PDB entry 5c1o

View 5c1o on RCSB PDB site
Description: Crystal structure of AMP-PNP 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: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.2 (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: d5c1oa1, d5c1oa2
  • 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: d5c1ob1, d5c1ob2
  • 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: d5c1oc1, d5c1oc2
  • 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: d5c1od1, d5c1od2
  • Heterogens: ANP, NA, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5c1oA (A:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
ilmlad

    Sequence, based on observed residues (ATOM records): (download) 
    >5c1oA (A:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshvgmskvdhaselqkalveafqhdsdvliekwls
gpeftvailgdevlpsiriqppgvfydysdktqyfcpsglsdeseqqlaalalqayhald
csgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5c1oB (B:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
ilmlad

    Sequence, based on observed residues (ATOM records): (download) 
    >5c1oB (B:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshesvgmskvdhaselqkalveafqhdsdvliekw
lsgpeftvailgdevlpsiriqpptqyfcpsglsdeseqqlaalalqayhaldcsgwgrv
dvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5c1oC (C:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
ilmlad

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5c1oD (D:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshegssvgmskvdhaselqkalveafqhdsdvlie
kwlsgpeftvailgdevlpsiriqppgvfydydakylsdktqyfcpsglsdeseqqlaal
alqayhaldcsgwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvar
ilmlad

    Sequence, based on observed residues (ATOM records): (download) 
    >5c1oD (D:)
maekvavllggtsaerevsllsgqavlaglkeagidaygvdtkdfpvtqlkeqgfdkvfi
alhgrggedgtlqgvleflqlpytgsgvmasaltmdklrtklvwqalglpispyvalnrq
qfetlspeelvacvaklglplivkpshesvgmskvdhaselqkalveafqhdsdvliekw
lsgpeftvailgdevlpsiriqppgvfdktqyfcpsglsdeseqqlaalalqayhaldcs
gwgrvdvmqdrdghfyllevntspgmtshslvpmaarqyglsfsqlvarilmlad