3QVB

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

Structural Biology Knowledgebase: 3QVB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QVB

Classification: TRANSFERASE

Total Structure Weight: 30365.32

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogenin-1 A 263 Homo sapiens EC#: 2.4.1.186 IUBMB
Fragment: glycogenin (residues 1-262)
Mutation: Y195F
Gene Name(s): GYG1 Gene View GYG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UDP
Query on UDP

A URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.199
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.40 α = 90.00
b = 100.97 β = 90.00
c = 48.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-25
  • Released Date: 2011-03-23
  • Deposition author(s): Chaikuad, A., Froese, D.S., Yue, W.W., Krysztofinska, E., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

  • 2012-01-11
    Type: Citation | Details: Citation update
  • 2011-12-28
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4