3EKM | pdb_00003ekm

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
F	d3ekmf1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d3ekme1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d3ekmd1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d3ekmc1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d3ekmb1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d3ekma1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	Diaminopimelate epimerase	Diaminopimelate epimerase	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	DAP_epimerase	e3ekmF3	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)
E	DAP_epimerase	e3ekmE3	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)
D	DAP_epimerase	e3ekmD3	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)
C	DAP_epimerase	e3ekmC5	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)
B	DAP_epimerase	e3ekmB3	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)
A	DAP_epimerase	e3ekmA5	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: DAP_epimerase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
E	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
D	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
C	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
B	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
A	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, 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	PF01678	Diaminopimelate epimerase (DAP_epimerase)	Diaminopimelate epimerase	Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.	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	Diaminopimelate epimerase, chloroplastic	isomerase activity racemase and epimerase activity diaminopimelate epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity	lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process lysine metabolic process oxoacid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process lysine biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast plastid stroma chloroplast stroma

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001653	Diaminopimelate epimerase, DapF	Family
A, B, C, D, E A, B, C, D, E, F	IPR018510	Diaminopimelate epimerase, active site	Active Site

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.