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Structure of NUDT15 in complex with 6-thio-gmp

Analyse Structure of NUDT15 in complex with 6-thio-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LPG
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable 8-oxo-dgtp diphosphatase NUDT15
EC: 3.6.1.55
UniProt: Q9NV35
Ligands: 71V, MG
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.55)	protein	156	21% helix, 36% strand	Q9NV35

Ligands and binding sites

71V · [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-sulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A
MG · Magnesium ion · metal · 5 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.65	0.83	31	MG, 71V
2	166	0.61	0.84	31	MG
3	53	0.30	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1669 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

5LPG · Structure of NUDT15 in complex with 6-thio-GMP · the same entry in another collection · chain A against A, TM-score 1.00
Q9NV35 · AlphaFold monomer V2.0 prediction for nucleotide triphosphate diphosphatase NUDT15… · a predicted model of the same protein · chain A 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 Q9NV35
Elsewhere: RCSB PDB 5LPG · PDBe 5LPG · UniProt Q9NV35

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