PDB entry 2zdg

View 2zdg on RCSB PDB site
Description: Crystal structure of D-Alanine:D-Alanine Ligase with ADP from Thermus thermophius HB8
Class: ligase
Keywords: D-Alanine-D-Alanine Ligase, Peptidoglycan Biosynthesis, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI
Deposited on 2007-11-22, released 2008-05-27
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.214
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2zdga1, d2zdga2
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2zdgb1, d2zdgb2
  • Chain 'C':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2zdgc1, d2zdgc2
  • Chain 'D':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2zdgd1, d2zdgd2
  • Heterogens: MG, ADP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2zdgA (A:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
    pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
    aggvaypellrrlvelalt
    

    Sequence, based on observed residues (ATOM records): (download)
    >2zdgA (A:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevrellipapldpgtqetvqelalka
    ykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvaypellrrlvela
    lt
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2zdgB (B:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
    pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
    aggvaypellrrlvelalt
    

    Sequence, based on observed residues (ATOM records): (download)
    >2zdgB (B:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeaellipapldtqetvqelalk
    aykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvaypellrrlvel
    alt
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2zdgC (C:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
    pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
    aggvaypellrrlvelalt
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2zdgD (D:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
    pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
    aggvaypellrrlvelalt
    

    Sequence, based on observed residues (ATOM records): (download)
    >2zdgD (D:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapaellipapltqetvqelal
    kaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvaypellrrlve
    lalt