PDB entry 3n8d

View 3n8d on RCSB PDB site
Description: Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase
Class: ligase
Keywords: vancomycin dependence, cell wall synthesis, D-Ala:D-Ala ligase, LIGASE
Deposited on 2010-05-28, released 2010-10-13
The last revision prior to the SCOPe 2.07 freeze date was dated 2010-10-13, with a file datestamp of 2010-10-08.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.204
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanine--d-alanine ligase
    Species: Staphylococcus aureus [TaxId:1280]
    Gene: ddl
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5HEB7
      • variant (259)
      • variant (282)
    Domains in SCOPe 2.07: d3n8da1, d3n8da2
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Staphylococcus aureus [TaxId:1280]
    Gene: ddl
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5HEB7 (Start-355)
      • variant (259)
      • variant (282)
      • expression tag (356-357)
    Domains in SCOPe 2.07: d3n8db1, d3n8db2, d3n8db3
  • Heterogens: ANP, SO4, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3n8dA (A:)
    mtkenicivfggksaehevsiltaqnvlnaidkdkyhvdiiyitndgdwrkqnnitaeik
    stdelhlengealeisqllkesssgqpydavfpllhgpngedgtiqglfevldvpyvgng
    vlsaassmdklvmkqlfehrglpqlpyisflrseyekyehnilklvndklnypvfvkpan
    lgssvgiskcnneaelkegikeafqfdrklvieqgvnareievavlgndypeatwpgevv
    kdvafydykskykdgkvqlkipadldedvqltlrnmaleafketdcsglvradffvtedn
    qiyinetnampgftafsmypklwenmglsypelitklielakerhqdkqknkykidlehh
    hhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3n8dA (A:)
    tkenicivfggksaehevsiltaqnvlnaidkdkyhvdiiyitndgdwrkqnnitaeiks
    tdelhleleisqllkesssgqpydavfpllngedgtiqglfevldvpyvgngvlsaassm
    dklvmkqlfehrglpqlpyisflrseyekyehnilklvndklnypvfvkpanlgssvgis
    kcnneaelkegikeafqfdrklvieqgvnareievavlgndypeatwpgevvvqlkipad
    ldedvqltlrnmaleafketdcsglvradffvtednqiyinetnampgftafsmypklwe
    nmglsypelitklielakerhqdkqknky
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3n8dB (B:)
    mtkenicivfggksaehevsiltaqnvlnaidkdkyhvdiiyitndgdwrkqnnitaeik
    stdelhlengealeisqllkesssgqpydavfpllhgpngedgtiqglfevldvpyvgng
    vlsaassmdklvmkqlfehrglpqlpyisflrseyekyehnilklvndklnypvfvkpan
    lgssvgiskcnneaelkegikeafqfdrklvieqgvnareievavlgndypeatwpgevv
    kdvafydykskykdgkvqlkipadldedvqltlrnmaleafketdcsglvradffvtedn
    qiyinetnampgftafsmypklwenmglsypelitklielakerhqdkqknkykidlehh
    hhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3n8dB (B:)
    tkenicivfggksaehevsiltaqnvlnaidkdkyhvdiiyitndgdwrkqnnitaeiks
    tdelhleeisqllkesssgqpydavfpllngedgtiqglfevldvpyvgngvlsaassmd
    klvmkqlfehrglpqlpyisflrseyekyehnilklvndklnypvfvkpanlvgiskcnn
    eaelkegikeafqfdrklvieqgvnareievavlgndypeatwpgevvkdvafqlkipad
    ldedvqltlrnmaleafketdcsglvradffvtednqiyinetnampgftafsmypklwe
    nmglsypelitklielakerhqdkqknkykidle