PDB entry 1yid

View 1yid on RCSB PDB site
Description: Crystal structure of tryptophanyl tRNA synthetase II from Deinococcus radiodurans in complex with ATP.
Class: ligase
Keywords: Tryptophanyl tRNA synthetase II, ATP, LIGASE
Deposited on 2005-01-11, released 2005-08-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.26
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tryptophanyl-tRNA synthetase
    Species: Deinococcus radiodurans [TaxId:1299]
    Gene: DR1093
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yida_
  • Chain 'B':
    Compound: Tryptophanyl-tRNA synthetase
    Species: Deinococcus radiodurans [TaxId:1299]
    Gene: DR1093
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yidb_
  • Chain 'C':
    Compound: Tryptophanyl-tRNA synthetase
    Species: Deinococcus radiodurans [TaxId:1299]
    Gene: DR1093
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yidc_
  • Heterogens: MG, ATP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1yidA (A:)
    mpfvdlevptmttptpaatparprvltgdrptgalhlghlagslqnrvrlqdeaelfvll
    advqaltdhfdrpeqvrenvlavaldylaagldpqkttcvvqsavpelaeltvyflnlvt
    vshlrqnptvkaeiaqkgygervpagffvypvsqaadiaafgatlvpvgddqlpmleqtr
    eivrrfnalyapvlaepqaqlsrvprlpgldgqakmskslgnaialgdsadevarkvmgm
    ytdpghlrasdpgrvegnpvftfldafdpdparvqalkdqyragglgdvkvkkhlidvln
    gvlapirtrraeyerdpdavlrfvtegtargrevaaqtlgqvrramrlfgh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yidA (A:)
    arprvltgdrptgalhlghlagslqnrvrlqdeaelfvlladvqaltdhfdrpeqvrenv
    lavaldylaagldpqkttcvvqsavpelaeltvyflnlvtvshlrqnptvkaeiaqkgyg
    ervpagffvypvsqaadiaafgatlvpvgddqlpmleqtreivrrfnalyapvlaepqaq
    lsrvprlpgldgqakmskslgnaialgdsadevarkvmgmytdpghlrasdpgrvegnpv
    ftfldafdpdparvqalkdqyragglgdvkvkkhlidvlngvlapirtrraeyerdpdav
    lrfvtegtargrevaaqtlgqvrramrlfgh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1yidB (B:)
    mpfvdlevptmttptpaatparprvltgdrptgalhlghlagslqnrvrlqdeaelfvll
    advqaltdhfdrpeqvrenvlavaldylaagldpqkttcvvqsavpelaeltvyflnlvt
    vshlrqnptvkaeiaqkgygervpagffvypvsqaadiaafgatlvpvgddqlpmleqtr
    eivrrfnalyapvlaepqaqlsrvprlpgldgqakmskslgnaialgdsadevarkvmgm
    ytdpghlrasdpgrvegnpvftfldafdpdparvqalkdqyragglgdvkvkkhlidvln
    gvlapirtrraeyerdpdavlrfvtegtargrevaaqtlgqvrramrlfgh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yidB (B:)
    arprvltgdrptgalhlghlagslqnrvrlqdeaelfvlladvqaltdhfdrpeqvrenv
    lavaldylaagldpqkttcvvqsavpelaeltvyflnlvtvshlrqnptvkaeiaqkgyg
    ervpagffvypvsqaadiaafgatlvpvgddqlpmleqtreivrrfnalyapvlaepqaq
    lsrvprlpgldgqakmskslgnaialgdsadevarkvmgmytdpghlrasdpgrvegnpv
    ftfldafdpdparvqalkdqyragglgdvkvkkhlidvlngvlapirtrraeyerdpdav
    lrfvtegtargrevaaqtlgqvrramrlfgh
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1yidC (C:)
    mpfvdlevptmttptpaatparprvltgdrptgalhlghlagslqnrvrlqdeaelfvll
    advqaltdhfdrpeqvrenvlavaldylaagldpqkttcvvqsavpelaeltvyflnlvt
    vshlrqnptvkaeiaqkgygervpagffvypvsqaadiaafgatlvpvgddqlpmleqtr
    eivrrfnalyapvlaepqaqlsrvprlpgldgqakmskslgnaialgdsadevarkvmgm
    ytdpghlrasdpgrvegnpvftfldafdpdparvqalkdqyragglgdvkvkkhlidvln
    gvlapirtrraeyerdpdavlrfvtegtargrevaaqtlgqvrramrlfgh
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yidC (C:)
    arprvltgdrptgalhlghlagslqnrvrlqdeaelfvlladvqaltdhfdrpeqvrenv
    lavaldylaagldpqkttcvvqsavpelaeltvyflnlvtvshlrqnptvkaeiaqkgyg
    ervpagffvypvsqaadiaafgatlvpvgddqlpmleqtreivrrfnalyapvlaepqaq
    lsrvprlpgldgqakmskslgnaialgdsadevarkvmgmytdpghlrasdpgrvegnpv
    ftfldafdpdparvqalkdqyragglgdvkvkkhlidvlngvlapirtrraeyerdpdav
    lrfvtegtargrevaaqtlgqvrramrlfgh