6AY1 | pdb_00006ay1

Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori

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)
H	d6ay1h_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
G	d6ay1g_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
E	d6ay1e_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
D	d6ay1d_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d6ay1c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
B	d6ay1b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A	d6ay1a1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A	d6ay1a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2B (2022-06-29)
E	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8061558	4001261	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061559	3001175	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)
H	XRCC4	e6ay1H1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
G	XRCC4	e6ay1G1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
F	XRCC4	e6ay1F1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
E	XRCC4	e6ay1E1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
D	XRCC4	e6ay1D1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
C	XRCC4	e6ay1C1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
B	XRCC4	e6ay1B1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)
A	XRCC4	e6ay1A1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: XRCC4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
G	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
F	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
E	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
D	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
C	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
B	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
A	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like 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	PF00334	Nucleoside diphosphate kinase (NDK)	Nucleoside diphosphate kinase		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	Nucleoside diphosphate kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleobase-containing compound kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	ribose phosphate metabolic process CTP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process pyrimidine ribonucleoside triphosphate biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process CTP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process pyrimidine ribonucleoside triphosphate biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process CTP metabolic process ribonucleoside triphosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine ribonucleoside triphosphate metabolic process nucleoside triphosphate metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process UTP biosynthetic process UTP metabolic process GTP metabolic process GTP biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine nucleotide metabolic process purine nucleoside triphosphate biosynthetic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine-containing compound metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001564	Nucleoside diphosphate kinase	Family

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.