PDB entry 3gp9

View 3gp9 on RCSB PDB site
Description: Crystal structure of the Mimivirus NDK complexed with GDP
Class: transferase
Keywords: phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on 2009-03-23, released 2009-08-11
The last revision prior to the SCOPe 2.08 freeze date was dated 2009-08-11, with a file datestamp of 2009-08-07.
Experiment type: XRAY
Resolution: 1.8 Å
R-factor: 0.19
AEROSPACI score: 0.52 (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 2.08: d3gp9a1, d3gp9a2
  • 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 2.08: d3gp9b1, d3gp9b2
  • 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 2.08: d3gp9c1, d3gp9c2
  • 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 2.08: d3gp9d1, d3gp9d2
  • 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 2.08: d3gp9e1, d3gp9e2
  • 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 2.08: d3gp9f1, d3gp9f2
  • Heterogens: GDP, PO4, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3gp9A (A:)
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qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9A (A:)
aglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsy
fndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsed
savdeisiwfpet

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3gp9B (B:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9B (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
vdeisiwfpe

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3gp9C (C:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9C (C:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3gp9D (D:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9D (D:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpe

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3gp9E (E:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9E (E:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3gp9F (F:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn

    Sequence, based on observed residues (ATOM records): (download) 
    >3gp9F (F:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfp