MolNFT v1 · #127531 · protein
Crystal structure of mouse MTH1 in complex with TH588
5MZG · 7,8-dihydro-8-oxoguanine triphosphatase: “Crystal structure of mouse MTH1 in complex with TH588”. X-ray diffraction, 3 ligands (2GE, SCN, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #127531 on GenesisL1: 3D structure…
- PDB
- 5MZG
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-8-oxoguanine triphosphatase
- EC
- 3.6.1.55, 3.6.1.56
- UniProt
- P53368
- Ligands
- 2GE, SCN, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 155 | 16% helix, 46% strand | P53368 |
| B | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 153 | 16% helix, 44% strand | P53368 |
Ligands and binding sites
- 2GE · N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.73 | 0.89 | 31 | 2GE, SO4 |
| 2 | 219 | 0.71 | 0.87 | 33 | 2GE, SO4 |
| 3 | 84 | 0.40 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MZG · Crystal structure of mouse MTH1 in complex with TH588 · the same entry in another collection · chain A against A, TM-score 1.00
- P53368 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P53368) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P53368
- Elsewhere: RCSB PDB 5MZG · PDBe 5MZG · UniProt P53368
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