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 2.08 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 2.08: 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 2.08: 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 2.08: 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 2.08: 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 2.08: 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 2.08: 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