5zic

X-ray diffraction
2.1Å resolution

Crystal structure of human GnT-V luminal domain in complex with acceptor sugar

Released:

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]
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-170784 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 523 amino acids
Theoretical weight: 59.8 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q09328 (Residues: 213-329, 345-741; Coverage: 69%)
Gene names: GGNT5, MGAT5
Sequence domains: Glycosyltransferase family 18

Ligands and Environments

Carbohydrate polymer : NEW Components: BMA, Z4Y, NAG
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 70.421Å b: 89.202Å c: 92.234Å
α: 90° β: 105.55° γ: 90°
R-values:
R R work R free
0.217 0.215 0.268
Expression system: Homo sapiens