5XGG | pdb_00005xgg

Crystal Structure C-terminal SH3 domain of Myosin IB from Entamoeba histolytica

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5xggc1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
C	d5xggc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
C	d5xggc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
D	d5xggd1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
D	d5xggd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
D	d5xggd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
F	d5xggf1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
F	d5xggf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
F	d5xggf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
E	d5xgge1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
E	d5xgge3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
E	d5xgge2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d5xggb1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d5xggb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d5xggb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
A	d5xgga1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
A	d5xgga3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
A	d5xgga2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	SH3-domain	8062081	3000153	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SH3-domain	8062081	3000153	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	SH3-domain	8062081	3000153	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SH3-domain	8062081	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8062081	3000153	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH3-domain	8062081	3000153	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)
C	SH3_1	e5xggC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
D	SH3_1	e5xggD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
F	SH3_1	e5xggF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
E	SH3_1	e5xggE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
B	SH3_1	e5xggB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
A	SH3_1	e5xggA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
D	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
F	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
E	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, E A, B, C, D, E, F	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, E A, B, C, D, E, F	Unconventional myosin IB	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding myosin light chain binding myosin binding phospholipid binding lipid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding myosin light chain binding myosin binding phospholipid binding lipid binding 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 polypeptide conformation or assembly isomerase activity isomerase activity cytoskeletal motor activity microfilament motor activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity	homeostatic process biological regulation phagosome maturation phagosome reneutralization regulation of intracellular pH cellular component organization organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis cellular process homeostatic process biological regulation phagosome maturation phagosome reneutralization regulation of intracellular pH cellular component organization organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis cellular process regulation of biological quality cellular component organization or biogenesis monoatomic cation homeostasis intracellular pH elevation regulation of cellular pH intracellular monoatomic ion homeostasis chemotaxis response to stimulus chemotaxis to cAMP taxis response to chemical response to external stimulus locomotion localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport cellular component disassembly plasma membrane bounded cell projection organization cell projection organization pseudopodium retraction lateral pseudopodium retraction pseudopodium organization actin filament-based process actin-mediated cell contraction actin filament-based movement actin-myosin filament sliding cellular localization establishment of localization in cell intracellular transport endosomal transport cellular component biogenesis filopodium assembly cellular component assembly plasma membrane bounded cell projection assembly cell projection assembly cell motility secretion by cell exocytosis secretion export from cell actin cytoskeleton organization actin filament organization supramolecular fiber organization cytoskeleton organization pinocytosis regulation of post-lysosomal vacuole size regulation of cellular component size regulation of vesicle size regulation of anatomical structure size	cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton actomyosin cytoplasm cytosol cell periphery plasma membrane membrane actin wave cell leading edge leading edge of lamellipodium lamellipodium phagocytic cup phagocytic cup lip macropinocytic cup cytoskeleton cell cortex cortical cytoskeleton macropinocytic cup cortical actin cytoskeleton membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle actin-based cell projection microvillus filopodium protein-containing complex myosin I complex myosin complex unconventional myosin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036961	Kinesin motor domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001609	Myosin head, motor domain-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010926	Class I myosin tail homology domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036072	Class I myosin, motor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001452	SH3 domain	Domain

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.