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, 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: 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 [TaxId:70601]
    Gene: ndk
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dyaa_
  • 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: d2dyab_
  • 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