PDB entry 2dy9

View 2dy9 on RCSB PDB site
Description: Crystal structure of nucleoside diphosphate kinase in complex with ADP
Class: transferase
Keywords: nucleoside binding, kinase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSFERASE
Deposited on 2006-09-08, released 2007-03-08
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.01 Å
R-factor: 0.122
AEROSPACI score: 0.52 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: ndk
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dy9a_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: ndk
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dy9b_
  • Heterogens: MG, CL, ADP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dy9A (A:)
    mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
    kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
    nvihasdskesaereislffkpeelfeypraadwfykkgi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy9A (A:)
    setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
    kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
    asdskesaereislffkpeelfeypraadwfykk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dy9B (B:)
    mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
    kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
    nvihasdskesaereislffkpeelfeypraadwfykkgi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy9B (B:)
    setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
    kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
    asdskesaereislffkpeelfeypraadwfykkgi