5YDB | pdb_00005ydb

Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter baumannii with dehydroquinic acid at 1.76 Angstrom resolution

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	d5ydbd_	Alpha and beta proteins (a/b)	Flavodoxin-like	Type II 3-dehydroquinate dehydratase	automated matches	automated matches	(Acinetobacter baumannii ATCC 17978 ) [TaxId: 400667 ],	SCOPe (2.08)
C	d5ydbc_	Alpha and beta proteins (a/b)	Flavodoxin-like	Type II 3-dehydroquinate dehydratase	automated matches	automated matches	(Acinetobacter baumannii ATCC 17978 ) [TaxId: 400667 ],	SCOPe (2.08)
B	d5ydbb_	Alpha and beta proteins (a/b)	Flavodoxin-like	Type II 3-dehydroquinate dehydratase	automated matches	automated matches	(Acinetobacter baumannii ATCC 17978 ) [TaxId: 400667 ],	SCOPe (2.08)
A	d5ydba_	Alpha and beta proteins (a/b)	Flavodoxin-like	Type II 3-dehydroquinate dehydratase	automated matches	automated matches	(Acinetobacter baumannii ATCC 17978 ) [TaxId: 400667 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Type II 3-dehydroquinate dehydratase	8077703	3001380	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type II 3-dehydroquinate dehydratase	8077703	3001380	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type II 3-dehydroquinate dehydratase	8077703	3001380	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type II 3-dehydroquinate dehydratase	8077703	3001380	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)
D		e5ydbD1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: KOW4_SPT5	F:	ECOD (20:10:01)
C		e5ydbC1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: KOW4_SPT5	F:	ECOD (20:10:01)
B		e5ydbB1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: KOW4_SPT5	F:	ECOD (20:10:01)
A		e5ydbA1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: KOW4_SPT5	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.9100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dehydroquinase, class II	CATH (4.3.0)
C	3.40.50.9100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dehydroquinase, class II	CATH (4.3.0)
B	3.40.50.9100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dehydroquinase, class II	CATH (4.3.0)
A	3.40.50.9100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dehydroquinase, class II	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	3-dehydroquinate dehydratase	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 3-dehydroquinate dehydratase activity	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process catabolic process oxoacid metabolic process quinate catabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process catabolic process oxoacid metabolic process quinate catabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process small molecule biosynthetic process dicarboxylic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process chorismate biosynthetic process dicarboxylic acid biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036441	Dehydroquinase, class II superfamily	Homologous Superfamily
A, B, C, D	IPR001874	Dehydroquinase, class II	Family
A, B, C, D	IPR018509	Dehydroquinase, class II, conserved site	Conserved 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.