GL1X · GenesisL1 explorer

MolNFT v1 · #19317 · protein

X-ray structure of yeast HAL2P

1QGX · 3',5'-adenosine bisphosphatase: “X-ray structure of yeast HAL2P”. X-ray diffraction, 4 ligands (AMP, MG, PO4), 3 pockets (best druggability 0.69). MolNFT v1 #19317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1QGX
Type
protein
Length
354 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
3',5'-adenosine bisphosphatase
EC
3.1.3.7
UniProt
P32179
Ligands
AMP, MG, PO4, SO4
Pockets
3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A3',5'-adenosine bisphosphatase (EC 3.1.3.7)protein35438% helix, 20% strandP32179

Ligands and binding sites

  • AMP · Adenosine monophosphate · ligand · chains A
  • MG · Magnesium ion · metal · 2 copies · chains A
  • PO4 · Phosphate ion · ion · chains A
  • SO4 · Sulfate ion · ion · chains A
  • BME · Beta-mercaptoethanol · additive · chains 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12780.690.8438MG, PO4, SO4, AMP
2680.360.7717empty
3500.280.7513empty

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

  • 1QGX · X-ray structure of yeast HAL2P · the same entry in another collection · chain A against A, TM-score 1.00
  • P32179 · AlphaFold monomer V2.0 prediction for 3'(2'),5'-bisphosphate nucleotidase (P32179) · a predicted model of the same protein · chain A against A, TM-score 0.99

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