MolNFT v1 · #104503 · protein
Crystal structure of vaccinia virus uracil-DNA glycosylase mutant R167AD4
4QCA: “Crystal structure of vaccinia virus uracil-DNA glycosylase mutant R167AD4”. X-ray diffraction, 2 ligands (K, CL), 8 pockets (best druggability 0.80). MolNFT v1 #104503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QCA
- Type
- protein
- Length
- 881 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
- K, CL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 221 | 42% helix, 17% strand | Q91UM2 |
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 41% helix, 17% strand | Q91UM2 |
| D | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 219 | 40% helix, 17% strand | Q91UM2 |
Ligands and binding sites
- K · Potassium ion · metal · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.80 | 0.82 | 99 | K |
| 2 | 267 | 0.66 | 0.83 | 38 | GOL |
| 3 | 216 | 0.61 | 0.81 | 33 | empty |
| 4 | 107 | 0.55 | 0.84 | 27 | GOL |
| 5 | 76 | 0.50 | 0.84 | 18 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 814 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 347 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 241 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QCA · Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant R167AD4 · the same entry in another collection · chain D against D, 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 4QCA · PDBe 4QCA · UniProt Q91UM2
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