MolNFT v1 · #6165 · protein
Crystal structure of E. COLI thymidylate synthase covalently modified at C146 with N-[tosyl-D-PROLINYL]AMINO-ethanethiol
1F4C: “Crystal structure of E. COLI thymidylate synthase covalently modified at C146 with…”. X-ray diffraction, 2 ligands (TP2, SO4), 8 pockets (best druggability 0.74). MolNFT v1 #6165 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1F4C
- Type
- protein
- Length
- 523 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
- TP2, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 34% helix, 27% strand | P0A884 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 36% helix, 27% strand | P0A884 |
Ligands and binding sites
- TP2 · N-[tosyl-D-prolinyl]amino-ethanethiol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 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 | 601 | 0.74 | 0.81 | 56 | SO4, TP2 |
| 2 | 552 | 0.69 | 0.79 | 50 | TP2, GOL |
| 3 | 108 | 0.42 | 0.77 | 22 | empty |
| 4 | 103 | 0.40 | 0.76 | 19 | empty |
| 5 | 76 | 0.39 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2316 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 1F4C · Crystal structure of E. COLI thymidylate synthase covalently modified at C146 with… · 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 1F4C · PDBe 1F4C · UniProt P0A884
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