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Pngase F complex with di-N-acetylchitobiose

Analyse Pngase F complex with di-N-acetylchitobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1PNF
Type
protein
Length
314 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptide-N(4)-(N-acetyl-beta-D-GLUCOSAMINYL)ASPARAGINE amidase F
EC
3.5.1.52
UniProt
P21163
Ligands
NDG, NAG, SO4
Pockets
3 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APeptide-N(4)-(N-acetyl-beta-D-GLUCOSAMINYL)ASPARAGINE amidase F (EC 3.5.1.52)protein3146% helix, 47% strandP21163

Ligands and binding sites

  • NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
  • SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11200.490.8021NDG
2760.310.7318empty
3590.300.7516SO4

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

  • 1PNF · Pngase F complex with di-N-acetylchitobiose · the same entry in another collection · chain A against A, TM-score 1.00
  • P21163 · AlphaFold monomer V2.0 prediction for peptide-N(4)-(N-acetyl-beta-D… · a predicted model of the same protein · chain A against A, TM-score 0.98

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