PDB entry 3ddi

View 3ddi on RCSB PDB site
Description: Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with TDP
Class: transferase
Keywords: TDP phosphotransferase, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-06-05, 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: 1.9 Å
R-factor: 0.175
AEROSPACI score: 0.49 (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 (5)
      • engineered (66)
      • see remark 999 (96-102)
      • engineered (115)
    Domains in SCOPe 2.03: d3ddia_
  • 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)
      • engineered (66)
      • see remark 999 (96-102)
      • engineered (115)
    Domains in SCOPe 2.03: d3ddib_
  • Heterogens: MG, TYD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3ddiA (A:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandigenli
    hasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ddiA (A:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandigenlihasds
    edsavdeisiwfp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3ddiB (B:)
    ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
    qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandigenli
    hasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ddiB (B:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandigenlihasds
    edsavdeisiwfp