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2OQ4

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, C
(C, E)
5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'polymer133958.62
2B, D
(D, F)
5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'polymer133863.52
3E, F
(A, B)
Endonuclease VIIIpolymer26229814.02UniProt (P50465)
Pfam (PF01149)
Pfam (PF06831)
Pfam (PF06827)
Escherichia coliDNA glycosylase/AP lyase Nei, DNA-apurinic or apyrimidinic site, lyase Nei
4G, M
(F, B)
SODIUM IONnon-polymer23.02Chemie (NA)
5H, J
(A, B)
ZINC IONnon-polymer65.42Chemie (ZN)
6I, K, L
(A, B)
SULFATE IONnon-polymer96.13Chemie (SO4)
7N, O, P, Q, R...
(C, D, E, F, A...)
waterwater18.093Chemie (HOH)
Sequence modifications
A, B: 1 - 262 (UniProt: P50465)
PDBExternal DatabaseDetails
Gln 2Glu 3engineered mutation
Thr 34Pro 35SEE REMARK 999
Arg 112Thr 113SEE REMARK 999
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains6
Total formula weight75272.2
Non-Polymers*Number of molecules7
Total formula weight465.0
All*Total formula weight75737.2
*Water molecules are not included.

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PDB entries from 2025-07-16

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