PDB entry 2xdm

View 2xdm on RCSB PDB site
Description: crystal structure of a complex between actinomadura r39 dd peptidase and a peptidoglycan mimetic boronate inhibitor
Deposited on 2010-05-04, released 2010-07-21
The last revision was dated 2011-11-23, with a file datestamp of 2011-11-18.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.20265
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA [TaxId:72570]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA [TaxId:72570]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA [TaxId:72570]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA [TaxId:72570]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: SO4, CO, BO8, MES, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records:
    >2xdmA (A:)
    rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
    evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
    dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
    dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
    paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
    ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
    vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
    sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqape
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >2xdmB (B:)
    rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
    evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
    dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
    dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
    paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
    ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
    vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
    sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqape
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >2xdmC (C:)
    rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
    evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
    dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
    dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
    paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
    ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
    vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
    sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqape
    

    Sequence, based on observed residues (ATOM records):
    >2xdmC (C:)
    rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
    evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
    dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
    dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
    paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
    ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
    vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
    sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqap
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >2xdmD (D:)
    rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
    evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
    dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
    dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
    paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
    ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
    vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
    sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqape