Research workbench
Enterococcus faecalis thymidylate synthase complex with methotrexate
Analyse Enterococcus faecalis thymidylate synthase complex with methotrexate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7W
- Type
- protein
- Length
- 1,183 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
- MTX, SO4
- Pockets
- 17 · best druggability 0.76
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 | 280 | 36% helix, 25% strand | Q834R3 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 273 | 38% helix, 26% strand | Q834R3 |
| C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 315 | 43% helix, 22% strand | Q834R3 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.76 | 0.84 | 50 | SO4, MTX |
| 2 | 497 | 0.75 | 0.83 | 55 | SO4, MTX |
| 3 | 604 | 0.68 | 0.77 | 56 | SO4 |
| 4 | 545 | 0.65 | 0.76 | 60 | SO4 |
| 5 | 166 | 0.53 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2428 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2383 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 656 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J7W · Enterococcus faecalis thymidylate synthase complex with methotrexate · 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 B 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 5J7W · PDBe 5J7W · UniProt Q834R3
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