4S0M | pdb_00004s0m

Crystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from acinetobacter baumannii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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 [auth I]	d4s0mi_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
G [auth H]	d4s0mh_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
F [auth G]	d4s0mg_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
E [auth F]	d4s0mf_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
D	d4s0md_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
C	d4s0mc_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
B	d4s0mb_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)
A	d4s0ma_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Acinetobacter baumannii ) [TaxId: 470 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth I]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	3001175	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8100886	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 [auth I]	Thymidylat_synt	e4s0mI1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
G [auth H]	Thymidylat_synt	e4s0mH1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
F [auth G]	Thymidylat_synt	e4s0mG1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
E [auth F]	Thymidylat_synt	e4s0mF1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
D	Thymidylat_synt	e4s0mD1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
C	Thymidylat_synt	e4s0mC1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
B	Thymidylat_synt	e4s0mB1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)
A	RNA_pol_Rpb2_6	e4s0mA1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: RNA_pol_Rpb2_6	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth I]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
G [auth H]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
F [auth G]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
E [auth F]	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	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 [auth F], A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E [auth F], A, B, C, D, E [auth F], F [auth G], G [auth H], H [auth I]	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.