PDB entry 2opf

View 2opf on RCSB PDB site
Description: Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate
Class: hydrolase/DNA
Keywords: Endonuclease VIII, oxidative damage, DNA repair, base excision, covalent intermediate, reaction mechanism, HYDROLASE-DNA COMPLEX
Deposited on 2007-01-29, released 2008-02-26
The last revision prior to the SCOPe 2.08 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 1.85 Å
R-factor: 0.24
AEROSPACI score: 0.45 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Endonuclease VIII
    Species: Escherichia coli [TaxId:562]
    Gene: nei
    Database cross-references and differences (RAF-indexed):
    • Uniprot P50465 (0-261)
      • see remark 999 (33)
      • see remark 999 (111)
      • engineered (251)
    Domains in SCOPe 2.08: d2opfa1, d2opfa2, d2opfa3
  • Chain 'B':
    Compound: 5'-d(*gp*gp*cp*tp*tp*cp*ap*tp*cp*cp*tp*g)-3'
  • Chain 'C':
    Compound: 5'-d(p*cp*ap*gp*gp*ap*(ped)p*gp*ap*ap*gp*cp*c)-3'
  • Heterogens: ZN, SO4, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2opfA (A:)
pegpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatrgqvdenkhhgalfrfkvfhrdgepcerc
gsiiekttlssapfywcpgcqh

    Sequence, based on observed residues (ATOM records): (download) 
    >2opfA (A:)
pegpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatrgqvdalfrfkvfhrdgepcercgsiiek
ttlssapfywcpgcqh

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.