3ZTR | pdb_00003ztr

Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE OF RADIATION DAMAGE)

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)
L	d3ztrl_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
K	d3ztrk_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
J	d3ztrj_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
I	d3ztri_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
H	d3ztrh_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
G	d3ztrg_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
F	d3ztrf_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E	d3ztre_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D	d3ztrd_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d3ztrc_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d3ztrb_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d3ztra_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	3001175	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061561	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)
L	RRM_1	e3ztrL1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
K	RRM_1	e3ztrK1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
J	RRM_1	e3ztrJ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
I	RRM_1	e3ztrI1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
H	RRM_1	e3ztrH1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
G	RRM_1	e3ztrG1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
F	RRM_1	e3ztrF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
E	RRM_1	e3ztrE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
D	RRM_1	e3ztrD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
C	RRM_1	e3ztrC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
B	RRM_1	e3ztrB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
A	RRM_1	e3ztrA1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
K	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
J	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
I	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
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, I, J, K, L	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, I, J, K, L	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	nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process ribose phosphate metabolic process nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process nucleoside triphosphate metabolic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process GTP metabolic process GTP biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process CTP biosynthetic process CTP metabolic 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, I, J, K, L	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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.