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Crystal structure of human MTH1(G2K/D120A mutant) in complex with 2- oxo-datp

Analyse Crystal structure of human MTH1(G2K/D120A 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
5GHP
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
NA
Pockets
3 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 44% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56)protein15616% helix, 44% strandP36639

Ligands and binding sites

  • NA · Sodium ion · metal · 2 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18010.790.8272empty
21640.700.8930NA
33280.650.8037NA

Interfaces

1 interface between chains.

  • A–B · 667 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

  • 5GHP · Crystal structure of human MTH1(G2K/D120A 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 B against A, TM-score 0.99

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