3CUP

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235

Yoshida, K.Corper, A.L.Puckett, C.Sim, J.Valerie, M.-D.Jabri, B.Wilson, I.A.Teyton, L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-D alpha chain
A
190Mus musculusGene Names: H2-Aa
Find proteins for P04228 (Mus musculus)
Go to UniProtKB:  P04228
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II H2-IA-beta chain linked to GAD221-235 peptide
B
222Rattus norvegicusMus musculus
This entity is chimeric
Gene Names: Gad2 (Gad65), H2-Ab1
EC: 4.1.1.15
Find proteins for Q05683 (Rattus norvegicus)
Go to UniProtKB:  Q05683
Find proteins for Q31135 (Mus musculus)
Go to UniProtKB:  Q31135
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.232 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.832α = 90.00
b = 55.832β = 90.00
c = 338.834γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 2.0: 2017-06-28
    Type: Advisory, Atomic model, Database references, Derived calculations, Refinement description, Source and taxonomy