PDB entry 2b8q

View 2b8q on RCSB PDB site
Description: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP
Class: transferase
Keywords: NDK, TDP, phosphotranferase, TRANSFERASE
Deposited on 2005-10-10, released 2005-11-15
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-08-25, with a file datestamp of 2009-08-21.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.199
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (3-5)
    Domains in SCOPe 2.07: d2b8qa1, d2b8qa2
  • Chain 'B':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (5)
    Domains in SCOPe 2.07: d2b8qb1, d2b8qb2
  • Chain 'C':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.07: d2b8qc1, d2b8qc2
  • Chain 'D':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.07: d2b8qd1, d2b8qd2
  • Chain 'E':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.07: d2b8qe1, d2b8qe2
  • Chain 'F':
    Compound: Probable nucleoside diphosphate kinase
    Species: Mimivirus [TaxId:315393]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.07: d2b8qf1, d2b8qf2
  • Heterogens: MG, PO4, TYD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2b8qA (A:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qA (A:)
    aglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsy
    fndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsed
    savdeisiwfpet
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2b8qB (B:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qB (B:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
    vdeisiwfpe
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2b8qC (C:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qC (C:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2b8qD (D:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qD (D:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2b8qE (E:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qE (E:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2b8qF (F:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2b8qF (F:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp