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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE 2 FROM ARABIDOPSIS
 
Authors :  Y. J. Im, J. -I. Kim, Y. Shen, Y. Na, Y. -J. Han, S. -H. Kim, P. -S. Song, S. H. Eom
Date :  20 Jan 04  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Transferase, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. J. Im, J. -I. Kim, Y. Shen, Y. Na, Y. -J. Han, S. -H. Kim, P. -S. Song, S. H. Eom
Structural Analysis Of Arabidopsis Thaliana Nucleoside Diphosphate Kinase-2 For Phytochrome-Mediated Light Signaling
J. Mol. Biol. V. 343 659 2004
PubMed-ID: 15465053  |  Reference-DOI: 10.1016/J.JMB.2004.08.054
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE II
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NDPK2
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: NUCLEOSIDE DIPHOSPHATE KINASE 2, NDK II, NDP KINASE II, NDPK II, NDPK IA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO418Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO418Ligand/IonSULFATE ION
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
1EPE4Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO49Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:167BINDING SITE FOR RESIDUE SO4 A 1001
02AC2SOFTWAREARG A:167 , THR A:173 , ARG A:184 , HIS A:197 , HOH A:1137 , HOH A:1176BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWARELYS A:172 , THR A:173 , HOH A:1114 , HOH A:1164BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREARG B:167 , HOH B:1179 , LYS D:206BINDING SITE FOR RESIDUE SO4 B 1004
05AC5SOFTWARELYS B:91 , ARG B:167 , THR B:173 , ARG B:184 , HIS B:197 , HOH B:1134BINDING SITE FOR RESIDUE SO4 B 1005
06AC6SOFTWARELYS B:172 , THR B:173 , HOH B:1178 , HOH B:1179 , ASP D:82 , LYS D:206 , HOH D:1193BINDING SITE FOR RESIDUE SO4 B 1006
07AC7SOFTWAREARG C:167 , HOH C:1156 , HOH C:1161BINDING SITE FOR RESIDUE SO4 C 1007
08AC8SOFTWARELYS C:91 , ARG C:184 , HIS C:197BINDING SITE FOR RESIDUE SO4 C 1008
09AC9SOFTWARELYS C:172 , THR C:173 , HOH C:1128BINDING SITE FOR RESIDUE SO4 C 1009
10BC1SOFTWAREARG D:167 , HOH D:1185 , HOH D:1189BINDING SITE FOR RESIDUE SO4 D 1010
11BC2SOFTWARELYS D:91 , ARG D:167 , ARG D:184 , HIS D:197 , HOH D:1134 , HOH D:1188 , HOH D:1212BINDING SITE FOR RESIDUE SO4 D 1011
12BC3SOFTWARELYS D:172 , THR D:173 , HOH D:1108BINDING SITE FOR RESIDUE SO4 D 1012
13BC4SOFTWAREARG E:167 , HOH E:1061 , HOH E:1082BINDING SITE FOR RESIDUE SO4 E 1013
14BC5SOFTWAREARG E:167 , THR E:173 , ARG E:184 , HOH E:1062 , HOH E:1076BINDING SITE FOR RESIDUE SO4 E 1014
15BC6SOFTWARELYS E:172 , THR E:173 , HOH E:1028 , HOH E:1058 , HOH E:1074BINDING SITE FOR RESIDUE SO4 E 1015
16BC7SOFTWAREARG F:167 , HOH F:1162BINDING SITE FOR RESIDUE SO4 F 1016
17BC8SOFTWAREARG F:167 , ARG F:184 , HIS F:197 , HOH F:1159 , HOH F:1179BINDING SITE FOR RESIDUE SO4 F 1017
18BC9SOFTWARELYS F:172 , THR F:173 , HOH F:1117BINDING SITE FOR RESIDUE SO4 F 1018
19CC1SOFTWAREGLU A:108 , GLY A:111 , PHE A:112 , LYS A:113 , TRP A:221 , SER A:223 , ALA A:226 , ARG A:230 , HOH A:1106 , HOH A:1110 , HOH A:1111 , HOH A:1152 , GLN D:96 , ARG D:97 , GLY D:98BINDING SITE FOR RESIDUE EPE A 1101
20CC2SOFTWAREGLU B:108 , GLY B:111 , TRP B:221 , SER B:223 , ALA B:226 , ARG B:230 , HOH B:1133 , HOH B:1138 , HOH B:1143 , HOH B:1147 , HOH B:1165 , HOH B:1170 , GLN F:96 , ARG F:97 , GLY F:98BINDING SITE FOR RESIDUE EPE B 1102
21CC3SOFTWAREGLU C:108 , GLY C:111 , PHE C:112 , LYS C:113 , TRP C:221 , SER C:223 , LEU C:229 , ARG C:230 , HOH C:1110 , HOH C:1131 , HOH C:1134 , HOH C:1142 , HOH C:1148 , HOH C:1164 , GLN E:96 , ARG E:97 , GLY E:98BINDING SITE FOR RESIDUE EPE C 1103
22CC4SOFTWAREGLN A:96 , ARG A:97 , GLY A:98 , GLU D:108 , GLY D:111 , PHE D:112 , LYS D:113 , TRP D:221 , SER D:223 , ALA D:226 , LEU D:229 , ARG D:230 , HOH D:1114 , HOH D:1115 , HOH D:1128 , HOH D:1200 , HOH D:1204 , HOH E:1035BINDING SITE FOR RESIDUE EPE D 1104
23CC5SOFTWAREGLN C:96 , ARG C:97 , GLY C:98 , HOH C:1127 , HOH C:1132 , HOH C:1160 , GLU E:108 , GLY E:111 , PHE E:112 , TRP E:221 , SER E:223 , ALA E:226 , HOH E:1067 , HOH E:1085BINDING SITE FOR RESIDUE EPE C 1105
24CC6SOFTWAREGLN B:96 , ARG B:97 , GLY B:98 , GLU F:108 , GLY F:111 , PHE F:112 , TRP F:221 , SER F:223 , LEU F:229 , HOH F:1114 , HOH F:1116 , HOH F:1142 , HOH F:1184BINDING SITE FOR RESIDUE EPE F 1106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S57)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S57)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S57)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK2_ARATH194-202
 
