Research workbench
Crystal structure of sumo-3-modified thymine-DNA glycosylase
Analyse Crystal structure of sumo-3-modified thymine-DNA glycosylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D07
- Type
- protein
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G/T mismatch-specific thymine DNA glycosylase; Ubiquitin-like protein SMT3B
- EC
- 3.2.2.-
- UniProt
- Q13569, P61956
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-) | protein | 215 | 40% helix, 19% strand | Q13569 |
| B | Ubiquitin-like protein SMT3B | protein | 76 | 20% helix, 37% strand | P61956 |
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 | 248 | 0.56 | 0.77 | 27 | empty |
| 2 | 180 | 0.51 | 0.78 | 33 | empty |
| 3 | 109 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 834 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2D07 · Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase · the same entry in another collection · chain A against A, TM-score 1.00
- Q13569 · AlphaFold monomer V2.0 prediction for G/T mismatch-specific thymine DNA glycosylase… · a predicted model of the same protein · chain A against A, TM-score 0.95
- P61956 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 2 (P61956) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q13569
- Every structure of UniProt P61956
- Elsewhere: RCSB PDB 2D07 · PDBe 2D07 · UniProt Q13569 · UniProt P61956
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