6AXF | pdb_00006axf

Structure of RasGRP2 in complex with Rap1B

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)
P	d6axfp_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N	d6axfn_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d6axfl_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6axfj_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6axfh_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6axff_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6axfd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6axfb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	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)
P	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	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)
P	Gelsolin	e6axfP1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
N	Gelsolin	e6axfN1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
L	Gelsolin	e6axfL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
J	Gelsolin	e6axfJ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
H	Gelsolin	e6axfH1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
F	Gelsolin	e6axfF1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
D	Gelsolin	e6axfD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
B	Gelsolin	e6axfB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
O	Gelsolin	e6axfO1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
M	Gelsolin	e6axfM1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
K	Gelsolin	e6axfK1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
I	Gelsolin	e6axfI1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
G	Gelsolin	e6axfG1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
E	Gelsolin	e6axfE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
C	Gelsolin	e6axfC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)
A	Gelsolin	e6axfA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gelsolin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
N	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
L	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)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
O	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
O	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
M	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
M	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
K	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
K	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
I	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
I	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
G	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
G	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
E	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
C	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
C	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)
A	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (utative)
A	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N, P	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
A, C, E, G, I A, C, E, G, I, K, M, O	PF00617	RasGEF domain (RasGEF)	RasGEF domain	-	Family
A, C, E, G, I A, C, E, G, I, K, M, O	PF00618	RasGEF N-terminal motif (RasGEF_N)	RasGEF N-terminal motif	A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	Ras-related protein Rap-1b	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 protein-containing complex 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 component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling regulation of biological process neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular response to stimulus small GTPase-mediated signal transduction response to stimulus intracellular signal transduction intracellular signaling cassette signal transduction Rap protein signal transduction calcium-ion regulated exocytosis positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of cellular process positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling cell population proliferation cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP regulation of calcium ion-dependent exocytosis negative regulation of calcium ion-dependent exocytosis positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly regulation of integrin activation integrin activation positive regulation of integrin activation regulation of cell junction assembly cell junction assembly developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm organelle membrane secretory granule membrane cytosol cell periphery plasma membrane synapse glutamatergic synapse lipid droplet membraneless organelle intracellular membraneless organelle
A, C, E, G, I A, C, E, G, I, K, M, O	RAS guanyl-releasing protein 2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding lipid binding diacylglycerol binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity transition metal ion binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding lipid binding diacylglycerol binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity transition metal ion binding zinc ion binding	positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity regulation of growth regulation of biological process regulation of cellular component organization regulation of cellular process growth positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity regulation of growth regulation of biological process regulation of cellular component organization regulation of cellular process growth regulation of cell growth cell growth cellular component organization cellular process cellular component organization or biogenesis cellular response to stimulus response to stimulus signaling signal transduction cell communication cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette	ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection cellular anatomical structure ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection cellular anatomical structure ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cytosol neuron projection synapse cell junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR005225	Small GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR020849	Small GTPase, Ras-type	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR001806	Small GTPase	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR038851	Ras-related protein Rap1	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR008937	Ras-like guanine nucleotide exchange factor	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002048	EF-hand domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR011992	EF-hand domain pair	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR046349	C1-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: P61224	Kabuki syndrome lung adenocarcinoma
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: Q7LDG7	platelet-type bleeding disorder 18 adrenal cortex carcinoma cutaneous lupus erythematosus interstitial cystitis malignant mesothelioma attention deficit hyperactivity disorder, inattentive type cystic fibrosis large cell medulloblastoma non-small cell lung carcinoma atypical teratoid rhabdoid tumor gout lung adenocarcinoma osteosarcoma