3U2U

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

Structural Biology Knowledgebase: 3U2U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3U2U

Classification: TRANSFERASE

Total Structure Weight: 62123.75

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

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UDP
Query on UDP

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

A, B ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B 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: 1.45 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.164
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.76 α = 79.36
b = 46.84 β = 88.45
c = 69.85 γ = 77.20

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-04
  • Released Date: 2011-11-02
  • Deposition author(s): 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)

Revision History

  • 2012-01-11
    Type: Citation | Details: Citation update
  • 2011-12-28
    Type: Citation | Details: Citation update