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 2.05 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.257
AEROSPACI score: 0.23 (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 2.05: d2nyga1
  • Chain 'B':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: 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 2.05: d2nygc_
  • 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 2.05: d2nygd_
  • Chain 'E':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2nyge_
  • Chain 'F':
    Compound: YokD protein
    Species: Bacillus subtilis [TaxId:1423]
    Gene: yokD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: 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