Research workbench
Etherocomplex of enteroccocus faecalis thymidylate synthase with 5- hydroxymethilene-6-hydrofolic acid and the phtalimidic inhibitor SS7
Analyse Etherocomplex of enteroccocus faecalis thymidylate synthase with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O7U
- Type
- protein
- Length
- 1,192 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
- THF, SS7, SO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 290 | 37% 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 | 272 | 37% helix, 26% strand | Q834R3 |
Ligands and binding sites
- THF · 5-hydroxymethylene-6-hydrofolic acid · ligand · chains B
- SS7 · 4-{[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]oxy}-3,5-dimethylphenyl acetate · ligand · chains D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, B, D
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 | 513 | 0.77 | 0.85 | 58 | SO4, SS7 |
| 2 | 484 | 0.74 | 0.83 | 55 | SO4, THF |
| 3 | 609 | 0.68 | 0.77 | 58 | SO4 |
| 4 | 529 | 0.67 | 0.77 | 48 | SO4 |
| 5 | 177 | 0.53 | 0.79 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2419 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2412 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 653 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 23 Ų buried · 0 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 Q834R3
- Elsewhere: RCSB PDB 4O7U · PDBe 4O7U · UniProt Q834R3
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