MolNFT v1 · #123841 · protein
Temperature sensitive D4 mutant L110F
5JX0 · Uracil-DNA glycosylase: “Temperature sensitive D4 mutant L110F”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.83). MolNFT v1 #123841 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JX0
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase
- EC
- 3.2.2.27
- UniProt
- P04303
- Ligands
- CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 218 | 36% helix, 17% strand | P04303 |
| B, C | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 216 | 36% helix, 17% strand | P04303 |
| D | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 213 | 38% helix, 17% strand | P04303 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.83 | 0.84 | 110 | empty |
| 2 | 124 | 0.61 | 0.86 | 35 | GOL |
| 3 | 106 | 0.61 | 0.87 | 31 | GOL |
| 4 | 86 | 0.57 | 0.87 | 22 | GOL |
| 5 | 104 | 0.52 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 405 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 385 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 224 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JX0 · Temperature sensitive D4 mutant L110F · the same entry in another collection · chain A 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 P04303
- Elsewhere: RCSB PDB 5JX0 · PDBe 5JX0 · UniProt P04303
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