PDB entry 5d8d

View 5d8d on RCSB PDB site
Description: Crystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii
Class: ligase
Keywords: D-alanine-D-alanine ligase, Acinetobacter baumannii, Apo structure, Drug target, LIGASE
Deposited on 2015-08-17, released 2016-08-17
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-08-17, with a file datestamp of 2016-08-12.
Experiment type: XRAY
Resolution: 2.19 Å
R-factor: N/A
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8da1, d5d8da2
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8db1, d5d8db2
  • Chain 'C':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8dc1, d5d8dc2
  • Chain 'D':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8dd1, d5d8dd2
  • Chain 'E':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8de1, d5d8de2
  • Chain 'F':
    Compound: d-alanine--d-alanine ligase
    Species: Acinetobacter baumannii ACICU [TaxId:405416]
    Gene: ddl, ACICU_03532
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5d8df1, d5d8df2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5d8dA (A:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dA (A:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhegsvgmskvekaedfaaaiekatqhdavvmaekwitgr
    eftisflngqplpvirlqygipcglseteekklqalclrafqavgaegwgridamqdeqg
    nfwllevntvpgmtshslvpkaakavgysfdelcvaileqtl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5d8dB (B:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dB (B:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhessvgmskvekaedfaaaiekatqhdavvmaekwitgr
    eftisflngqplpvirlqygipcglseteekklqalclrafqavgaegwgridamqdeqg
    nfwllevntvpgmtshslvpkaakavgysfdelcvaileqtl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5d8dC (C:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dC (C:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhevgmskfaaaiekatqhdavvmaekwitgreftisfln
    gqplpvirlqygipcglseteekklqalclrafqavgaegwgridamqdeqgnfwllevn
    tvpgmtshslvpkaakavgysfdelcvaileqtl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5d8dD (D:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dD (D:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwitg
    reftisflngqplpvirlqygipcglseteekklqalclrafqavgaegwgridamqdeq
    gnfwllevntvpgmtshslvpkaakavgysfdelcvaileqtle
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5d8dE (E:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dE (E:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhvgmskvaedfaaaiekatavvmaekwitgreftisfln
    gqplpvirlqgipcglseteekklqalclrafqavgaegwgridamqdeqgnfwllevnt
    vpgmtshslvpkaakavgysfdelcvaileqtlegt
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5d8dF (F:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tketdldsviaelglpviikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwit
    greftisflngqplpvirlqppadvafydyeakyqrndveygipcglseteekklqalcl
    rafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvail
    eqtlegta
    

    Sequence, based on observed residues (ATOM records): (download)
    >5d8dF (F:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriie
    tdldsviaeliikpvhegssvgmskvekaedfaaaiekatqhdavvmaekwitgreftis
    flngqplpvirlqygipcglseteekklqalclrafqavgaegwgridamqdeqgnfwll
    evntvpgmtshslvpkaakavgysfdelcvaileqtle