MolNFT v1 · #104502 · protein
Crystal structure of vaccinia virus uracil-DNA glycosylase mutant 3GD4
4QC9: “Crystal structure of vaccinia virus uracil-DNA glycosylase mutant 3GD4”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.74). MolNFT v1 #104502 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QC9
- Type
- protein
- Length
- 875 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
- Q91UM2
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 219 | 34% helix, 18% strand | Q91UM2 |
| C | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 218 | 34% helix, 18% strand | Q91UM2 |
| D | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 34% helix, 19% strand | Q91UM2 |
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 218 | 36% helix, 17% strand | Q91UM2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, D, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.74 | 0.80 | 57 | empty |
| 2 | 543 | 0.71 | 0.80 | 57 | empty |
| 3 | 193 | 0.65 | 0.84 | 43 | SO4 |
| 4 | 154 | 0.64 | 0.86 | 28 | empty |
| 5 | 99 | 0.63 | 0.89 | 29 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 921 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 903 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 563 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 522 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QC9 · Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4 · 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 Q91UM2
- Elsewhere: RCSB PDB 4QC9 · PDBe 4QC9 · UniProt Q91UM2
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