Research workbench
Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in complex with fdump
Analyse Crystal structure of enteroccocus faecalis thymidylate synthase (efts) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QXS
- Type
- protein
- Length
- 1,214 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
- UFP, FFO, SO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thymidylate synthase (EC 2.1.1.45) | protein | 292 | 39% helix, 24% strand | Q834R3 |
| B, D | Thymidylate synthase (EC 2.1.1.45) | protein | 315 | 43% helix, 22% strand | Q834R3 |
Ligands and binding sites
- UFP · 5-fluoro-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 · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.81 | 0.87 | 53 | empty |
| 2 | 492 | 0.77 | 0.85 | 55 | UFP, FFO |
| 3 | 415 | 0.76 | 0.86 | 47 | UFP, FFO |
| 4 | 244 | 0.61 | 0.80 | 32 | SO4 |
| 5 | 332 | 0.59 | 0.77 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2427 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2363 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 572 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6QXS · Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with… · the same entry in another collection · chain C against C, 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 6QXS · PDBe 6QXS · UniProt Q834R3
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