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(-) Description

Title :  PLASMODIUM FALCIPARUM NUCLEOSIDE DIPHOSPHATE KINASE B
 
Authors :  M. A. Robien, J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogen Protozoa Consortium (Sgpp)
Date :  21 Sep 04  (Deposition) - 12 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein Structure Initiative, Structural Genomics, Sgpp, Psi, Structural Genomics Of Pathogenic Protozoa Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa
Crystal Structure Of Nucleoside Diphosphate Kinase B From Plasmodium Falciparum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE B
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR/DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF13_0349
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XIQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XIQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1XIQ)

(-) Sequences/Alignments

Asymmetric/Biological 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 Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqa_ A: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqA00 A:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh......hhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq A   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqb_ B: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqB00 B:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh......hhhhhhhh..eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq B   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain C from PDB  Type:PROTEIN  Length:149
 aligned with Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqc_ C: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqC00 C:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh.....hhhhhhhhh.eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq C   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain D from PDB  Type:PROTEIN  Length:149
 aligned with Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqd_ D: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqD00 D:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhh............hhhhhhhhh.eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq D   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain E from PDB  Type:PROTEIN  Length:149
 aligned with Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqe_ E: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqE00 E:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhh.....hhhhhhhhh.eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq E   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain F from PDB  Type:PROTEIN  Length:149
 aligned with Q8ID43_PLAF7 | Q8ID43 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q8ID43_PLAF7     1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
               SCOP domains d1xiqf_ F: Nucleoside diphosphate kinase, NDK                                                                                                         SCOP domains
               CATH domains 1xiqF00 F:1-149  [code=3.30.70.141, no name defined]                                                                                                  CATH domains
           Pfam domains (1) -NDK-1xiqF01 F:2-136                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) -NDK-1xiqF02 F:2-136                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) -NDK-1xiqF03 F:2-136                                                                                                                    ------------- Pfam domains (3)
           Pfam domains (4) -NDK-1xiqF04 F:2-136                                                                                                                    ------------- Pfam domains (4)
           Pfam domains (5) -NDK-1xiqF05 F:2-136                                                                                                                    ------------- Pfam domains (5)
           Pfam domains (6) -NDK-1xiqF06 F:2-136                                                                                                                    ------------- Pfam domains (6)
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xiq F   1 MEKSFIMIKPDGVQRGLVGTIIKRFEKKGYKLIAIKMLNPTEEILKEHYKELSDQPFFKNLVAYISKGPVVAMVWEGVDMVKQGRKLIGETNPLTSNTGTIRGDFCLEVSKNVIHGSDSVASANKEINIWFKAEELTQWKHHMKEWICS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: NDK] (40)
(-)
Family: NDK (40)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q8ID43_PLAF7 | Q8ID43)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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.
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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