MolNFT v1 · #150599 · protein
Mouse thymidylate synthase crystal soaked in phenolphthalein
6GYJ: “Mouse thymidylate synthase crystal soaked in phenolphthalein”. X-ray diffraction, 2 ligands (FGT, SO4), 9 pockets (best druggability 0.68). MolNFT v1 #150599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GYJ
- Type
- protein
- Length
- 558 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
- FGT, SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 35% helix, 24% strand | P07607 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 278 | 35% helix, 24% strand | P07607 |
Ligands and binding sites
- FGT · 3,3-bis(4-hydroxyphenyl)-2-benzofuran-1-one · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
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 | 442 | 0.68 | 0.80 | 49 | SO4, FGT, DMS |
| 2 | 405 | 0.66 | 0.79 | 41 | SO4 |
| 3 | 132 | 0.51 | 0.80 | 20 | empty |
| 4 | 108 | 0.47 | 0.79 | 17 | empty |
| 5 | 76 | 0.42 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2318 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
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 6GYJ · PDBe 6GYJ · UniProt P07607
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