Research workbench
E. COLI thymidylate synthase mutant I264AM
Analyse E. COLI thymidylate synthase mutant I264AM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CDZ
- Type
- protein
- Length
- 526 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
- CB3, UMP, UMC
- 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 | 263 | 33% helix, 26% strand | P0A884 |
Ligands and binding sites
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 2 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A, B
- UMC · 2'-deoxy-5'-uridylic acid · ligand · 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 | 723 | 0.77 | 0.81 | 58 | CB3, UMP |
| 2 | 430 | 0.75 | 0.84 | 40 | CB3, UMC |
| 3 | 104 | 0.41 | 0.77 | 22 | empty |
| 4 | 101 | 0.40 | 0.77 | 17 | empty |
| 5 | 84 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2342 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (carboxylation, covalent ligand).
Compared structures
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 6CDZ · PDBe 6CDZ · UniProt P0A884
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.