MolNFT v1 · #110300 · protein
Complex structure of thymidylate synthase from varicella zoster virus
4XSE: “Complex structure of thymidylate synthase from varicella zoster virus”. X-ray diffraction, 1 ligand (PO4), 17 pockets (best druggability 0.72). MolNFT v1 #110300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XSE
- Type
- protein
- Length
- 1,116 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q4JQW2
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 29% helix, 23% strand | Q4JQW2 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 30% helix, 22% strand | Q4JQW2 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 27% helix, 22% strand | Q4JQW2 |
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 30% helix, 23% strand | Q4JQW2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.72 | 0.79 | 55 | PO4 |
| 2 | 443 | 0.72 | 0.82 | 49 | PO4 |
| 3 | 463 | 0.72 | 0.81 | 50 | PO4 |
| 4 | 378 | 0.65 | 0.79 | 47 | PO4 |
| 5 | 312 | 0.61 | 0.78 | 41 | empty |
Interfaces
3 interfaces between chains.
- B–A · 2115 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2072 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 607 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4XSE · Complex structure of thymidylate synthase from varicella zoster virus · the same entry in another collection · chain C against C, 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 Q4JQW2
- Elsewhere: RCSB PDB 4XSE · PDBe 4XSE · UniProt Q4JQW2
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