Research workbench
Crystal structure of E. COLI thymidylate synthase complexed with sp- 876
Analyse Crystal structure of E. COLI thymidylate synthase complexed with sp- 876 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F4G
- 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
- TP4, SO4
- Pockets
- 7 · best druggability 0.72
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
- TP4 · N-[4-[[glutamic acid]-carbonyl]-benzene-sulfonyl-D-prolinyl]-3-amino-propanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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
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 | 500 | 0.72 | 0.82 | 51 | SO4, TP4 |
| 2 | 574 | 0.69 | 0.78 | 51 | GOL, TP4 |
| 3 | 118 | 0.41 | 0.76 | 19 | empty |
| 4 | 109 | 0.40 | 0.76 | 17 | empty |
| 5 | 51 | 0.38 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2250 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation, oxidation).
Compared structures
- 1F4G · Crystal structure of E. COLI thymidylate synthase complexed with sp-876 · 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 1F4G · PDBe 1F4G · UniProt P0A884
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