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Complex structure of thymidylate synthase from varicella zoster virus with a phosphorylated bvdu
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
- 4XSC
- Type
- protein
- Length
- 1,093 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
- BVP
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 31% helix, 26% strand | Q4JQW2 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 284 | 33% helix, 23% strand | Q4JQW2 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 26% strand | Q4JQW2 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 30% helix, 23% strand | Q4JQW2 |
Ligands and binding sites
- BVP · (E)-5-(2-bromovinyl)-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.70 | 0.79 | 61 | BVP, 1PE |
| 2 | 275 | 0.69 | 0.84 | 34 | empty |
| 3 | 409 | 0.69 | 0.81 | 40 | BVP, 1PE |
| 4 | 660 | 0.66 | 0.75 | 55 | empty |
| 5 | 367 | 0.66 | 0.80 | 37 | BVP, 1PE |
Interfaces
3 interfaces between chains.
- A–B · 2233 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2175 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 696 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4XSC · Complex structure of thymidylate synthase from varicella zoster virus with a… · 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 4XSC · PDBe 4XSC · UniProt Q4JQW2
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