MolNFT v1 · #52513 · protein + DNA
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair
2W36: “Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #52513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2W36
- Type
- protein + DNA
- Length
- 478 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; 5'-D(*GP*CP*BRUP*AP*CP*IP*GP*AP*BRUP*CP*GP)-3'…
- EC
- 3.1.21.7
- UniProt
- Q9X2H9
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease V (EC 3.1.21.7) | protein | 223 | 26% helix, 27% strand | Q9X2H9 |
| C, E | 5'-D(*GP*CP*BRUP*AP*CP*IP*GP*AP*BRUP*CP*GP)-3' | dna | 11 | — | — |
| D, F | 5'-D(*CP*GP*AP*TP*CP*TP*GP*TP*AP*GP*CP)-3' | dna | 5 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.54 | 0.80 | 20 | empty |
| 2 | 175 | 0.52 | 0.78 | 19 | empty |
| 3 | 54 | 0.29 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–C · 745 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 742 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 241 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- C–D · 228 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–D · 211 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2W36 · 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 1.00
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 2W36 · PDBe 2W36 · UniProt Q9X2H9
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