4GLM | pdb_00004glm

Crystal structure of the SH3 Domain of DNMBP protein [Homo sapiens]

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)
D	d4glmd1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4glmd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4glmc_	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4glmb1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4glmb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4glma1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4glma3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4glma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
D	SCOP2B Superfamily	SH3-domain	8090160	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH3-domain	8090160	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8090160	3000153	SCOP2B (2022-06-29)
A	SCOP2 Family	SH3-domain	8088336	4000369	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH3-domain	8090160	3000153	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	RuBisCO_large_N	e4glmD2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (v294.1)
C	RuBisCO_large_N	e4glmC2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (v294.1)
B	RuBisCO_large_N	e4glmB2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (v294.1)
A	TGT	e4glmA1	A: a/b three-layered sandwiches	X: Globin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: TGT	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
C	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dynamin-binding protein	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular process cellular component organization or biogenesis cilium organization cell projection assembly developmental process organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular process cellular component organization or biogenesis cilium organization cell projection assembly developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular response to stimulus regulation of signaling regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system Golgi stack cytoplasm cell-cell junction anchoring junction cell junction cytosol presynapse synapse nucleoplasm cytoskeleton nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004148	BAR domain	Domain
A, B, C, D	IPR035820	Dynamin-binding protein, first C-terminal SH3 domain	Domain
A, B, C, D	IPR035819	Dynamin-binding protein, third N-terminal SH3 domain	Domain
A, B, C, D	IPR000219	Dbl homology domain	Domain
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A, B, C, D	IPR051492	Dynamin-binding and Rho GEF	Family
A, B, C, D	IPR001331	Guanine-nucleotide dissociation stimulator, CDC24, conserved site	Conserved Site
A, B, C, D	IPR035818	Dynamin-binding protein, second N-terminal SH3 domain	Domain
A, B, C, D	IPR001452	SH3 domain	Domain
A, B, C, D	IPR035899	Dbl homology (DH) domain superfamily	Homologous Superfamily
A, B, C, D	IPR035817	Dynamin-binding protein, first N-terminal SH3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q6XZF7	atypical teratoid rhabdoid tumor glioblastoma malignant mesothelioma psoriasis B-cell chronic lymphocytic leukemia interstitial cystitis non-alcoholic fatty liver disease tuberculosis cataract lung cancer osteosarcoma

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.