3R5A | pdb_00003r5a

Pseudomonas aeruginosa DapD (PA3666) in complex with D-2-aminopimelate

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8050589	3001804	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	Hexapep_2	e3r5aA2	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
A	THDPS_N	e3r5aA1	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
B	Hexapep_2	e3r5aB1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
B	THDPS_N	e3r5aB2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
C	Hexapep_2	e3r5aC1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
C	THDPS_N	e3r5aC2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
D	Hexapep_2	e3r5aD1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
D	THDPS_N	e3r5aD2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
E	Hexapep_2	e3r5aE1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
E	THDPS_N	e3r5aE2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)
F	Hexapep_2	e3r5aF1	A: beta duplicates or obligate multimers	X: Single-stranded left-handed beta-helix	H: Trimeric LpxA-like enzymes (From Topology)	T: Trimeric LpxA-like enzymes	F: Hexapep_2	ECOD (1.6)
F	THDPS_N	e3r5aF2	A: a+b complex topology	X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	H: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain (From Topology)	T: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain	F: THDPS_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
B	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
C	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
D	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
D	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
E	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
E	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
F	3.30.70.2010	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
F	3.30.60.70	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
F	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	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	PF14790	Tetrahydrodipicolinate N-succinyltransferase N-terminal (THDPS_N)	Tetrahydrodipicolinate N-succinyltransferase N-terminal	This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF14789	Tetrahydrodipicolinate N-succinyltransferase middle (THDPS_M)	Tetrahydrodipicolinate N-succinyltransferase middle	This is the middle domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF14602	Hexapeptide repeat of succinyl-transferase (Hexapep_2)	Hexapeptide repeat of succinyl-transferase	-	Repeat

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	Tetrahydrodipicolinate N-succinyletransferase	N-succinyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity succinyltransferase activity catalytic activity N-acyltransferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding	diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process diaminopimelate metabolic process amino acid biosynthetic process diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process diaminopimelate metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process lysine metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process alpha-amino acid metabolic process lysine biosynthetic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR011004	Trimeric LpxA-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038361	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR026586	Type 2 tetrahydrodipicolinate N-succinyltransferase family	Family
A, B, C, D, E A, B, C, D, E, F	IPR032784	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019876	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria	Family
A, B, C, D, E A, B, C, D, E, F	IPR001451	Hexapeptide repeat	Repeat

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.