1K5G

Crystal structure of Ran-GDP-AlFx-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)
A	d1k5ga_	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	d1k5gd_	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	d1k5gg_	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)
J	d1k5gj_	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)
B	d1k5gb_	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	d1k5ge_	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	d1k5gh_	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)
K	d1k5gk_	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)
C	d1k5gc_	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	d1k5gf_	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	d1k5gi_	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)
L	d1k5gl_	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)

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	8057412	3002022	SCOP2B (2022-06-29)
D	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)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PH domain-like	8037820	3000134	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RNI-like	8038588	3000990	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RNI-like	8038588	3000990	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	e1k5gA2	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)
D	Ras	e1k5gD2	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)
G	Ras	e1k5gG2	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)
J	Ras	e1k5gJ2	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	Ran_BP1	e1k5gB1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: Ran_BP1	ECOD (1.6)
E	Ran_BP1	e1k5gE1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: Ran_BP1	ECOD (1.6)
H	Ran_BP1	e1k5gH1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: Ran_BP1	ECOD (1.6)
K	Ran_BP1	e1k5gK1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: Ran_BP1	ECOD (1.6)
C	LRR_8_4	e1k5gC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
F	LRR_8_4	e1k5gF1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
I	LRR_8_4	e1k5gI1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
L	LRR_8_4	e1k5gL1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	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)
D	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)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
E	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)
K	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B, E, H, K	PF00638	RanBP1 domain (Ran_BP1)	RanBP1 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	GTP-binding nuclear protein RAN	chromatin binding binding protein heterodimerization activity protein binding 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 chromatin binding binding protein heterodimerization activity protein binding 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 cell adhesion molecule binding cadherin 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	cellular process cell cycle mitotic cell cycle cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process cellular process cell cycle mitotic cell cycle cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process RNA transport negative regulation of metabolic process nucleic acid transport biological regulation pre-miRNA export from nucleus intracellular transport regulation of macromolecule metabolic process gene expression establishment of localization 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 macromolecule localization post-transcriptional gene silencing regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus protein-containing complex localization cellular component biogenesis ribosome biogenesis ribosomal small subunit export from nucleus organelle localization cellular component organization or biogenesis ribosome localization protein localization establishment of protein localization protein export from nucleus protein transport cellular macromolecule localization intracellular protein transport viral process cell division ribosomal large subunit export from nucleus protein localization to nucleus import into nucleus establishment of protein localization to organelle protein localization to organelle protein import into nucleus mitotic nuclear division organelle fission chromosome organization sister chromatid segregation cellular component organization organelle organization nuclear division mitotic cell cycle process mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cell cycle process protein localization to nucleolus regulation of localization 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 transport positive regulation of protein localization to nucleus 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 microtubule cytoskeleton organization mitotic spindle organization microtubule-based process cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization nucleobase-containing compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process RNA import into nucleus snRNA import into nucleus snRNA transport 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 ribonucleoside triphosphate metabolic process regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding	midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen membrane pigment granule intracellular vesicle melanosome cytoplasmic vesicle cytoplasm vesicle protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex organelle envelope nuclear envelope endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle microtubule organizing center cytoskeleton centriole microtubule cytoskeleton cytosol nuclear protein-containing complex nuclear pore nucleoplasm chromatin chromosome endosome recycling endosome
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
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 protein localization establishment of protein localization nitrogen compound transport protein export from nucleus localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process nuclear export establishment of localization protein localization establishment of protein localization nitrogen compound transport protein export from nucleus protein transport cellular macromolecule localization macromolecule 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR002041	Ran GTPase	Family
A, D, G, J	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, D, G, J	IPR005225	Small GTP-binding domain	Domain
A, D, G, J	IPR001806	Small GTPase	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
C, F, I, L	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C, F, I, L	IPR027038	Ran GTPase-activating protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
B, E, H, K	Pharos: P43487	HIV infectious disease HIV Coinfection kidney neoplasm schizophrenia kidney cancer

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.