Research workbench
Lactobacillus casei thymidylate synthase ternary complex with dump and the phtalimidic derivative C00
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
- 3BZ0
- Type
- protein
- Length
- 306 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 0.65
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 306 | 39% helix, 21% 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 | 538 | 0.65 | 0.76 | 38 | UMP, C00 |
| 2 | 50 | 0.28 | 0.75 | 11 | empty |
Compared structures
- 3BZ0 · 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 0.98
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 3BZ0 · PDBe 3BZ0 · UniProt P00469
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