Research workbench
Crystal structure of human MTH1 in complex with O6-methyl-dgmp
Analyse Crystal structure of human MTH1 in complex with O6-methyl-dgmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OTM
- Type
- protein
- Length
- 314 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
- P36639
- Ligands
- 6OG, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 157 | 16% helix, 43% strand | P36639 |
Ligands and binding sites
- 6OG · 6-O-methyl guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- ACT · Acetate ion · additive · chains A
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 | 157 | 0.73 | 0.91 | 25 | 6OG |
| 2 | 170 | 0.72 | 0.90 | 26 | 6OG |
| 3 | 107 | 0.38 | 0.75 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 470 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5OTM · Crystal structure of human MTH1 in complex with O6-methyl-dGMP · the same entry in another collection · chain A against A, TM-score 1.00
- P36639 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P36639) · a predicted model of the same protein · chain A 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 P36639
- Elsewhere: RCSB PDB 5OTM · PDBe 5OTM · UniProt P36639
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