	Domain
A, D, G, J	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E, H, K	Pharos: P43487	HIV infectious disease HIV Coinfection kidney neoplasm schizophrenia kidney cancer
A, D, G, J	Pharos: P62826	keloid carcinoma HIV infectious disease Mammary Neoplasms, Experimental sarcomatoid carcinoma pemphigus undifferentiated carcinoma acute myeloid leukemia mammary neoplasms, animal nasopharyngeal carcinoma plasma cell myeloma amyotrophic lateral sclerosis lymphoplasmacytic lymphoma osteoarthritis ovarian cancer keloid carcinoma HIV infectious disease Mammary Neoplasms, Experimental sarcomatoid carcinoma pemphigus undifferentiated carcinoma acute myeloid leukemia mammary neoplasms, animal nasopharyngeal carcinoma plasma cell myeloma amyotrophic lateral sclerosis lymphoplasmacytic lymphoma osteoarthritis ovarian cancer invasive ductal breast carcinoma myopathy osteoarthritis susceptibility 1

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.