Research workbench
Replacement of VAL3 in human thymidylate synthase affects its kinetic properties and intracellular stability
Analyse Replacement of VAL3 in human thymidylate synthase affects its kinetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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