MolNFT v1 · #73739 · protein
Human thymidylate synthase R163K with cys 195 covalently modified by glutathione
3OB7: “Human thymidylate synthase R163K with cys 195 covalently modified by glutathione”. X-ray diffraction, 2 ligands (GSH, PO4), 15 pockets (best druggability 0.81). MolNFT v1 #73739 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3OB7
- Type
- protein
- Length
- 1,403 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
- GSH, PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 25% strand | P04818 |
| C, E | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 33% helix, 23% strand | P04818 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B, D, E
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.81 | 0.82 | 79 | GSH |
| 2 | 848 | 0.72 | 0.77 | 82 | PO4 |
| 3 | 613 | 0.67 | 0.77 | 51 | empty |
| 4 | 505 | 0.66 | 0.77 | 55 | PO4 |
| 5 | 391 | 0.61 | 0.77 | 48 | PO4 |
Interfaces
5 interfaces between chains.
- A–B · 2243 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2236 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 650 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 252 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3OB7 · Human Thymidylate Synthase R163K with Cys 195 covalently modified by Glutathione · 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 3OB7 · PDBe 3OB7 · UniProt P04818
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