MolNFT v1 · #62575 · protein
Replacement of VAL3 in human thymidylate synthase affects its kinetic properties and intracellular stability
3EJL: “Replacement of VAL3 in human thymidylate synthase affects its kinetic properties and intracellular stability”. X-ray diffraction, 2 ligands (UFP, PO4), 16 pockets (best druggability 0.69). MolNFT v1 #62575 on GenesisL1: 3D…
- PDB
- 3EJL
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UFP, PO4
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 283 | 30% helix, 23% strand | P04818 |
Ligands and binding sites
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · chains C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, 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 | 574 | 0.69 | 0.78 | 47 | PO4 |
| 2 | 571 | 0.68 | 0.77 | 43 | PO4 |
| 3 | 494 | 0.67 | 0.78 | 55 | UFP |
| 4 | 440 | 0.62 | 0.76 | 36 | PO4 |
| 5 | 157 | 0.52 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2262 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3EJL · Replacement of Val3 in Human Thymidylate Synthase Affects Its Kinetic Properties and… · the same entry in another collection · chain A against A, TM-score 1.00
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 P04818
- Elsewhere: RCSB PDB 3EJL · PDBe 3EJL · UniProt P04818
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