1K2D

Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A

Structural Biology Knowledgebase: 1K2D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.248

Literature

Macromolecules
Sequence Display for 1K2D

Classification: IMMUNE SYSTEM

Total Structure Weight: 46947.39

Macromolecule Entities
Molecule Chains Length Organism Details
H-2 class II histocompatibility antigen, A-U alpha chain A 189 Mus musculus Fragment: EXTRACELLULAR ALPHA-1 AND ALPHA-2 DOMAINS
Gene Name(s): H2-Aa
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
H-2 class II histocompatibility antigen, A-U beta chain B 189 Mus musculus Fragment: EXTRACELLULAR BETA-1 AND BETA-2 DOMAINS
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Myelin Basic Protein peptide with 8 residue linker peptide P 23 Homo sapiens Fragment: 11 residue peptide with 8 residue linker peptide
Mutation: M0G
Gene Name(s): MBP Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.248
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 99.15 α = 90.00
b = 110.59 β = 90.00
c = 94.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-26
  • Released Date: 2003-03-04
  • Deposition author(s): He, X.L., Radu, C., Ward, E.S., Garcia, K.C.

Revision History

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