PDB entry 2zdh

View 2zdh on RCSB PDB site
Description: Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine 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 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: 0.207
AEROSPACI score: 0.46 (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 2.06: d2zdha1, d2zdha2
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2zdhb1, d2zdhb2
  • Chain 'C':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2zdhc1, d2zdhc2
  • Chain 'D':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2zdhd1, d2zdhd2
  • Heterogens: MG, ADP, DAL, HOH

PDB Chain Sequences:

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >2zdhB (B:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfypgraellipapldpgtq
    etvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvayp
    ellrrlvelalt
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2zdhC (C:)
    mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
    gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
    rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
    rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfytkytpgraellipapld
    pgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeagg
    vaypellrrlvelalt
    

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