6YJQ

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation

PDB DOI: https://doi.org/10.2210/pdb6YJQ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2020-04-04 Released: 2020-08-05
Deposition Author(s): Wu, L., Darby, J.F., Gilio, A.K., Davies, G.J.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.237
R-Value Work: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V

Darby, J.F., Gilio, A.K., Piniello, B., Roth, C., Blagova, E., Rovira, C., Hubbard, R.E., Davies, G.J., Wu, L.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.0c02222

Macromolecule Content

Total Structure Weight: 119.67 kDa
Atom Count: 8,372
Modelled Residue Count: 986
Deposited Residue Count: 1,030
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A	A [auth AAA], B [auth BBB]	515	Homo sapiens	Mutation(s): 0 Gene Names: MGAT5, GGNT5 EC: 2.4.1.155
UniProt & NIH Common Fund Data Resources
Find proteins for Q09328 (Homo sapiens) Explore Q09328 Go to UniProtKB: Q09328
PHAROS: Q09328 GTEx: ENSG00000152127
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09328
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth BBB]	Go to GlyGen: Q09328-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth BBB] MOL2 format, chain N [auth BBB] mmCIF format, chain N [auth BBB]	N [auth BBB]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth BBB] Interactions & Density Focus chain N [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain U [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain U [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain U [auth BBB]	F [auth AAA] G [auth AAA] H [auth AAA] I [auth AAA] P [auth BBB] F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB], U [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain J [auth BBB] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain O [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain O [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain J [auth BBB] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain O [auth BBB]	C [auth AAA] D [auth AAA] E [auth AAA] J [auth BBB] K [auth BBB] C [auth AAA], D [auth AAA], E [auth AAA], J [auth BBB], K [auth BBB], L [auth BBB], M [auth BBB], O [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain O [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain O [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.237
R-Value Work: 0.194
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47	α = 108.36
b = 68.17	β = 92.28
c = 90.99	γ = 106.86

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	ErC-2012-AdG-322942

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary