PDB entry 2vgk

View 2vgk on RCSB PDB site
Description: crystal structure of actinomadura r39 dd-peptidase complexed with a peptidoglycan-mimetic cephalosporin
Class: hydrolase
Keywords: cell wall biogenesis/degradation, antibiotic resistance, peptidoglycan synthesis, protease, secreted, hydrolase, cell shape, carboxypeptidase, penicillin-binding, actinomadura, peptidoglycan, transpeptidase
Deposited on 2007-11-14, released 2008-11-25
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.25 Å
R-factor: 0.233
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA SP. [TaxId:72570]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vgka_
  • Chain 'B':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA SP. [TaxId:72570]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vgkb_
  • Chain 'C':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA SP. [TaxId:72570]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vgkc_
  • Chain 'D':
    Compound: d-alanyl-d-alanine carboxypeptidase
    Species: ACTINOMADURA SP. [TaxId:72570]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vgkd_
  • Heterogens: REZ, SO4, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2vgkA (A:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapegarmmrgpvqgsge
lecswvqac

    Sequence, based on observed residues (ATOM records): (download) 
    >2vgkA (A:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapeg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2vgkB (B:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapegarmmrgpvqgsge
lecswvqac

    Sequence, based on observed residues (ATOM records): (download) 
    >2vgkB (B:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqape

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2vgkC (C:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapegarmmrgpvqgsge
lecswvqac

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

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2vgkD (D:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapegarmmrgpvqgsge
lecswvqac

    Sequence, based on observed residues (ATOM records): (download) 
    >2vgkD (D:)
rltelredidailedpalegavsgvvvvdtatgeelysrdggeqllpasnmklftaaaal
evlgadhsfgtevaaesapgrrgevqdlylvgrgdptlsaedldamaaevaasgvrtvrg
dlyaddtwfdserlvddwwpedepyaysaqisaltvahgerfdtgvtevsvtpaaegepa
dvdlgaaegyaeldnravtgaagsantlvidrpvgtntiavtgslpadaapvtalrtvde
paalaghlfeealesngvtvkgdvglggvpadwqdaevladhtsaelseilvpfmkfsnn
ghaemlvksigqetagagtwdaglvgveealsglgvdtaglvlndgsglsrgnlvtadtv
vdllgqagsapwaqtwsaslpvagesdpfvggtlanrmrgtaaegvveaktgtmsgvsal
sgyvpgpegelafsivnnghsgpaplavqdaiavrlaeyaghqapeg