PDB entry 5bph

View 5bph on RCSB PDB site
Description: Crystal structure of AMP 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 2015-05-28, 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: 1.7 Å
R-factor: N/A
AEROSPACI score: 0.4 (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: d5bpha1, d5bpha2
  • 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: d5bphb1, d5bphb2
  • 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: d5bphc1, d5bphc2
  • 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: d5bphd1, d5bphd2
  • Heterogens: AMP, NA, ACT, GOL, HOH

PDB Chain Sequences:

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >5bphB (B:)
    aekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfia
    lhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrqq
    fetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvliek
    wlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaala
    lqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvari
    lmlad
    

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >5bphD (D:)
    maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
    alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
    qfetlspeelvacvaklglplivkpshessvgmskvdhaselqkalveafqhdsdvliek
    wlsgpeftvailgdevlpsiriqppgvfydydaksdktqyfcpsglsdeseqqlaalalq
    ayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilm
    lad