PDB entry 5dmx

View 5dmx on RCSB PDB site
Description: Crystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii, space group p212121
Class: ligase
Keywords: D-alanine-D-alanine ligase, Acinetobacter baumannii, drug target protein, apo structure, LIGASE
Deposited on 2015-09-09, 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: 2.81 Å
R-factor: N/A
AEROSPACI score: 0.16 (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: d5dmxa1, d5dmxa2
  • 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: d5dmxb1, d5dmxb2
  • 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: d5dmxc1, d5dmxc2
  • 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: d5dmxd1, d5dmxd2
  • 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: d5dmxe1, d5dmxe2
  • 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: d5dmxf1, d5dmxf2
  • Heterogens: HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxA (A:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    vvmaekwitgreftisflngqplpvirlqygipcglseteekklqalclrafqavgaegw
    gridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvaileqtle
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxB (B:)
    snatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydra
    fivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriit
    ketdldsviaelglpviikpvhegavvmaekwitgreftisflngqplpvirlqygipcg
    lseteekklqalclrafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaak
    avgysfdelcvaileqtle
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxC (C:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyrii
    tldsviaelglpviikpvhegmaekwitgreftisflngqplpvirlqygipcglsetee
    kklqalclrafqavgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysf
    delcvaileqtle
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxD (D:)
    atkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydrafi
    vlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyriitke
    tdldsviaelglpviikpvhevgmskvekaedfaaaiekatqhdavvmaekwitgrefti
    sflngqplpvirlgipcglseteekklqalclrafqavgaegwgridamqdeqgnfwlle
    vntvpgmtshslvpkaakavgysfdelcvaileqtl
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxE (E:)
    atkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydrafi
    vlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyftisfl
    ngqplpvirlqygipclsekklqalclrafqavgaegrievntvpgmtshslvpkaakav
    gysfdelcvaileqtle
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5dmxF (F:)
    msnatkfgkvavllggksaeravsldsgqavldallrsgvqaeafdpqdrsvtelvnydr
    afivlhgrggedgqiqgvlewlnipytgtgvqgsaigmdkvktkqiwqgsdlptapyril
    dsviaelglpaekwitgreftisflngqplpvirlqygipcglseteekklqalclrafq
    avgaegwgridamqdeqgnfwllevntvpgmtshslvpkaakavgysfdelcvaileqtl
    e