GL1X · GenesisL1 explorer

MolNFT v1 · #138904 · protein

Crystal structure of ATNUDX1 (E56A)

5WY6 · Nudix hydrolase 1: “Crystal structure of ATNUDX1 (E56A)”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.73). MolNFT v1 #138904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5WY6
Type
protein
Length
277 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Nudix hydrolase 1
EC
3.6.1.55, 3.6.1.67, 3.6.1.22
UniProt
Q9CA40
Ligands
SO4
Pockets
3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ENudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)protein13915% helix, 41% strandQ9CA40
ANudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)protein13815% helix, 41% strandQ9CA40

Ligands and binding sites

  • SO4 · Sulfate ion · ion · chains E, A
  • PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains E, A
  • GOL · Glycerol · additive · 2 copies · chains E, A

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
13190.730.8534empty
23070.730.8534empty
33760.640.7841empty

Interfaces

1 interface between chains.

  • E–A · 356 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

  • 5WY6 · Crystal structure of AtNUDX1 (E56A) · the same entry in another collection · chain E against E, TM-score 1.00
  • Q9CA40 · AlphaFold monomer V2.0 prediction for nudix hydrolase 1 (Q9CA40) · a predicted model of the same protein · chain A against A, TM-score 0.98

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