Research workbench
Structures of thymidylate synthase R163K with substrates and inhibitors show subunit asymmetry
Analyse Structures of thymidylate synthase R163K with substrates and inhibitors show… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HB8
- Type
- protein
- Length
- 1,405 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 33% helix, 24% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.78 | 0.80 | 84 | UMP |
| 2 | 754 | 0.72 | 0.78 | 67 | PO4, EDO |
| 3 | 678 | 0.68 | 0.76 | 56 | empty |
| 4 | 453 | 0.63 | 0.77 | 48 | UMP, EDO |
| 5 | 384 | 0.62 | 0.77 | 31 | PO4, EDO |
Interfaces
5 interfaces between chains.
- A–B · 2244 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 2211 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 298 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HB8 · Structures of Thymidylate Synthase R163K with Substrates and Inhibitors Show Subunit… · 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 P04818
- Elsewhere: RCSB PDB 3HB8 · PDBe 3HB8 · UniProt P04818
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