5VRB | pdb_00005vrb

Crystal structure of a transketolase from Neisseria gonorrhoeae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d5vrbd1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
D	d5vrbd3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
C	d5vrbc1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
C	d5vrbc3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
B	d5vrbb1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
B	d5vrbb3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
A	d5vrba1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
A	d5vrba3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Transketolase_C_1	e5vrbD2	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
D	Transketolase_N	e5vrbD1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transketolase_N	ECOD (1.6)
D	Transket_pyr	e5vrbD3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
C	Transketolase_C_1	e5vrbC3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
C	Transketolase_N	e5vrbC2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transketolase_N	ECOD (1.6)
C	Transket_pyr	e5vrbC1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
B	Transketolase_C_1	e5vrbB2	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
B	Transketolase_N	e5vrbB1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transketolase_N	ECOD (1.6)
B	Transket_pyr	e5vrbB3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
A	Transketolase_C_1	e5vrbA3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
A	Transketolase_N	e5vrbA2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transketolase_N	ECOD (1.6)
A	Transket_pyr	e5vrbA1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
D	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
C	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
A	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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	Transketolase	transketolase activity transketolase or transaldolase activity transferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process generation of precursor metabolites and energy nucleotide metabolic process NADP+ metabolic process aldehyde metabolic process purine-containing compound metabolic process NADPH regeneration organophosphate metabolic process metabolic process cellular process pentose-phosphate shunt, non-oxidative branch	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR033247	Transketolase family	Family
A, B, C, D	IPR005474	Transketolase, N-terminal	Domain
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
A, B, C, D	IPR049557	Transketolase conserved site	Conserved Site
A, B, C, D	IPR005478	Transketolase, bacterial-like	Family
A, B, C, D	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
A, B, C, D	IPR055152	Transketolase-like, C-terminal domain	Domain
A, B, C, D	IPR020826	Transketolase binding site	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.