1YJD

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)

Structural Biology Knowledgebase: 1YJD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YJD

Classification: IMMUNE SYSTEM / SIGNALING PROTEIN

Total Structure Weight: 63945.91

Macromolecule Entities
Molecule Chains Length Organism Details
Fab fragment of 5.11A1 antibody light chain L 212 Mus musculus
Fab fragment of 5.11A1 antibody heavy chain H 222 Mus musculus Fragment: IgV and IgC1 domains
T-cell-specific surface glycoprotein CD28 C 140 Homo sapiens Fragment: Extracellular region
Gene Name(s): CD28 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.239
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 191.22 α = 90.00
b = 47.42 β = 94.45
c = 71.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-14
  • Released Date: 2005-02-15
  • Deposition author(s): Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Sorensen, P., Stuart, D.I., Davis, S.J.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4