MolNFT v1 · #81617 · protein
Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in complex with 5-formyl tetrahydrofolate
3UWL: “Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in complex with 5-formyl…”. X-ray diffraction, 2 ligands (FFO, SO4), 16 pockets (best druggability 0.73). MolNFT v1 #81617 on GenesisL1: 3D structure, binding…
- PDB
- 3UWL
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- Q834R3
- Ligands
- FFO, SO4
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 292 | 40% helix, 24% strand | Q834R3 |
| B, D | Thymidylate synthase (EC 2.1.1.45) | protein | 315 | 42% helix, 22% strand | Q834R3 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 38% helix, 25% strand | Q834R3 |
Ligands and binding sites
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.73 | 0.83 | 50 | FFO |
| 2 | 400 | 0.71 | 0.82 | 45 | FFO |
| 3 | 631 | 0.69 | 0.77 | 58 | SO4 |
| 4 | 587 | 0.68 | 0.77 | 53 | SO4 |
| 5 | 348 | 0.60 | 0.77 | 39 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2391 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2380 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 658 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 3UWL · Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q834R3 · AlphaFold monomer V2.0 prediction for thymidylate synthase (Q834R3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q834R3
- Elsewhere: RCSB PDB 3UWL · PDBe 3UWL · UniProt Q834R3
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