1LKD | pdb_00001lkd

CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1lkda1	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Extradiol dioxygenases	2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme)	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Extradiol dioxygenases	8030659	4001093	SCOP2 (2022-06-29)
A	SCOP2 Family	Extradiol dioxygenases	8030660	4001093	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8043038	3000739	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8043039	3000739	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)
A		e1lkdA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22632	Dihydroxybiphenyl dioxygenase BphC D1 (BphC_D1)	Dihydroxybiphenyl dioxygenase BphC D1	This domain is found in dihydroxybiphenyl dioxygenase BphC and related proteins. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs).	Domain
A	PF00903	Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (Glyoxalase)	Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen biphenyl-2,3-diol 1,2-dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding	cellular response to stimulus catabolic process response to stimulus cellular response to xenobiotic stimulus xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus response to chemical metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000486	Extradiol ring-cleavage dioxygenase, class I /II	Conserved Site
A	IPR037523	Vicinal oxygen chelate (VOC), core domain	Domain
A	IPR017626	Biphenyl-2,3-diol 1,2-dioxygenase	Family
A	IPR029068	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Homologous Superfamily
A	IPR004360	Glyoxalase/fosfomycin resistance/dioxygenase domain	Domain

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.