Research workbench
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2- oxo-datp
Analyse Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2- oxo-datp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GHN
- Type
- protein
- Length
- 312 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
- 6U4, NA
- Pockets
- 3 · best druggability 0.79
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 | 156 | 16% helix, 43% strand | P36639 |
Ligands and binding sites
- 6U4 · [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.79 | 0.82 | 72 | empty |
| 2 | 305 | 0.61 | 0.79 | 36 | 6U4, NA |
| 3 | 189 | 0.60 | 0.82 | 32 | 6U4, NA |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5GHN · Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP · 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 5GHN · PDBe 5GHN · UniProt P36639
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