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Biol. Unit 1 - sites (Jmol Viewer)

Title :   X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED WITH ADP AT 2 A RESOLUTION

Authors :   Y. Chen, S. Gallois-Montbrun, B. Schneider, M. Veron, S. Morera, D. Dev Bonne, J. Janin

Date :   16 Apr 03 (Deposition) - 30 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)

Keywords :   Mutant Complexe Adp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Chen, S. Gallois-Montbrun, B. Schneider, M. Veron, S. Morera, D. Deville-Bonne, J. Janin
Nucleotide Binding To Nucleoside Diphosphate Kinases: X-Ray Structure Of Human Ndpk-A In Complex With Adp And Compariso To Protein Kinases
J. Mol. Biol. V. 332 915 2003
PubMed-ID: 12972261 | Reference-DOI: 10.1016/J.JMB.2003.07.004

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE A
	Chains	:	A, B, C
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJC20
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	5	Ligand/Ion	CALCIUM ION
3	PO4	3	Ligand/Ion	PHOSPHATE ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	ADP	6	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	PO4	6	Ligand/Ion	PHOSPHATE ION
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:10 , LYS A:12 , HIS A:51 , TYR A:52 , GLY A:118 , GLY A:119 , CA A:1162 , HOH A:1226	BINDING SITE FOR RESIDUE PO4 A 1161
02	AC2	SOFTWARE	GLY A:119 , ASP A:121 , ADP A:1160 , PO4 A:1161 , HOH A:1192 , HOH A:1226	BINDING SITE FOR RESIDUE CA A 1162
03	AC3	SOFTWARE	LYS B:12 , HIS B:51 , TYR B:52 , GLY B:118 , GLY B:119 , HOH B:2236 , HOH B:2261	BINDING SITE FOR RESIDUE PO4 B 2161
04	AC4	SOFTWARE	GLY B:119 , ADP B:2160 , HOH B:2236 , HOH B:2261	BINDING SITE FOR RESIDUE CA B 2162
05	AC5	SOFTWARE	HIS C:51 , TYR C:52 , GLY C:118 , GLY C:119 , HOH C:3223	BINDING SITE FOR RESIDUE PO4 C 3161
06	AC6	SOFTWARE	ADP C:3160 , HOH C:3223 , HOH C:3224	BINDING SITE FOR RESIDUE CA C 3162
07	AC7	SOFTWARE	GLY C:131 , HOH C:3204 , HOH C:3205 , HOH C:3206	BINDING SITE FOR RESIDUE CA C 1001
08	AC8	SOFTWARE	GLY B:131 , PHE B:134 , HOH B:2241 , HOH B:2289 , HOH B:2313 , HOH B:2314	BINDING SITE FOR RESIDUE CA B 1002
09	AC9	SOFTWARE	LYS A:12 , LEU A:55 , TRP A:60 , LEU A:64 , ARG A:88 , THR A:94 , ARG A:105 , VAL A:112 , ASN A:115 , ASP A:121 , CA A:1162 , HOH A:1190	BINDING SITE FOR RESIDUE ADP A 1160
10	BC1	SOFTWARE	LYS B:12 , LEU B:55 , TRP B:60 , ARG B:88 , THR B:94 , ARG B:105 , VAL B:112 , ASN B:115 , CA B:2162 , HOH B:2211 , HOH B:2261	BINDING SITE FOR RESIDUE ADP B 2160
11	BC2	SOFTWARE	LYS C:12 , TRP C:60 , LEU C:64 , ARG C:88 , THR C:94 , ARG C:105 , VAL C:112 , ASN C:115 , CA C:3162 , HOH C:3223	BINDING SITE FOR RESIDUE ADP C 3160
12	BC3	SOFTWARE	GLU B:152 , HOH B:2312 , GLU C:152	BINDING SITE FOR RESIDUE TRS B 1003

Asymmetric Unit

No.	Residues
1	A:4	-	A:4

(no "Cis Peptide Bond" information available for 1UCN)

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_004625	S	120	G	NDKA_HUMAN	Polymorphism	121917887	A/B/C	S	120	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_004625	S	120	G	NDKA_HUMAN	Polymorphism	121917887	A/B/C	S	120	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKA_HUMAN	115-123	3	A:115-123 B:115-123 C:115-123

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKA_HUMAN	115-123	6	A:115-123 B:115-123 C:115-123

Asymmetric Unit (4, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000393196	1a	ENSE00001874573	chr17:49230897-49231023	127	NDKA_HUMAN	-	0	0	-	-
1.4b	ENST00000393196	4b	ENSE00002182518	chr17:49233012-49233141	130	NDKA_HUMAN	1-42	42	3	A:2-42 B:2-42 C:2-42	41 41 41
1.5a	ENST00000393196	5a	ENSE00002174061	chr17:49237341-49237442	102	NDKA_HUMAN	43-76	34	3	A:43-76 B:43-76 C:43-76	34 34 34
1.6c	ENST00000393196	6c	ENSE00002147222	chr17:49238521-49238633	113	NDKA_HUMAN	77-114	38	3	A:77-114 B:77-114 C:77-114	38 38 38
1.6i	ENST00000393196	6i	ENSE00001956093	chr17:49239089-49239556	468	NDKA_HUMAN	114-152	39	3	A:114-152 B:114-152 C:114-152	39 39 39

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:151
 aligned with NDKA_HUMAN | P15531 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           NDKA_HUMAN     2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
               SCOP domains d1ucna_ A: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1ucnA00 A:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------G-------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: A:2-42 UniProt: 1-42     Exon 1.5a  PDB: A:43-76           Exon 1.6c  PDB: A:77-114              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------Exon 1.6i  PDB: A:114-152               Transcript 1 (2)
                 1ucn A   2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPWFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIGGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with NDKA_HUMAN | P15531 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           NDKA_HUMAN     2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
               SCOP domains d1ucnb_ B: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1ucnB00 B:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------G-------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:2-42 UniProt: 1-42     Exon 1.5a  PDB: B:43-76           Exon 1.6c  PDB: B:77-114              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------Exon 1.6i  PDB: B:114-152               Transcript 1 (2)
                 1ucn B   2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPWFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIGGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with NDKA_HUMAN | P15531 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
           NDKA_HUMAN     2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
               SCOP domains d1ucnc_ C: Nucleoside diphosphate kinase, NDK                                                                                                           SCOP domains
               CATH domains 1ucnC00 C:2-152  [code=3.30.70.141, no name defined]                                                                                                    CATH domains
           Pfam domains (1) ---NDK-1ucnC01 C:5-139                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) ---NDK-1ucnC02 C:5-139                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) ---NDK-1ucnC03 C:5-139                                                                                                                    ------------- Pfam domains (3)
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------G-------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: C:2-42 UniProt: 1-42     Exon 1.5a  PDB: C:43-76           Exon 1.6c  PDB: C:77-114              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------Exon 1.6i  PDB: C:114-152               Transcript 1 (2)
                 1ucn C   2 ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPWFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIGGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Nucleoside diphosphate kinase, NDK (129)

Family: Nucleoside diphosphate kinase, NDK (112)

Protein domain: Nucleoside diphosphate kinase, NDK (66)

Human (Homo sapiens), NDKA [TaxId: 9606] (6)

1a	d1ucna_	A:
1b	d1ucnb_	B:
1c	d1ucnc_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.141, no name defined] (46)

Human (Homo sapiens) (5)

1a	1ucnA00	A:2-152
1b	1ucnB00	B:2-152
1c	1ucnC00	C:2-152

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NDK] (40)

Family: NDK (40)

Homo sapiens (Human) (6)

1a	NDK-1ucnC01	C:5-139
1b	NDK-1ucnC02	C:5-139
1c	NDK-1ucnC03	C:5-139

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NDKA_HUMAN | P15531)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0043015	gamma-tubulin binding	Interacting selectively and non-covalently with the microtubule constituent protein gamma-tubulin.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0019215	intermediate filament binding	Interacting selectively and non-covalently with an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0043024	ribosomal small subunit binding	Interacting selectively and non-covalently with any part of the small ribosomal subunit.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006241	CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006183	GTP biosynthetic process	The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
	GO:0006228	UTP biosynthetic process	The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0071398	cellular response to fatty acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0021766	hippocampus development	The progression of the hippocampus over time from its initial formation until its mature state.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	GO:0030879	mammary gland development	The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0002762	negative regulation of myeloid leukocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009142	nucleoside triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0043388	positive regulation of DNA binding	Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0014075	response to amine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
	GO:0051591	response to cAMP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005882	intermediate filament	A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

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	NDKA_HUMAN \| P15531	:	1jxv 2hvd 2hve 3l7u 4eno

1nue	X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 A RESOLUITION

Description

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Ligands, Modified Residues, Ions (4, 12)

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