3UHJ | pdb_00003uhj

Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021

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)
D	d3uhjd_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
F	d3uhjf_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
H	d3uhjh_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
G	d3uhjg_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
E	d3uhje_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
C	d3uhjc_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
B	d3uhjb_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)
A	d3uhja_	Multi-domain proteins (alpha and beta)	Dehydroquinate synthase-like	Dehydroquinate synthase-like	automated matches	automated matches	(Sinorhizobium meliloti ) [TaxId: 382 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2B (2022-06-29)
B	SCOP2 Family	Iron-containing alcohol dehydrogenase	8080098	4003591	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Dehydroquinate synthase-like	8080099	3001905	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Dehydroquinate synthase-like	8080099	3001905	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	CblD	e3uhjD3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
F	PK_Tyr_Ser-Thr	e3uhjF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
H	CblD	e3uhjH3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
G	CblD	e3uhjG3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
E	CblD	e3uhjE3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
C	CblD	e3uhjC3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
B	CblD	e3uhjB3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
A	LMWPc	e3uhjA1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: Bet v1-like	T: Bet v1-like	F: LMWPc	ECOD (v294.1)
A	Glyco_hydro_106	e3uhjA2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
F	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
H	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
G	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
E	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
C	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
B	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	CATH (4.3.0)
A	3.40.50.1970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.20.1090.10	Mainly Alpha	Up-down Bundle	Dehydroquinate synthase-like, alpha domain	Dehydroquinate synthase-like - alpha domain	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, G, H	PF00465	Iron-containing alcohol dehydrogenase (Fe-ADH)	Iron-containing alcohol dehydrogenase		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, G, H	Probable glycerol dehydrogenase	cation binding ion binding binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity glycerol dehydrogenase (NAD+) activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016205	Glycerol dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018211	Alcohol dehydrogenase, iron-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001670	Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA	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.