Research workbench
Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI (E2Q) 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
- 2OQ4
- Type
- protein + DNA
- Length
- 545 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- P50465
- Ligands
- NA, ZN, SO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' | dna | 11 | — | — |
| D | 5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | dna | 12 | — | — |
| E | 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' | dna | 9 | — | — |
| F | 5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | dna | 11 | — | — |
| A | Endonuclease VIII (EC 3.2.2.-, 4.2.99.18) | protein | 252 | 31% helix, 23% strand | P50465 |
| B | Endonuclease VIII (EC 3.2.2.-, 4.2.99.18) | protein | 250 | 29% helix, 23% strand | P50465 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains E, F, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.60 | 0.79 | 25 | empty |
| 2 | 308 | 0.54 | 0.75 | 30 | empty |
| 3 | 259 | 0.52 | 0.75 | 30 | SO4 |
| 4 | 185 | 0.47 | 0.76 | 30 | NA |
| 5 | 138 | 0.45 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- F–B · 604 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–A · 600 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 508 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- E–F · 406 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- C–A · 364 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2OQ4 · Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in… · 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 0.99
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 2OQ4 · PDBe 2OQ4 · UniProt P50465
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.