MolNFT v1 · #59467 · protein
Lactobacillus casei thymidylate synthase ternary complex with dump and the phtalimidic derivative C00 in multiple binding modes
3BYX: “Lactobacillus casei thymidylate synthase ternary complex with dump and the phtalimidic derivative C00 in…”. X-ray diffraction, 2 ligands (UMP, C00), 2 pockets (best druggability 0.75). MolNFT v1 #59467 on GenesisL1: 3D structure…
- PDB
- 3BYX
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P00469
- Ligands
- UMP, C00
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 313 | 41% helix, 22% strand | P00469 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A
- C00 · 2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.75 | 0.79 | 78 | UMP, C00 |
| 2 | 59 | 0.27 | 0.73 | 16 | empty |
Compared structures
- 3BYX · Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic… · the same entry in another collection · chain A against A, TM-score 1.00
- P00469 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P00469) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00469
- Elsewhere: RCSB PDB 3BYX · PDBe 3BYX · UniProt P00469
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