Research workbench
Crystal structure of the thymidylate synthase K48Q
Analyse Crystal structure of the thymidylate synthase K48Q in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B5B
- 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, NDN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 33% helix, 26% strand | P0A884 |
Ligands and binding sites
- NDU · 2'-deoxy-5-nitrouridine 5'-monophosphate · ligand · chains A, B
- NDN · 2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate) · ligand · 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 | 518 | 0.77 | 0.84 | 48 | NDN |
| 2 | 529 | 0.76 | 0.83 | 48 | NDU |
| 3 | 109 | 0.39 | 0.76 | 19 | empty |
| 4 | 87 | 0.39 | 0.76 | 12 | empty |
| 5 | 98 | 0.38 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2364 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct, covalent ligand).
Compared structures
- 3B5B · Crystal structure of the thymidylate synthase k48q · the same entry in another collection · chain A against A, TM-score 1.00
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 3B5B · PDBe 3B5B · UniProt P0A884
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