3SI9 | pdb_00003si9

Crystal structure of Dihydrodipicolinate Synthase from Bartonella Henselae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3si9d1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
D	d3si9d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
C	d3si9c1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
C	d3si9c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
B	d3si9b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
B	d3si9b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
A	d3si9a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)
A	d3si9a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bartonella henselae ) [TaxId: 38323 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Aldolase	8059135	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8059135	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8059135	3000445	SCOP2B (2022-06-29)
A	SCOP2 Family	Class I aldolase	8059134	4003216	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8059135	3000445	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	Carb_anhydrase	e3si9D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Carb_anhydrase	ECOD (v294.1)
C	Carb_anhydrase	e3si9C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Carb_anhydrase	ECOD (v294.1)
B	Carb_anhydrase	e3si9B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Carb_anhydrase	ECOD (v294.1)
A		e3si9A1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	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	Dihydrodipicolinate synthase	4-hydroxy-tetrahydrodipicolinate synthase activity amine-lyase activity lyase activity catalytic activity carbon-nitrogen lyase activity	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 amino acid biosynthetic process 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 amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process lysine metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process alpha-amino acid metabolic process L-lysine biosynthetic process via diaminopimelate L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005263	4-hydroxy-tetrahydrodipicolinate synthase, DapA	Family
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR020625	Schiff base-forming aldolase, active site	Active Site
A, B, C, D	IPR002220	DapA-like	Family

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.