8CE3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
A, B
515Homo sapiensMutation(s): 0 
Gene Names: MGAT5GGNT5
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09328
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UE0 (Subject of Investigation/LOI)
Query on UE0

Download Ideal Coordinates CCD File 
E [auth A](3~{S})-1-ethanoyl-3-(4-methylphenyl)piperidine-3-carboxylic acid
C15 H19 N O3
FZGIXDHLUQHJKF-OAHLLOKOSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.86α = 107.3
b = 68.54β = 92.16
c = 91.31γ = 107.05
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N008332/1
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union675899
Royal SocietyUnited KingdomINF/R1/191028

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary