PDB entry 3eic

View 3eic on RCSB PDB site
Description: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP
Class: transferase
Keywords: NDK Phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-09-15, released 2009-06-16
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-08-25, with a file datestamp of 2009-08-21.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.19
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (3-5)
    Domains in SCOPe 2.01: d3eica_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (5)
    Domains in SCOPe 2.01: d3eicb_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.01: d3eicc_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.01: d3eicd_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.01: d3eice_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: NDK, MIMI_R418
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (4-5)
    Domains in SCOPe 2.01: d3eicf_
  • Heterogens: MG, UDP, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >3eicA (A:)
    aglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsy
    fndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsed
    savdeisiwfpet
    

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

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

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

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

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

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

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

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

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

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