 
 
 
 		  6A:194-202
B:194-202
C:194-202
D:194-202
E:194-202
F:194-202
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK2_ARATH194-202
 
 
 
 
 		  6A:194-202
B:194-202
C:194-202
D:194-202
E:194-202
F:194-202
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK2_ARATH194-202
 
 
 
 
 		  6A:194-202
B:194-202
C:194-202
D:194-202
E:194-202
F:194-202

(-) Exons   (0, 0)

(no "Exon" information available for 1S57)

(-) Sequences/Alignments

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:153
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:153
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
           NDK2_ARATH    79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57a_ A: Nucleoside diphosphate kinase, NDK                                                                                                             SCOP domains
               CATH domains 1s57A00 A:79-231  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 A  79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:149
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         
           NDK2_ARATH    83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57b_ B: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1s57B00 B:83-231  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 B  83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         


Chain C from PDB  Type:PROTEIN  Length:149
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:149
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         
           NDK2_ARATH    83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57c_ C: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1s57C00 C:83-231  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 C  83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         


Chain D from PDB  Type:PROTEIN  Length:153
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:153
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
           NDK2_ARATH    79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57d_ D: Nucleoside diphosphate kinase, NDK                                                                                                             SCOP domains
               CATH domains 1s57D00 D:79-231  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 D  79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   


Chain E from PDB  Type:PROTEIN  Length:149
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:149
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         
           NDK2_ARATH    83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57e_ E: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1s57E00 E:83-231  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 E  83 VEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222         


Chain F from PDB  Type:PROTEIN  Length:153
 aligned with NDK2_ARATH | O64903 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:153
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
           NDK2_ARATH    79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
               SCOP domains d1s57f_ F: Nucleoside diphosphate kinase, NDK                                                                                                             SCOP domains
               CATH domains 1s57F00 F:79-231  [code=3.30.70.141, no name defined]                                                                                                     CATH domains
           Pfam domains (1) -----NDK-1s57F01 F:84-218                                                                                                                   ------------- Pfam domains (1)
           Pfam domains (2) -----NDK-1s57F02 F:84-218                                                                                                                   ------------- Pfam domains (2)
           Pfam domains (3) -----NDK-1s57F03 F:84-218                                                                                                                   ------------- Pfam domains (3)
           Pfam domains (4) -----NDK-1s57F04 F:84-218                                                                                                                   ------------- Pfam domains (4)
           Pfam domains (5) -----NDK-1s57F05 F:84-218                                                                                                                   ------------- Pfam domains (5)
           Pfam domains (6) -----NDK-1s57F06 F:84-218                                                                                                                   ------------- Pfam domains (6)
         Sec.struct. author .....eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s57 F  79 SMEDVEETYIMVKPDGIQRGLVGEIISRFEKKGFKLIGLKMFQCPKELAEEHYKDLSAKSFFPNLIEYITSGPVVCMAWEGVGVVASARKLIGKTDPLQAEPGTIRGDLAVQTGRNIVHGSDSPENGKREIGLWFKEGELCKWDSALATWLRE 231
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: NDK] (40)
(-)
Family: NDK (40)
(-)
Arabidopsis thaliana (Mouse-ear cress) (3)
1aNDK-1s57F01F:84-218
1bNDK-1s57F02F:84-218
1cNDK-1s57F03F:84-218
1dNDK-1s57F04F:84-218
1eNDK-1s57F05F:84-218
1fNDK-1s57F06F:84-218

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NDK2_ARATH | O64903)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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: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:0009734    auxin-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription.
    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: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:0009585    red, far-red light phototransduction    The sequence of reactions within a cell required to convert absorbed photons from red or far-red light into a molecular signal; the red, far-red light range is defined as having a wavelength within the range 660-730 nm.
    GO:0009411    response to UV    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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0042542    response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009941    chloroplast envelope    The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        NDK2_ARATH | O64903: 1s59

(-) Related Entries Specified in the PDB File

1s59 THE SAME PROTEIN COMPLEXED WITH DGTP