MolNFT v1 · #47407 · protein + DNA
Crystal structure of a UNG2/MODIFIED DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping
2OXM · DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3'): “Crystal structure of a UNG2/MODIFIED DNA complex that represent a stabilized short-lived extrahelical state…”. X-ray diffraction, 2 pockets (best druggability 0.59). MolNFT v1 #47407 on…
- PDB
- 2OXM
- Type
- protein + DNA
- Length
- 242 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- P13051
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3') (EC 3.2.2.-) | dna | 9 | — | — |
| C | DNA (5'-D(*AP*AP*AP*GP*AP*TP*(4MF)P*AP*CP*A)-3') | dna | 10 | — | — |
| A | Uracil-DNA glycosylase | protein | 223 | 36% helix, 11% strand | P13051 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.59 | 0.82 | 30 | empty |
| 2 | 313 | 0.53 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–A · 571 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 444 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- C–A · 204 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2OXM · Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived… · the same entry in another collection · chain B against B, TM-score 1.00
- P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13051
- Elsewhere: RCSB PDB 2OXM · PDBe 2OXM · UniProt P13051
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.