Research workbench
Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI (R252A) in complex with ap-site containing DNA substrate
Analyse Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OPF
- Type
- protein + DNA
- Length
- 279 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'; 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- P50465
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' | dna | 11 | — | — |
| C | 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | dna | 12 | — | — |
| A | Endonuclease VIII (EC 3.2.2.-, 4.2.99.18) | protein | 256 | 31% helix, 26% strand | P50465 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.71 | 0.79 | 47 | empty |
| 2 | 224 | 0.48 | 0.75 | 32 | GOL |
Interfaces
3 interfaces between chains.
- C–A · 609 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 483 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–A · 392 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2OPF · Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A)… · the same entry in another collection · chain B against B, TM-score 1.00
- P50465 · AlphaFold monomer V2.0 prediction for endonuclease 8 (P50465) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P50465
- Elsewhere: RCSB PDB 2OPF · PDBe 2OPF · UniProt P50465
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