PDB entry 2dya

View 2dya on RCSB PDB site
Description: Crystal structure of complex between Adenine nucleotide and nucleoside diphosphate kinase
Class: transferase
Keywords: nucleoside binding, kinase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI
Deposited on 2006-09-08, released 2007-03-08
The last revision prior to the SCOP 1.73 freeze date was dated 2007-03-08, with a file datestamp of 2007-06-04.
Experiment type: XRAY
Resolution: 1.77 Å
R-factor: 0.114
AEROSPACI score: 0.59 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Pyrococcus horikoshii
    Gene: ndk
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d2dyaa1
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Pyrococcus horikoshii
    Gene: ndk
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d2dyab1
  • Heterogens: MG, CL, ADP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dyaA (A:)
    mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
    kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
    nvihasdskesaereislffkpeelfeypraadwfykkgi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dyaA (A:)
    setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
    kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
    asdskesaereislffkpeelfeypraadwfykk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dyaB (B:)
    mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
    kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
    nvihasdskesaereislffkpeelfeypraadwfykkgi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dyaB (B:)
    setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
    kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
    asdskesaereislffkpeelfeypraadwfykkg