MolNFT v1 · #22214 · protein
E. COLI thymidylate synthase in complex with BW1843U89 and 2'-deoxyuridine 5'-monophosphate (dump)
1SYN: “E. COLI thymidylate synthase in complex with BW1843U89 and 2'-deoxyuridine 5'-monophosphate (dump)”. X-ray diffraction, 2 ligands (UMP, F89), 7 pockets (best druggability 0.78). MolNFT v1 #22214 on GenesisL1: 3D structure, binding…
- PDB
- 1SYN
- 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, F89
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 35% helix, 25% strand | P0A884 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- F89 · S)-2-(5(((1,2-dihydro-3-methyl-1-oxobenzo(f)quinazolin-9-yl)methyl)amino)1-oxo-2-isoindolinyl)glutaric acid · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 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 | 467 | 0.78 | 0.86 | 46 | UMP, F89 |
| 2 | 481 | 0.77 | 0.85 | 48 | UMP, F89 |
| 3 | 106 | 0.40 | 0.76 | 19 | empty |
| 4 | 92 | 0.39 | 0.77 | 18 | empty |
| 5 | 91 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2358 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 1SYN · E. COLI thymidylate synthase in complex with BW1843U89 and 2'-deoxyuridine… · 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 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 P0A884
- Elsewhere: RCSB PDB 1SYN · PDBe 1SYN · UniProt P0A884
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