Research workbench
Complex structure of thymidylate synthase from varicella zoster virus with a dump
Analyse Complex structure of thymidylate synthase from varicella zoster virus with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XSD
- Type
- protein
- Length
- 1,081 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
- UMP
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 31% helix, 24% strand | Q4JQW2 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 277 | 29% helix, 22% strand | Q4JQW2 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 27% helix, 24% strand | Q4JQW2 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 30% helix, 22% strand | Q4JQW2 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.67 | 0.80 | 37 | UMP |
| 2 | 471 | 0.67 | 0.79 | 48 | UMP |
| 3 | 463 | 0.66 | 0.78 | 53 | UMP |
| 4 | 277 | 0.64 | 0.81 | 28 | empty |
| 5 | 363 | 0.62 | 0.77 | 34 | UMP |
Interfaces
3 interfaces between chains.
- A–B · 2157 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2078 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4XSD · Complex structure of thymidylate synthase from varicella zoster virus with a dUMP · 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 Q4JQW2
- Elsewhere: RCSB PDB 4XSD · PDBe 4XSD · UniProt Q4JQW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.