PDB entry 2dby

View 2dby on RCSB PDB site
Description: Crystal structure of the GTP-binding protein YchF in complexed with GDP
Class: hydrolase
Keywords: GTP-binding protein, GDP, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE
Deposited on 2005-12-16, released 2006-06-16
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: 1.76 Å
R-factor: 0.191
AEROSPACI score: 0.52 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: GTP-binding protein
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5SJ29 (0-End)
      • modified residue (0)
      • modified residue (316)
    Domains in SCOPe 2.07: d2dbya1, d2dbya2
  • Heterogens: GDP, FMT, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dbyA (A:)
    mlavgivglpnvgkstlfnaltranalaanypfatidknvgvvplederlyalqrtfakg
    ervppvvpthvefvdiaglvkgahkgeglgnqflahirevaaiahvlrcfpdpdvvhvmg
    rvdpledaevvetellladlatlerrlerlrkearadrerlplleaaeglyvhlqegkpa
    rtfppseavarflketplltakpviyvanvaeedlpdgrgnpqveavrrkaleegaevvv
    vsarleaelaelsgeearellaayglqesglqrlaragyraldlltfftagekevrawtv
    rrgtkapraageihsdmergfiraevipwdklveaggwarakergwvrlegkdyevqdgd
    viyvlfna
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dbyA (A:)
    mlavgivglpnvgkstlfnaltranalaanypfatidknvgvvplederlyalqrtfakg
    ervppvvpthvefvdiaglvkgahkgeglgnqflahirevaaiahvlrcfpdpledaevv
    etellladlatlerrlerlrkearadrerlplleaaeglyvhlqegkpartfppseavar
    flketplltakpviyvanvaeedlpdgrgnpqveavrrkaleegaevvvvsarleaelae
    lsgeearellaayglqesglqrlaragyraldlltfftagekevrawtvrrgtkapraag
    eihsdmergfiraevipwdklveaggwarakergwvrlegkdyevqdgdviyvlf