› 3hdl

X-ray diffraction
1.85Å resolution

Crystal Structure of Highly Glycosylated Peroxidase from Royal Palm Tree

Released:
DOI: 10.2210/pdb3hdl/pdb
PDB entry 3hdl coloured by chain, front view.
PDB entry 3hdl coloured by chain, side view.
PDB entry 3hdl coloured by chain, top view.
Source organism: Roystonea regia
Primary publication:
Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).
Watanabe L, de Moura PR, Bleicher L, Nascimento AS, Zamorano LS, Calvete JJ, Sanz L, Pérez A, Bursakov S, Roig MG, Shnyrov VL, Polikarpov I
J Struct Biol 169 226-42 (2010)
PMID: 19854274

Function and Biology Details

Reaction catalysed: 
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112321 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (6 distinct):
Peroxidase Chain: A
Molecule details ›
Chain: A
Length: 304 amino acids
Theoretical weight: 31.87 KDa
Source organism: Roystonea regia
UniProt:
  • Canonical: D1MPT2 (Residues: 1-304; Coverage: 100%)
Sequence domains: Peroxidase
Structure domains:

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
Carbohydrate polymer : NEW Components: NAG, MAN, XYZ, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, FUC
Carbohydrate polymer
6 bound ligands:
Ligand CA 2 x CA
Ligand PEO 1 x PEO
Ligand SO4 8 x SO4
Ligand MES 1 x MES
Ligand EDO 16 x EDO
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: P3121
Unit cell:
a: 117.821Å b: 117.821Å c: 93.447Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.176 0.187

Quick links

Citations

4 review citations

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010.
Harvey DJ. (2015)
3 more

6 mentions without citation

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions.
Lüthje et al. (2018)
5 more