PDB entry 2d5n

View 2d5n on RCSB PDB site
Description: Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis
Class: hydrolase, oxidoreductase
Keywords: alpha/beta/alpha; two separate functional domains, HYDROLASE, OXIDOREDUCTASE
Deposited on 2005-11-02, released 2005-11-29
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.97 Å
R-factor: 0.224
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Riboflavin biosynthesis protein ribD
    Species: Bacillus subtilis [TaxId:1423]
    Gene: RibG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2d5na1, d2d5na2
  • Chain 'B':
    Compound: Riboflavin biosynthesis protein ribD
    Species: Bacillus subtilis [TaxId:1423]
    Gene: RibG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2d5nb1, d2d5nb2
  • Chain 'C':
    Compound: Riboflavin biosynthesis protein ribD
    Species: Bacillus subtilis [TaxId:1423]
    Gene: RibG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2d5nc1, d2d5nc2
  • Chain 'D':
    Compound: Riboflavin biosynthesis protein ribD
    Species: Bacillus subtilis [TaxId:1423]
    Gene: RibG
    Database cross-references and differences (RAF-indexed):
    • Uniprot P17618 (12-End)
      • cloning artifact (11)
    Domains in SCOPe 2.06: d2d5nd1, d2d5nd2, d2d5nd3
  • Heterogens: ZN, NDP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2d5nA (A:)
    mrgshhhhhhgsmeeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygea
    haevhaihmagahaegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvag
    rgismmkeagievregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdsk
    witseaarqdaqqyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsiped
    akvicdqiaptwifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvy
    veggsavhgsfvkegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqi
    grdikltakptke
    

    Sequence, based on observed residues (ATOM records): (download)
    >2d5nA (A:)
    meeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygeahaevhaihmaga
    haegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvagrgismmkeagie
    vregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdskwitseaarqdaq
    qyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsipedakvicdqiaptw
    ifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvyveggsavhgsfv
    kegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqigrdikltakpt
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2d5nB (B:)
    mrgshhhhhhgsmeeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygea
    haevhaihmagahaegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvag
    rgismmkeagievregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdsk
    witseaarqdaqqyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsiped
    akvicdqiaptwifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvy
    veggsavhgsfvkegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqi
    grdikltakptke
    

    Sequence, based on observed residues (ATOM records): (download)
    >2d5nB (B:)
    meeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygeahaevhaihmaga
    haegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvagrgismmkeagie
    vregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdskwitseaarqdaq
    qyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsipedakvicdqiaptw
    ifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvyveggsavhgsfv
    kegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqigrdikltakpt
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2d5nC (C:)
    mrgshhhhhhgsmeeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygea
    haevhaihmagahaegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvag
    rgismmkeagievregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdsk
    witseaarqdaqqyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsiped
    akvicdqiaptwifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvy
    veggsavhgsfvkegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqi
    grdikltakptke
    

    Sequence, based on observed residues (ATOM records): (download)
    >2d5nC (C:)
    meeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygeahaevhaihmaga
    haegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvagrgismmkeagie
    vregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdskwitseaarqdaq
    qyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsipedakvicdqiaptw
    ifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvyveggsavhgsfv
    kegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqigrdikltakpt
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2d5nD (D:)
    mrgshhhhhhgsmeeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygea
    haevhaihmagahaegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvag
    rgismmkeagievregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdsk
    witseaarqdaqqyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsiped
    akvicdqiaptwifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvy
    veggsavhgsfvkegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqi
    grdikltakptke
    

    Sequence, based on observed residues (ATOM records): (download)
    >2d5nD (D:)
    smeeyymklaldlakqgegqtesnplvgavvvkdgqivgmgahlkygeahaevhaihmag
    ahaegadiyvtlepcshygktppcaeliinsgikrvfvamrdpnplvagrgismmkeagi
    evregiladqaerlnekflhfmrtglpyvtlkaaasldgkiatstgdskwitseaarqda
    qqyrkthqsilvgvgtvkadnpsltcrlpnvtkqpvrvildtvlsipedakvicdqiapt
    wifttaradeekkkrlsafgvniftleteriqipdvlkilaeegimsvyveggsavhgsf
    vkegcfqeiifyfapkliggthapslisgegfqsmkdvpllqftditqigrdikltakpt