PDB entry 3fbf

View 3fbf on RCSB PDB site
Description: Crystal structure of the Mimivirus NDK N62L mutant complexed with dTDP
Class: transferase
Keywords: phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-11-19, released 2009-08-11
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-08-11, with a file datestamp of 2009-08-07.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.181
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbfa_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbfb_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbfc_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbfd_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbfe_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
      • engineered (66)
    Domains in SCOPe 2.03: d3fbff_
  • Heterogens: MG, TYD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3fbfA (A:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfA (A:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
    vdeisiwfpe
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3fbfB (B:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfB (B:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
    vdeisiwfpe
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3fbfC (C:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfC (C:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3fbfD (D:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfD (D:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3fbfE (E:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfE (E:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3fbfF (F:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3fbfF (F:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp