4F36 | pdb_00004f36

Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form

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)
A	d4f36a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
B [auth C]	d4f36c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
C [auth B]	d4f36b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
F	d4f36f_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
E	d4f36e1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
E	d4f36e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)
D	d4f36d_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Trypanosoma brucei brucei TREU927 ) [TaxId: 185431 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8061522	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8061523	3001175	SCOP2 (2022-06-29)
B [auth C]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061523	3001175	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061523	3001175	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061523	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061523	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8061523	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)
A		e4f36A1	A: P-loop domains-like	X: RIFT-related	H: FMN-binding split barrel 2	T: Pribosyltran_N	F:	ECOD (20:10:01)
B [auth C]		e4f36C1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)
C [auth B]		e4f36B1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)
F		e4f36F1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)
E		e4f36E1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)
D		e4f36D1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: 14-3-3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
B [auth C]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
C [auth B]	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	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 [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	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	ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic 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 metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic 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 nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process metabolic process cellular 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 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 CTP biosynthetic process CTP metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process post-transcriptional regulation of gene expression regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle cell projection cellular anatomical structure intracellular anatomical structure ciliary plasm organelle cilium cytoplasm plasma membrane bounded cell projection intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B [auth C], C [auth B], D, E, A, B [auth C], C [auth B], D, E, F	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.