Research workbench
Mouse thymidylate synthase cocrystallized with dump and soaked in phenolphthalein
Analyse Mouse thymidylate synthase cocrystallized with dump and soaked in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKO
- Type
- protein
- Length
- 571 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, FGT
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | P07607 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 34% helix, 23% strand | P07607 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- FGT · 3,3-bis(4-hydroxyphenyl)-2-benzofuran-1-one · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.78 | 0.85 | 44 | UMP, FGT, DMS |
| 2 | 578 | 0.77 | 0.83 | 46 | UMP, FGT, DMS |
| 3 | 113 | 0.45 | 0.78 | 20 | empty |
| 4 | 85 | 0.44 | 0.80 | 17 | empty |
| 5 | 81 | 0.40 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2259 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6GKO · Mouse thymidylate synthase cocrystallized with dUMP and soaked in phenolphthalein · 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 0.99
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 6GKO · PDBe 6GKO · UniProt P07607
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