4A72 | pdb_00004a72

Crystal structure of the omega transaminase from Chromobacterium violaceum in a mixture of apo and PLP-bound states

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)
D	d4a72d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Chromobacterium violaceum ) [TaxId: 536 ],	SCOPe (2.08)
C	d4a72c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Chromobacterium violaceum ) [TaxId: 536 ],	SCOPe (2.08)
B	d4a72b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Chromobacterium violaceum ) [TaxId: 536 ],	SCOPe (2.08)
A	d4a72a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Chromobacterium violaceum ) [TaxId: 536 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8071942	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8071942	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8071942	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8071942	3000954	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)
D	Tiam_CC_Ex	e4a72D1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Tiam_CC_Ex	ECOD (develop294)
C	Tiam_CC_Ex	e4a72C1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Tiam_CC_Ex	ECOD (develop294)
B	PI3K_C2	e4a72B1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (develop294)
A	PI3K_C2	e4a72A1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00202	Aminotransferase class-III (Aminotran_3)	Aminotransferase class-III		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	OMEGA TRANSAMINASE	transferase activity, transferring nitrogenous groups transaminase activity adenosylmethionine-8-amino-7-oxononanoate transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding identical protein binding transferase activity, transferring nitrogenous groups transaminase activity adenosylmethionine-8-amino-7-oxononanoate transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding identical protein binding protein binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR049704	Aminotransferases class-III pyridoxal-phosphate attachment site	Conserved Site
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR005814	Aminotransferase class-III	Family
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily

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.