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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM RICE
 
Authors :  J. -Y. Huang, C. -Y. Chang, T. Chang, C. -J. Chen
Date :  06 Jun 03  (Deposition) - 22 Feb 05  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  Nucleoside Diphosphate Kinase, Rice, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Huang, T. Chang, C. Y. Chang, C. J. Chen
Crystal Structure Of Nucleoside Diphosphate Kinase Required For Coleoptile Elongation In Rice (Oryza Sativa L. ).
J. Struct. Biol. V. 150 309 2005
PubMed-ID: 15890279  |  Reference-DOI: 10.1016/J.JSB.2005.02.010

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE I
    ChainsA, B, C, D, E, F, G, H, I, J, K, L
    EC Number2.7.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHAT12
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonRICE
    Organism ScientificORYZA SATIVA
    Organism Taxid4530
    SynonymNUCLEOSIDE DIPHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)ABCDEF      
Biological Unit 2 (1x)      GHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PKU)

(-) Sites  (0, 0)

(no "Site" information available for 1PKU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 12)

Asymmetric Unit (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK1_ORYSJ112-120
 
 
 
 
 
 
 
 
 
 
 
  12A:115-123
B:115-123
C:115-123
D:115-123
E:115-123
F:115-123
G:115-123
H:115-123
I:115-123
J:115-123
K:115-123
L:115-123
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK1_ORYSJ112-120
 
 
 
 
 
 
 
 
 
 
 
  6A:115-123
B:115-123
C:115-123
D:115-123
E:115-123
F:115-123
-
-
-
-
-
-
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK1_ORYSJ112-120
 
 
 
 
 
 
 
 
 
 
 
  6-
-
-
-
-
-
G:115-123
H:115-123
I:115-123
J:115-123
K:115-123
L:115-123

(-) Exons   (0, 0)

(no "Exon" information available for 1PKU)

(-) 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:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains -d1pkua1 A:4-151 Nucleoside diphosphate kinase, NDK                                                                                                   SCOP domains
               CATH domains 1pkuA00 A:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku A   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkub_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuB00 B:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku B   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkuc_ C: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuC00 C:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku C   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkud_ D: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuD00 D:3-151  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhh..........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku D   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain E from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkue_ E: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuE00 E:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku E   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain F from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkuf_ F: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuF00 F:3-151  [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
                 1pku F   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain G from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkug_ G: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuG00 G:3-151  [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..........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku G   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain H from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkuh_ H: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuH00 H:3-151  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhh....hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku H   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain I from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkui_ I: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuI00 I:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku I   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain J from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkuj_ J: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuJ00 J:3-151  [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..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku J   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain K from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkuk_ K: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuK00 K:3-151  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku K   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

Chain L from PDB  Type:PROTEIN  Length:149
 aligned with NDK1_ORYSJ | Q07661 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           NDK1_ORYSJ     - -MEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 148
               SCOP domains d1pkul_ L: automated matches                                                                                                                          SCOP domains
               CATH domains 1pkuL00 L:3-151  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
           Pfam domains (1) --NDK-1pkuL01 L:5-138                                                                                                                   ------------- Pfam domains (1)
           Pfam domains (2) --NDK-1pkuL02 L:5-138                                                                                                                   ------------- Pfam domains (2)
           Pfam domains (3) --NDK-1pkuL03 L:5-138                                                                                                                   ------------- Pfam domains (3)
           Pfam domains (4) --NDK-1pkuL04 L:5-138                                                                                                                   ------------- Pfam domains (4)
           Pfam domains (5) --NDK-1pkuL05 L:5-138                                                                                                                   ------------- Pfam domains (5)
           Pfam domains (6) --NDK-1pkuL06 L:5-138                                                                                                                   ------------- Pfam domains (6)
           Pfam domains (7) --NDK-1pkuL07 L:5-138                                                                                                                   ------------- Pfam domains (7)
           Pfam domains (8) --NDK-1pkuL08 L:5-138                                                                                                                   ------------- Pfam domains (8)
           Pfam domains (9) --NDK-1pkuL09 L:5-138                                                                                                                   ------------- Pfam domains (9)
          Pfam domains (10) --NDK-1pkuL10 L:5-138                                                                                                                   ------------- Pfam domains (10)
          Pfam domains (11) --NDK-1pkuL11 L:5-138                                                                                                                   ------------- Pfam domains (11)
          Pfam domains (12) --NDK-1pkuL12 L:5-138                                                                                                                   ------------- Pfam domains (12)
         Sec.struct. author ..eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pku L   3 RMEQSFIMIKPDGVQRGLIGDIISRFEKKGFYLRGMKFMNVERSFAQQHYADLSDKPFFPGLVEYIISGPVVAMVWEGKDVVATGRRIIGATRPWEAAPGTIRADYAVEVGRNVIHGSDSVDNGKKEIALWFPEGLAEWRSNLHPWIYE 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         

   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  (2, 12)

Asymmetric Unit

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a1pkuA00A:3-151
1b1pkuB00B:3-151
1c1pkuK00K:3-151
1d1pkuL00L:3-151
1e1pkuC00C:3-151
1f1pkuD00D:3-151
1g1pkuE00E:3-151
1h1pkuF00F:3-151
1i1pkuG00G:3-151
1j1pkuH00H:3-151
1k1pkuI00I:3-151
1l1pkuJ00J:3-151

(-) Pfam Domains  (1, 12)

Asymmetric Unit
(-)
Family: NDK (40)
1aNDK-1pkuL01L:5-138
1bNDK-1pkuL02L:5-138
1cNDK-1pkuL03L:5-138
1dNDK-1pkuL04L:5-138
1eNDK-1pkuL05L:5-138
1fNDK-1pkuL06L:5-138
1gNDK-1pkuL07L:5-138
1hNDK-1pkuL08L:5-138
1iNDK-1pkuL09L:5-138
1jNDK-1pkuL10L:5-138
1kNDK-1pkuL11L:5-138
1lNDK-1pkuL12L:5-138

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (NDK1_ORYSJ | Q07661)
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: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: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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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