PDB entry 3b6b

View 3b6b on RCSB PDB site
Description: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP
Class: transferase
Keywords: NDK, PHOSPHOTRANSFERASE, NUCLEOTIDE BINDING PROTEIN, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphorylation
Deposited on 2007-10-28, released 2008-11-04
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-07-07, with a file datestamp of 2009-07-02.
Experiment type: XRAY
Resolution: 2 Å
R-factor: 0.201
AEROSPACI score: 0.44 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.06: d3b6ba1, d3b6ba2
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (20)
    Domains in SCOPe 2.06: d3b6bb1, d3b6bb2
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.06: d3b6bc1, d3b6bc2
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.06: d3b6bd1, d3b6bd2
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.06: d3b6be1, d3b6be2
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
    Gene: ndk
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5UQL3 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.06: d3b6bf1, d3b6bf2
  • Heterogens: MG, DGI, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3b6bA (A:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bA (A:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpe
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3b6bB (B:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bB (B:)
    lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
    dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
    vdeisiwfp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3b6bC (C:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bC (C:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpet
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3b6bD (D:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bD (D:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpe
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3b6bE (E:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bE (E:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfpe
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3b6bF (F:)
    syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
    aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
    dlandirenlihasdsedsavdeisiwfpetkmetdn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3b6bF (F:)
    glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
    ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
    avdeisiwfp