MolNFT v1 · #92648 · protein
E. COLI thymidylate synthase Y209W variant in complex with substrate and a cofactor analog
4GEV: “E. COLI thymidylate synthase Y209W variant in complex with substrate and a cofactor analog”. X-ray diffraction, 2 ligands (UMC, CB3), 8 pockets (best druggability 0.77). MolNFT v1 #92648 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GEV
- 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
- UMC, CB3
- Pockets
- 8 · best druggability 0.77
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
- UMC · 2'-deoxy-5'-uridylic acid · ligand · 2 copies · chains A, B
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.77 | 0.86 | 46 | UMC, CB3 |
| 2 | 455 | 0.75 | 0.84 | 47 | UMC, CB3 |
| 3 | 128 | 0.42 | 0.76 | 23 | empty |
| 4 | 105 | 0.39 | 0.76 | 19 | empty |
| 5 | 91 | 0.39 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2369 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 4GEV · E. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog · 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 4GEV · PDBe 4GEV · UniProt P0A884
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