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
- 1OE5
- 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
- URA, DUR
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-) | protein | 243 | 48% helix, 12% strand | Q9YGN6 |
| B | Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-) | protein | 245 | 49% 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*3DRP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*GP)-3' | dna | 13 | — | — |
Ligands and binding sites
- URA · Uracil · ligand · chains A
- DUR · 2'-deoxyuridine · ligand · chains F
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.75 | 0.80 | 74 | URA, GOL |
| 2 | 295 | 0.60 | 0.78 | 33 | empty |
| 3 | 113 | 0.51 | 0.81 | 20 | empty |
| 4 | 148 | 0.42 | 0.74 | 19 | EPE |
| 5 | 143 | 0.41 | 0.74 | 18 | EPE |
Interfaces
5 interfaces between chains.
- E–F · 507 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–E · 308 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 255 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–F · 181 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1OE5 · 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 1OE5 · PDBe 1OE5 · UniProt Q9YGN6
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