PDB entry 2nyg

View 2nyg on RCSB PDB site
Description: Crystal structure of YokD protein from Bacillus subtilis
Class: structural genomics, unknown function
Keywords: pfam02522, NYSGXRC, 10116c, Aminoglycoside 3-N-acetyltransferase, PSI-2, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, UNKNOWN FUNCTION
Deposited on 2006-11-20, released 2006-12-12
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-03, with a file datestamp of 2021-01-29.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: N/A
AEROSPACI score: 0.25 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O32003 (2-End)
      • cloning artifact (1)
    Domains in SCOPe 2.08: d2nyga1, d2nyga2
  • Chain 'B':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2nygb_
  • Chain 'C':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O32003 (2-End)
      • cloning artifact (1)
    Domains in SCOPe 2.08: d2nygc2, d2nygc3
  • Chain 'D':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O32003 (2-End)
      • cloning artifact (1)
    Domains in SCOPe 2.08: d2nygd2, d2nygd3
  • Chain 'E':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2nyge_
  • Chain 'F':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2nygf_
  • Heterogens: COA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2nygA (A:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygA (A:)
    lkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvt
    eegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfrs
    ypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdss
    tcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvgk
    vgsancrlfslteavdfaekwfinndskni
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2nygB (B:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygB (B:)
    prtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvteegtivmpsq
    svelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfrsypevkrsnhp
    nysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdsstcfhlaeyri
    pyqkiinrgapiivegkrvwkeykelefreelfqevgqafeakvgkvgsancrlfsltea
    vdfaekwfinn
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2nygC (C:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygC (C:)
    lkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvt
    eegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfrs
    ypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdss
    tcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvgk
    vgsancrlfslteavdfaekwfinndskni
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2nygD (D:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygD (D:)
    lkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvt
    eegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfrs
    ypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdss
    tcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvgk
    vgsancrlfslteavdfaekwfinndsk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2nygE (E:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygE (E:)
    prtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvteegtivmpsq
    svelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfrsypevkrsnhp
    nysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdsstcfhlaeyri
    pyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvgkvgsancrlfs
    lteavdfaekwfinndskni
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2nygF (F:)
    slkkivesttfprtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvv
    teegtivmpsqsvelsdpkewgnppvpeewwdiiresmpaynsnytpttrgmgqivelfr
    sypevkrsnhpnysfvawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfds
    stcfhlaeyripyqkiinrgapiivegkrvwkeykelefreelfqevgqafeaehnmkvg
    kvgsancrlfslteavdfaekwfinndsknikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nygF (F:)
    rtkqsitedlkalglkkgmtvlvhsslssigwvnggavaviqalidvvteegtivmpsqs
    velsdpkewpvpeewwdiiresmpaynsnytpttrgmgqivelfrsypevkrsnhpnysf
    vawgkhknkilnqhplefglgeqsplgklyiresyvlllgadfdsstcfhlaeyripyqk
    iinrgapiivegkrvwkeykelefreelfqevgqafeaekvgkvgsancrlfslteavdf
    aekwfinn