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 2.06 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 2.06: 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 2.06: 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 2.06: 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 2.06: 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 2.06: 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 2.06: 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