3U2X

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and 1'-deoxyglucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and 1'-deoxyglucose

Chaikuad, A.Froese, D.S.Krysztofinska, E.von Delft, F.Weigelt, J.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Oppermann, U.Yue, W.W.Structural Genomics Consortium (SGC)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogenin-1 AB263Homo sapiensMutation(s): 0 
Gene Names: GYGGYG1
EC: 2.4.1.186
Find proteins for P46976 (Homo sapiens)
Explore P46976 
Go to UniProtKB:  P46976
NIH Common Fund Data Resources
PHAROS:  P46976
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
ASO
Query on ASO

Download Ideal Coordinates CCD File 
A, B
1,5-anhydro-D-glucitol
C6 H12 O5
MPCAJMNYNOGXPB-SLPGGIOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.7α = 79.57
b = 46.86β = 88.96
c = 69.7γ = 77.25
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary