6IWR

Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7.

Yu, C.Liang, L.Yin, Y.

(2019) Biochem. Biophys. Res. Commun. 510: 266-271


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylgalactosaminyltransferase 7
A, B, C, D, E, F
597Homo sapiensMutation(s): 0 
Gene Names: GALNT7
EC: 2.4.1.-
Find proteins for Q86SF2 (Homo sapiens)
Go to Gene View: GALNT7
Go to UniProtKB:  Q86SF2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UD2
Query on UD2

Download SDF File 
Download CCD File 
D
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-NESSUJCYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 137.435α = 90.00
b = 158.264β = 90.00
c = 251.484γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-12-06 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Yu, C., Yin, Y.X.

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references