PDB entry 5c1p

View 5c1p on RCSB PDB site
Description: Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
Class: ligase
Keywords: D-alanine-D-alanine ligase, DDL, drug target, bacterial cell wall synthesis, LIGASE
Deposited on 2015-06-15, released 2016-03-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-03-02, with a file datestamp of 2016-02-26.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanine--d-alanine ligase
    Species: Yersinia pestis [TaxId:632]
    Gene: ddl, ddlB, YPO0557, y3624, YP_3627
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5c1pa1, d5c1pa2
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Yersinia pestis [TaxId:632]
    Gene: ddl, ddlB, YPO0557, y3624, YP_3627
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5c1pb1, d5c1pb2
  • Chain 'C':
    Compound: d-alanine--d-alanine ligase
    Species: Yersinia pestis [TaxId:632]
    Gene: ddl, ddlB, YPO0557, y3624, YP_3627
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5c1pc1, d5c1pc2
  • Chain 'D':
    Compound: d-alanine--d-alanine ligase
    Species: Yersinia pestis [TaxId:632]
    Gene: ddl, ddlB, YPO0557, y3624, YP_3627
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5c1pd1, d5c1pd2
  • Heterogens: NA, GOL, ADP, ACT, DAL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5c1pA (A:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
    kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
    alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
    ilmlad
    

    Sequence, based on observed residues (ATOM records): (download)
    >5c1pA (A:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshsvgmskvdhaselqkalveafqhdsdvliekwl
    sgpeftvailgdevlpsiriqpktqyfcpsglsdeseqqlaalalqayhaldcsgwgrvd
    vmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5c1pB (B:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
    kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
    alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
    ilmlad
    

    Sequence, based on observed residues (ATOM records): (download)
    >5c1pB (B:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshvgmskvdhaselqkalveafqhdsdvliekwls
    gpeftvailgdevlpsiriqppgvfydydakktqyfcpsglsdeseqqlaalalqayhal
    dcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5c1pC (C:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
    kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
    alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
    ilmlad
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5c1pD (D:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
    kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
    alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
    ilmlad
    

    Sequence, based on observed residues (ATOM records): (download)
    >5c1pD (D:)
    aekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfia
    lhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrqq
    fetlspeelvacvaklglplivkpshevgmskvdhaselqkalveafqhdsdvliekwls
    gpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaalalqa
    yhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilml
    ad