4GRX | pdb_00004grx

Structure of an omega-aminotransferase from Paracoccus denitrificans

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4grxd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Paracoccus denitrificans PD1222 ) [TaxId: 318586 ],	SCOPe (2.08)
C	d4grxc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Paracoccus denitrificans PD1222 ) [TaxId: 318586 ],	SCOPe (2.08)
B	d4grxb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Paracoccus denitrificans PD1222 ) [TaxId: 318586 ],	SCOPe (2.08)
A	d4grxa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Paracoccus denitrificans PD1222 ) [TaxId: 318586 ],	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	8071944	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8071944	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8071944	3000954	SCOP2B (2022-06-29)
A	SCOP2 Family	GABA-aminotransferase-like	8071943	4000675	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8071944	3000954	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	DHH	e4grxD1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: DHH	ECOD (v294.1)
C	Ribosomal_L24e	e4grxC1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (v294.1)
B	DHH	e4grxB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: DHH	ECOD (v294.1)
A	EXOSC1	e4grxA1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: EXOSC1	ECOD (v294.1)

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	Aminotransferase	transferase activity, transferring nitrogenous groups S-adenosyl-L-methionine:8-amino-7-oxononanoate transaminase activity 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	oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process GABA metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process GABA metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process small molecule biosynthetic process vitamin biosynthetic process organic acid biosynthetic process biotin biosynthetic process carboxylic acid biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process sulfur compound metabolic process	-

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.