3QQM | pdb_00003qqm

Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
F	SCOP2 Family	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100429	4002874	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	D-aminoacid aminotransferase-like PLP-dependent enzymes	8100430	3001836	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)
A	AHSA1	e3qqmA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F: AHSA1	ECOD (v294.1)
A	TPK_catalytic	e3qqmA3	A: a/b three-layered sandwiches	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: TPK_catalytic	ECOD (v294.1)
B	AAA	e3qqmB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
C	AAA	e3qqmC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
D	AAA	e3qqmD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
E	AAA	e3qqmE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
F	AAA	e3qqmF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
G	AAA	e3qqmG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
H	AAA	e3qqmH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
B	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
C	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
D	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
E	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
E	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
F	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
F	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
G	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
G	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)
H	3.30.470.10	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
H	3.20.10.10	Alpha Beta	Alpha-Beta Barrel	D-amino Acid Aminotransferase	Chain A, domain 2	CATH (4.3.0)

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, G, H	Mlr3007 protein	transferase activity, transferring nitrogenous groups branched-chain-amino-acid transaminase activity transaminase activity transferase activity catalytic activity	small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process biosynthetic process branched-chain amino acid biosynthetic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050571	Class-IV Pyridoxal-Phosphate-Dependent Aminotransferase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043132	Branched-chain-amino-acid aminotransferase-like, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043131	Branched-chain-amino-acid aminotransferase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001544	Aminotransferase class IV	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036038	Aminotransferase-like, PLP-dependent enzymes	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018300	Aminotransferase, class IV, conserved site	Conserved Site

Protein Modification Annotation

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

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.