Research workbench
Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI: the R252A mutant at 2.05 resolution.
Analyse Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q3B
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease VIII
- EC
- 3.2.2.-
- UniProt
- P50465
- Ligands
- MG, ZN
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease VIII (EC 3.2.2.-) | protein | 259 | 32% helix, 21% strand | P50465 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.52 | 0.80 | 32 | empty |
| 2 | 215 | 0.50 | 0.76 | 28 | empty |
| 3 | 85 | 0.36 | 0.76 | 18 | empty |
Compared structures
- 1Q3B · Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The… · the same entry in another collection · chain A against A, 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 0.55
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 1Q3B · PDBe 1Q3B · UniProt P50465
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