PDB entry 3elh

View 3elh on RCSB PDB site
Description: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dUDP
Class: transferase
Keywords: nucleoside diphosphate kinase mimivirus phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-09-22, 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: 0.195
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: MIMI_R418, NDK
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (6-End)
      • expression tag (3-5)
    Domains in SCOPe 2.03: d3elha_
  • 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)
    Domains in SCOPe 2.03: d3elhb_
  • 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)
    Domains in SCOPe 2.03: d3elhc_
  • 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)
    Domains in SCOPe 2.03: d3elhd_
  • 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)
    Domains in SCOPe 2.03: d3elhe_
  • 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)
    Domains in SCOPe 2.03: d3elhf_
  • Heterogens: DUD, MG, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

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

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

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