MolNFT v1 · #26758 · protein
Crystal structure of SUMO1-conjugated thymine DNA glycosylase
1WYW · G/T mismatch-specific thymine DNA glycosylase: “Crystal structure of SUMO1-conjugated thymine DNA glycosylase”. X-ray diffraction, 3 ligands (MG, NA, CL), 4 pockets (best druggability 0.67). MolNFT v1 #26758 on GenesisL1: 3D…
- PDB
- 1WYW
- Type
- protein
- Length
- 295 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 SMT3C
- EC
- 3.2.2.-
- UniProt
- Q13569, P63165
- Ligands
- MG, NA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-) | protein | 216 | 42% helix, 15% strand | Q13569 |
| B | Ubiquitin-like protein SMT3C | protein | 79 | 23% helix, 34% strand | P63165 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.67 | 0.83 | 37 | CL |
| 2 | 214 | 0.61 | 0.82 | 22 | empty |
| 3 | 339 | 0.58 | 0.76 | 35 | empty |
| 4 | 65 | 0.36 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 939 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1WYW · Crystal Structure of SUMO1-conjugated 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 0.97
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P63165
- Elsewhere: RCSB PDB 1WYW · PDBe 1WYW · UniProt Q13569 · UniProt P63165
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