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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA NUCLEOSIDE DIPHOSPHATE KINASE B WITH UNORDERED NUCLEOTIDE-BINDING LOOP.
 
Authors :  D. M. Trindade, T. A. C. B. Sousa, C. C. C. Tonoli, C. R. Santos, R. K. Arni, A. H. C. Oliveira, M. T. Murakami
Date :  13 Jun 10  (Deposition) - 27 Apr 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Ndkb, Phosphate Ion, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Souza, D. M. Trindade, C. C. Tonoli, C. R. Santos, R. J. Ward, R. K. Arni, A. H. Oliveira, M. T. Murakami
Molecular Adaptability Of Nucleoside Diphosphate Kinase B From Trypanosomatid Parasites: Stability, Oligomerization And Structural Determinants Of Nucleotide Binding.
Mol Biosyst V. 7 2189 2011
PubMed-ID: 21528129  |  Reference-DOI: 10.1039/C0MB00307G

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    ChainsA
    EC Number2.7.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneL1648.07, LMJF32.2950, NDKB
    Organism ScientificLEISHMANIA MAJOR
    Organism Taxid5664

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , ARG A:87 , THR A:93 , ARG A:104 , HIS A:117BINDING SITE FOR RESIDUE PO4 A 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NGR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NGR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NGR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NGR)

(-) Exons   (0, 0)

(no "Exon" information available for 3NGR)

(-) 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    
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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:117
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
         Q9U1E1_LEIMA     1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSH 144
               SCOP domains d3ngra_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---NDK-3ngrA01 A:4-138                                                                                                                    ------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeeee.---------------------------...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee......hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngr A   1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQ---------------------------SGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSH 144
                                    10        20        30        40|        -         -        70        80        90       100       110       120       130       140    
                                                                   41                          69                                                                           

   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NGR)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Family: NDK (40)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9U1E1_LEIMA | Q9U1E1)
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: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: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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 Related Entries

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

UniProtKB/TrEMBL
        Q9U1E1_LEIMA | Q9U1E13ngs 3ngt 3ngu 5c7p 5caa 5cab

(-) Related Entries Specified in the PDB File

3ngs THE SAME PROTEIN WITH ORDERED NUCLEOTIDE-BINDING LOOP
3ngt THE SAME PROTEIN COMPLEXED WITH AMP.
3ngu THE SAME PROTEIN COMPLEXED WITH ADP.