Research workbench
Lactobacillus casei thymidylate synthase ternary complex with dump and the phtalimidic derivative C00 in multiple binding modes
Analyse Lactobacillus casei thymidylate synthase ternary complex with dump and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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