MolNFT v1 · #170212 · protein
Mouse thymidylate synthase cocrystallized with dump and soaked in sulfamethoxazole
6Y08: “Mouse thymidylate synthase cocrystallized with dump and soaked in sulfamethoxazole”. X-ray diffraction, 2 ligands (UMP, 08D), 9 pockets (best druggability 0.68). MolNFT v1 #170212 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y08
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P07607
- Ligands
- UMP, 08D
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 279 | 35% helix, 24% strand | P07607 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 278 | 36% helix, 24% strand | P07607 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- 08D · Sulfamethoxazole · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.68 | 0.80 | 45 | UMP, 08D |
| 2 | 430 | 0.66 | 0.79 | 45 | UMP, 08D |
| 3 | 170 | 0.50 | 0.77 | 20 | empty |
| 4 | 82 | 0.42 | 0.79 | 15 | empty |
| 5 | 81 | 0.40 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2267 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6Y08 · Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole · the same entry in another collection · chain A against A, TM-score 1.00
- P07607 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P07607) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P07607
- Elsewhere: RCSB PDB 6Y08 · PDBe 6Y08 · UniProt P07607
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