PDB entry 3fc9

View 3fc9 on RCSB PDB site
Description: Crystal structure of the Mimivirus NDK +Kpn-N62L double mutant complexed with CDP
Class: transferase
Keywords: phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-11-21, released 2009-08-25
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: 2.8 Å
R-factor: 0.188
AEROSPACI score: 0.28 (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)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9a_
  • 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)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9b_
  • 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 (5)
      • engineered (66)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9c_
  • 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 (5)
      • engineered (66)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9d_
  • 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 (5)
      • engineered (66)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9e_
  • 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 (5)
      • engineered (66)
      • see remark 999 (96-102)
    Domains in SCOPe 2.03: d3fc9f_
  • Heterogens: CTP, MG, CDP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3fc9A (A:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9A (A:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfpe

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3fc9B (B:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9B (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfp

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3fc9C (C:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9C (C:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfp

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3fc9D (D:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9D (D:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfpe

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3fc9E (E:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9E (E:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfp

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3fc9F (F:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenli
hasdsedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3fc9F (F:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgntnplasapgtirgdlandirenlihasds
edsavdeisiwfp