5UD6 | pdb_00005ud6

Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound

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)
B	d5ud6b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	Red alga (Cyanidioschyzon merolae strain 10D ) [TaxId: 280699 ],	SCOPe (2.08)
D	d5ud6d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	Red alga (Cyanidioschyzon merolae strain 10D ) [TaxId: 280699 ],	SCOPe (2.08)
C	d5ud6c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	Red alga (Cyanidioschyzon merolae strain 10D ) [TaxId: 280699 ],	SCOPe (2.08)
A	d5ud6a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	Red alga (Cyanidioschyzon merolae strain 10D ) [TaxId: 280699 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Aldolase	8059109	3000445	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8059109	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8059109	3000445	SCOP2B (2022-06-29)
A	SCOP2 Family	Class I aldolase	8059108	4003216	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8059109	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)
B	SBP_bac_1	e5ud6B1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
D	SBP_bac_1	e5ud6D1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
C	Spa1_C	e5ud6C1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Spa1_C	ECOD (v294.1)
A	SBP_bac_1	e5ud6A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
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)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00701	Dihydrodipicolinate synthetase family (DHDPS)	Dihydrodipicolinate synthetase family	This family has a TIM barrel structure.	Domain

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 cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle plastid organelle intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020624	Schiff base-forming aldolase, conserved site	Conserved Site
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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	KPI	Parent Component: LYS RESID: AA0287 PSI-MOD : N6-pyruvic acid 2-iminyl-L-lysine MOD:00292

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.