Research workbench
E. COLI thymidylate synthase bound to dump and LY338529, a PYRROLO(2, 3-D)PYRIMIDINE-based antifolate
Analyse E. COLI thymidylate synthase bound to dump and LY338529, a PYRROLO(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JUT
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P0A884
- Ligands
- UMP, LYD
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 35% helix, 26% strand | P0A884 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- LYD · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-3-methyl-butyric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.78 | 0.85 | 44 | UMP, LYD |
| 2 | 428 | 0.75 | 0.84 | 47 | UMP, LYD |
| 3 | 100 | 0.42 | 0.78 | 17 | empty |
| 4 | 102 | 0.40 | 0.77 | 18 | empty |
| 5 | 109 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2303 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (carboxylation, covalent ligand).
Compared structures
- 1JUT · E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrolo(2,3-d)pyrimidine-based… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · a predicted model of the same protein · chain B 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 P0A884
- Elsewhere: RCSB PDB 1JUT · PDBe 1JUT · UniProt P0A884
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.