PDB entry 3fbe

View 3fbe on RCSB PDB site
Description: Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP
Class: transferase
Keywords: phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2008-11-19, released 2009-06-16
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-07-24, with a file datestamp of 2019-07-19.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (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)
      • engineered (66)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbea1, d3fbea2
  • 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)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbeb1, d3fbeb2
  • 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)
      • engineered (66)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbec1, d3fbec2
  • 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)
      • engineered (66)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbed1, d3fbed2
  • 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)
      • engineered (66)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbee1, d3fbee2
  • 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)
      • engineered (66)
      • engineered (111)
    Domains in SCOPe 2.08: d3fbef1, d3fbef2
  • Heterogens: MG, GDP, HOH

PDB Chain Sequences:

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >3fbeB (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dlcdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandigenlihasdsedsa
vdeisiwfp

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

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

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

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

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

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

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

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