8CE3 | pdb_00008ce3

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

PDB DOI: https://doi.org/10.2210/pdb8CE3/pdb

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

Deposited: 2023-02-01 Released: 2024-02-21
Deposition Author(s): Gilio, A.K., Darby, J.F., Wu, L., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Marie Sklodowska-Curie Actions, FragNET ITN, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design, Modular Synthesis and Screening of 58 Shape-Diverse 3-D Fragments

Downes, T.D., Jones, S.P., Firth, J.D., Darby, J.F., Gilio, A.K., Klein, H.F., Blakemore, D.C., de Fusco, C., Roughley, S.D., Vidler, L.R., Whatton, M.A., Woolford, A.J.A., Wrigley, G.L., Hubbard, R.E., Wu, L., Davies, G.J., O'Brien, P.

(2025) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2025-mxs07

Macromolecule Content

Total Structure Weight: 119.94 kDa
Atom Count: 8,494
Modeled Residue Count: 992
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	A, B	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UE0 (Subject of Investigation/LOI) Query on UE0 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(3~{S})-1-ethanoyl-3-(4-methylphenyl)piperidine-3-carboxylic acid C₁₅ H₁₉ N O₃ FZGIXDHLUQHJKF-OAHLLOKOSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	C [auth A] D [auth A] M [auth A] N [auth A] O [auth A] C [auth A], D [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.86	α = 107.3
b = 68.54	β = 92.16
c = 91.31	γ = 107.05

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N008332/1
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	675899
Royal Society	United Kingdom	INF/R1/191028