PDB entry 5bpf

View 5bpf on RCSB PDB site
Description: Crystal structure of ADP 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, Yersinia pestis, LIGASE
Deposited on 2015-05-28, released 2016-03-02
The last revision prior to the SCOPe 2.06 freeze date was dated 2016-03-02, with a file datestamp of 2016-02-26.
Experiment type: XRAY
Resolution: 2.28 Å
R-factor: N/A
AEROSPACI score: 0.25 (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 2.06: d5bpfa1, d5bpfa2
  • 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 2.06: d5bpfb1, d5bpfb2
  • 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 2.06: d5bpfc1, d5bpfc2
  • 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 2.06: d5bpfd1, d5bpfd2
  • Heterogens: NA, GOL, ADP, ACT, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >5bpfA (A:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshesvgmskvdhaselqkalveafqhdsdvliekw
    lsgpeftvailgdevlpsiriqppktqyfcpsglsdeseqqlaalalqayhaldcsgwgr
    vdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5bpfB (B:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshsvgmskvdhaselqkalveafqdsdvliekwls
    gpeftvailgdevlpsiriqppgvfydydaklsdktqyfcpsglsdeseqqlaalalqay
    haldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmla
    d
    

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >5bpfD (D:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshsvgmskvdhaselqkalveafqhdsdvliekwl
    sgpeftvailgdevlpsiriqppgvfysdktqyfcpsglsdeseqqlaalalqayhaldc
    sgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad