MolNFT v1 · #127530 · protein

Crystal structure of dog MTH1 protein

5MZF: “Crystal structure of dog MTH1 protein”. X-ray diffraction, 2 ligands (SO4, CL), 12 pockets (best druggability 0.71). MolNFT v1 #127530 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MZF
Type: protein
Length: 637 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MTH1 protein
UniProt: F1P963
Ligands: SO4, CL
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MTH1 protein	protein	155	16% helix, 46% strand	F1P963
B	MTH1 protein	protein	164	15% helix, 48% strand	F1P963
C	MTH1 protein	protein	154	18% helix, 46% strand	F1P963
D	MTH1 protein	protein	164	17% helix, 45% strand	F1P963

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
CL · Chloride ion · ion · chains B
ACT · Acetate ion · additive · 6 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.71	0.90	29	ACT
2	150	0.71	0.90	29	ACT
3	207	0.67	0.85	35	ACT, CL
4	179	0.64	0.85	37	SO4, ACT
5	152	0.62	0.85	24	GOL

Interfaces

5 interfaces between chains.

B–D · 777 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 530 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 375 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5MZF · Crystal structure of dog MTH1 protein · the same entry in another collection · chain D against D, TM-score 1.00
F1P963 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (F1P963) · a predicted model of the same protein · chain C 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 F1P963
Elsewhere: RCSB PDB 5MZF · PDBe 5MZF · UniProt F1P963

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