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MolNFT v1 · #128180 · protein

Glucose oxidase mutant A2

5NIT: “Glucose oxidase mutant A2”. X-ray diffraction, 5 ligands (FAD, NAG, BMA), 2 pockets (best druggability 0.84). MolNFT v1 #128180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5NIT
Type
protein
Length
581 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Glucose oxidase
EC
1.1.3.4
UniProt
P13006
Ligands
FAD, NAG, BMA, MAN, OXY
Pockets
2 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AGlucose oxidase (EC 1.1.3.4)protein58134% helix, 24% strandP13006

Ligands and binding sites

  • FAD · Flavin-adenine dinucleotide · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
  • BMA · beta-D-mannopyranose · sugar
  • MAN · alpha-D-mannopyranose · sugar
  • OXY · Oxygen molecule · ion · chains A
  • DIO · 1,4-diethylene dioxide · additive · 18 copies · chains A
  • EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16520.840.8984FAD, OXY, DIO
2660.310.7518empty

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

  • 5NIT · Glucose oxidase mutant A2 · the same entry in another collection · chain A against A, TM-score 1.00
  • P13006 · AlphaFold monomer V2.0 prediction for glucose oxidase (P13006) · a predicted model of the same protein · chain A against A, TM-score 1.00

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