MolNFT v1 · #119858 · protein
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8- oxo-dgtp at pH 7.0
5GHM · 7,8-dihydro-8-oxoguanine triphosphatase: “Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8- oxo-dgtp at pH 7.0”. X-ray diffraction, 2 ligands (8DG, NA), 4 pockets (best druggability 0.77). MolNFT v1 #119858 on…
- PDB
- 5GHM
- 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
- 8DG, NA
- Pockets
- 4 · best druggability 0.77
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
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.77 | 0.82 | 71 | empty |
| 2 | 318 | 0.65 | 0.80 | 34 | 8DG, NA |
| 3 | 262 | 0.65 | 0.82 | 30 | 8DG |
| 4 | 63 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5GHM · Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 7.0 · 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 B against A, TM-score 0.99
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 5GHM · PDBe 5GHM · UniProt P36639
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