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Binding mode of hydroxylamine to arthromyces ramosus peroxidase

Analyse Binding mode of hydroxylamine to arthromyces ramosus peroxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1C8I
Type
protein
Length
336 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Protein (peroxidase)
EC
1.11.1.7
UniProt
P28313
Ligands
HEM, HOA, NAG, BMA, CA
Pockets
1 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProtein (peroxidase) (EC 1.11.1.7)protein33643% helix, 7% strandP28313

Ligands and binding sites

  • HEM · Protoporphyrin IX containing Fe · ligand · chains A
  • HOA · Hydroxyamine · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · chains A
  • CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14230.790.8743HEM, HOA

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).

Compared structures

  • 1C8I · Binding mode of hydroxylamine to arthromyces ramosus peroxidase · the same entry in another collection · chain A against A, TM-score 1.00
  • P28313 · AlphaFold monomer V2.0 prediction for peroxidase (P28313) · a predicted model of the same protein · chain A against A, TM-score 1.00

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