Research workbench
Xenopus SMUG1, an anti-mutator uracil-DNA glycosylase
Analyse Xenopus SMUG1, an anti-mutator uracil-DNA glycosylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OE6
- Type
- protein + DNA
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-strand selective monofunctional uracil DNA glycosylase…
- EC
- 3.2.2.-
- UniProt
- Q9YGN6
- Ligands
- HMU
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-) | protein | 244 | 46% helix, 11% strand | Q9YGN6 |
| B | Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-) | protein | 245 | 47% helix, 11% strand | Q9YGN6 |
| E | 5'-D(*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3' | dna | 12 | — | — |
| F | 5'-D(*CP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- HMU · 5-hydroxymethyl uracil · ligand · 2 copies · chains A
- GOL · Glycerol · additive · chains A, E
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.73 | 0.80 | 56 | HMU, GOL |
| 2 | 379 | 0.65 | 0.79 | 36 | empty |
| 3 | 247 | 0.56 | 0.79 | 27 | empty |
| 4 | 129 | 0.50 | 0.80 | 22 | empty |
| 5 | 158 | 0.43 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- E–F · 520 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–E · 300 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 297 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–B · 234 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 174 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (additive adduct, nucleotide modification).
Compared structures
- 1OE6 · Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YGN6 · AlphaFold monomer V2.0 prediction for single-strand selective monofunctional uracil DNA… · a predicted model of the same protein · chain B 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 Q9YGN6
- Elsewhere: RCSB PDB 1OE6 · PDBe 1OE6 · UniProt Q9YGN6
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