› 8ce3

X-ray diffraction
1.89Å resolution

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548

Released:
DOI: 10.2210/pdb8ce3/pdb
PDB entry 8ce3 coloured by chain, front view.
PDB entry 8ce3 coloured by chain, side view.
PDB entry 8ce3 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Gilio AK, Darby JF, Wu L, Davies GJ

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-glucosamine + beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->4))-alpha-D-Man-(1->3)-(beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein] = UDP + beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->4))-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-(beta-D-GlcNAc-(1->6))-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein]
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-240284 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 515 amino acids
Theoretical weight: 59 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q09328 (Residues: 214-741; Coverage: 70%)
Gene names: GGNT5, MGAT5
Sequence domains: Glycosyltransferase family 18

Ligands and Environments

3 bound ligands:
Ligand EDO 7 x EDO
Ligand UE0 1 x UE0
Ligand SO4 13 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P1
Unit cell:
a: 46.86Å b: 68.54Å c: 91.31Å
α: 107.3° β: 92.16° γ: 107.05°
R-values:
R R work R free
0.192 0.19 0.233
Expression system: Trichoplusia ni

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