PDB entry 3ee3

View 3ee3 on RCSB PDB site
Description: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with CDP
Class: transferase
Keywords: phosphotransferase ATP-binding mimivirus, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-09-04, released 2009-06-16
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-08-25, with a file datestamp of 2009-08-21.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.196
AEROSPACI score: 0.34 (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 (4-5)
    Domains in SCOPe 2.03: d3ee3a_
  • 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 (4-5)
    Domains in SCOPe 2.03: d3ee3b_
  • 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 2.03: d3ee3c_
  • 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 2.03: d3ee3d_
  • 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 2.03: d3ee3e_
  • 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 2.03: d3ee3f_
  • Heterogens: CDP, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3ee3A (A:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3A (A:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3ee3B (B:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3B (B:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3ee3C (C:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3C (C:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3ee3D (D:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3D (D:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3ee3E (E:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3E (E:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3ee3F (F:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
    sedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ee3F (F:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp