MolNFT v1 · #162090 · protein
Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in complex with dump
6QYA: “Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in complex with dump”. X-ray diffraction, 4 ligands (UMP, FFO, SO4), 14 pockets (best druggability 0.72). MolNFT v1 #162090 on GenesisL1: 3D structure, binding…
- PDB
- 6QYA
- Type
- protein
- Length
- 1,190 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
- UMP, FFO, SO4, CL
- Pockets
- 14 · best druggability 0.72
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 | 278 | 36% helix, 24% strand | Q834R3 |
| B, D | Thymidylate synthase (EC 2.1.1.45) | protein | 315 | 43% helix, 22% strand | Q834R3 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 282 | 39% helix, 24% strand | Q834R3 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- 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 · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.72 | 0.83 | 44 | FFO |
| 2 | 463 | 0.72 | 0.82 | 47 | FFO |
| 3 | 519 | 0.66 | 0.77 | 51 | UMP |
| 4 | 473 | 0.65 | 0.77 | 39 | UMP |
| 5 | 140 | 0.48 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2479 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2448 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 641 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact, oxidation).
Compared structures
- 6QYA · Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q834R3 · AlphaFold monomer V2.0 prediction for thymidylate synthase (Q834R3) · a predicted model of the same protein · chain C 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 Q834R3
- Elsewhere: RCSB PDB 6QYA · PDBe 6QYA · UniProt Q834R3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.