Research workbench
E.COLI thymidylate synthase complexes with 5-NO2DUMP and tetrahydrofolate at 1.4 a resolution
Analyse E.COLI thymidylate synthase complexes with 5-NO2DUMP and tetrahydrofolate at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BHL
- 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
- NDU, THG, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 26% strand | P0A884 |
Ligands and binding sites
- NDU · 2'-deoxy-5-nitrouridine 5'-monophosphate · ligand · 2 copies · chains A, B
- THG · (6S)-5,6,7,8-tetrahydrofolate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.77 | 0.85 | 49 | NDU, THG |
| 2 | 385 | 0.77 | 0.87 | 47 | NDU, THG |
| 3 | 103 | 0.42 | 0.78 | 19 | empty |
| 4 | 98 | 0.39 | 0.77 | 18 | empty |
| 5 | 86 | 0.37 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2330 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 3BHL · E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A… · the same entry in another collection · chain B against B, 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 3BHL · PDBe 3BHL · UniProt P0A884
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