› 6tes

X-ray diffraction
2.2Å resolution

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Glucuronic Acid

Released:
DOI: 10.2210/pdb6tes/pdb
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PDB entry 6tes coloured by chain, front view.
PDB entry 6tes coloured by chain, side view.
PDB entry 6tes coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity
Mattoteia D, Chiapparino A, Fumagalli M, De Marco M, De Giorgi F, Negro L, Pinnola A, Faravelli S, Roscioli T, Scietti L, Forneris F
Int J Mol Sci (2023)

Function and Biology Details

Reactions catalysed: 
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2)
UDP-alpha-D-galactose + [procollagen]-(2S,5R)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine
UDP-alpha-D-glucose + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(alpha-D-glucosyl-(1->2)-beta-D-galactosyl)-5-hydroxy-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130034 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 Chain: A
Molecule details ›
Chain: A
Length: 718 amino acids
Theoretical weight: 82.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60568 (Residues: 25-738; Coverage: 100%)
Gene name: PLOD3
Sequence domains: 2OG-Fe(II) oxygenase superfamily

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand AKG 1 x AKG
Ligand FE2 2 x FE2
Ligand MN 1 x MN
Ligand UGA 1 x UGA
Ligand NAG 1 x NAG
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 98.202Å b: 100.505Å c: 224.745Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.19 0.238
Expression system: Homo sapiens

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