1YO8

Structure of the C-terminal domain of human thrombospondin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1YO8

Classification: CELL ADHESION

Total Structure Weight: 73582.11

Macromolecule Entities
Molecule Chains Length Organism Details
thrombospondin-2 A 634 Homo sapiens Fragment: C-terminal domain
Mutation: M675M, M964M, M1041M, M1134M, M1159M
Gene Name(s): THBS2 Gene View TSP2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.218
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 93.44 α = 90.00
b = 121.59 β = 90.00
c = 155.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-26
  • Released Date: 2005-09-27
  • Deposition author(s): Carlson, C.B., Bernstein, D.A., Annis, D.S., Misenheimer, T.M., Hannah, B.A., Mosher, D.F., Keck, J.L.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Non-polymer description, Version format compliance