PDB entry 2dd0

View 2dd0 on RCSB PDB site
Description: The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine
Class: hydrolase
Keywords: D-stereospecific, Amidase, D-Phe, penicillin recognize protein
Deposited on 2006-01-18, released 2006-02-07
The last revision prior to the SCOPe 2.07 freeze date was dated 2006-05-09, with a file datestamp of 2007-04-25.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.191
AEROSPACI score: 0.34 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704 (Start-362)
    Domains in SCOPe 2.07: d2dd0a_
  • Chain 'B':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704 (Start-362)
    Domains in SCOPe 2.07: d2dd0b_
  • Chain 'C':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704
    Domains in SCOPe 2.07: d2dd0c_
  • Chain 'D':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704 (Start-362)
    Domains in SCOPe 2.07: d2dd0d_
  • Chain 'E':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704
    Domains in SCOPe 2.07: d2dd0e_
  • Chain 'F':
    Compound: D-amino acid amidase
    Species: Ochrobactrum anthropi
    Gene:
    Database cross-references and differences (RAF-indexed):
    • GB BAA94704 (Start-362)
    Domains in SCOPe 2.07: d2dd0f_
  • Heterogens: BA, DPN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dd0A (A:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0A (A:)
    sdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasc
    tksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmis
    dkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifapl
    gmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgana
    agdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmrygs
    selkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikns
    rs
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dd0B (B:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0B (B:)
    sdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasc
    tksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmis
    dkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifapl
    gmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgana
    agdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmrygs
    selkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikns
    rs
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2dd0C (C:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0C (C:)
    dlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasct
    ksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmisd
    kswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifaplg
    mkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsganaa
    gdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmrygss
    elkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaiknsr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2dd0D (D:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0D (D:)
    sdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasc
    tksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmis
    dkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifapl
    gmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgana
    agdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmrygs
    selkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikns
    rs
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2dd0E (E:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0E (E:)
    sdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasc
    tksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmis
    dkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifapl
    gmkdtwvgthetfpiereargymhadvsgagdpvdgvwdstewfplsganaagdmvstpr
    divkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmrygsselkghlgq
    ipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikns
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2dd0F (F:)
    msdlnnaiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfrias
    ctksfiatglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmi
    sdkswtaqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifap
    lgmkdtwvgthetfpiereargymhaaaddenpqwdvsgagdpvdgvwdstewfplsgan
    aagdmvstprdivkflnalfdgrildqkrlwemkdnikpaffpgsntvanghglllmryg
    sselkghlgqipghtsimgrdeetgaalmliqnsgagdfesfylkgvnepvdrvleaikn
    srs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dd0F (F:)
    aiqgilddhvargvvgvslalclpgeetslyqsgyadkfnkmpmtgdhlfriasctksfi
    atglhllvqdgtvdldepitrwfpdlpkaaqmpvrillnhrsglpdfetsmpmisdkswt
    aqeivdfsfrhgvqkepwhgmeysntgyvlagmiiahetgkpysdhlrsrifaplgmkdt
    wvgthetfpiereargymhwdstewfplsganaagdmvstprdivkflnalfdgrildqk
    rlwemkdnikpaffpgsntvanghglllmrygsselkghlgqipghtsimgrdeetgaal
    mliqnsgagdfesfylkgvnepvdrvleaikrs