MolNFT v1 · #52512 · protein + DNA
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair
2W35: “Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.28). MolNFT v1 #52512 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2W35
- Type
- protein + DNA
- Length
- 467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3'; 5'-D(*AP*GP*CP*CP*GP*TP)-3'
- EC
- 3.1.21.7
- UniProt
- Q9X2H9
- Ligands
- MG
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease V (EC 3.1.21.7) | protein | 223 | 27% helix, 27% strand | Q9X2H9 |
| C | 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' | dna | 4 | — | — |
| D | 5'-D(*AP*GP*CP*CP*GP*TP)-3' | dna | 4 | — | — |
| F | 5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' | dna | 7 | — | — |
| G | 5'-D(*AP*GP*CP*CP*GP*TP)-3' | dna | 6 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, D, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.28 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 537 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 526 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 219 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–G · 189 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–D · 119 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 2W35 · Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair · the same entry in another collection · chain C against C, TM-score 1.00
- Q9X2H9 · AlphaFold monomer V2.0 prediction for endonuclease V (Q9X2H9) · 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 Q9X2H9
- Elsewhere: RCSB PDB 2W35 · PDBe 2W35 · UniProt Q9X2H9
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