Research workbench
High-resolution structure of wild-type E. COLI thymidylate synthase
Analyse High-resolution structure of wild-type E. COLI thymidylate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NNR
- 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
- UMC, CB3, NA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 36% helix, 26% strand | P0A884 |
Ligands and binding sites
- UMC · 2'-deoxy-5'-uridylic acid · ligand · 2 copies · chains A, B
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic 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 | 418 | 0.78 | 0.87 | 52 | UMC, CB3 |
| 2 | 419 | 0.76 | 0.85 | 47 | UMC, CB3 |
| 3 | 92 | 0.40 | 0.77 | 20 | empty |
| 4 | 110 | 0.39 | 0.76 | 19 | empty |
| 5 | 83 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2361 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
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 6NNR · PDBe 6NNR · UniProt P0A884
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