1D5X

X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures.

Bolin, D.R.Swain, A.L.Sarabu, R.Berthel, S.J.Gillespie, P.Huby, N.J.Makofske, R.Orzechowski, L.Perrotta, A.Toth, K.Cooper, J.P.Jiang, N.Falcioni, F.Campbell, R.Cox, D.Gaizband, D.Belunis, C.J.Vidovic, D.Ito, K.Crowther, R.Kammlott, U.Zhang, X.Palermo, R.Weber, D.Guenot, J.Nagy, Z.Olson, G.L.

(2000) J.Med.Chem. 43: 2135-2148

  • Primary Citation of Related Structures:  1D5M, 1D5Z, 1D6E

  • PubMed Abstract: 
  • Molecular features of ligand binding to MHC class II HLA-DR molecules have been elucidated through a combination of peptide structure-activity studies and structure-based drug design, resulting in analogues with nanomolar affinity in binding assays. ...

    Molecular features of ligand binding to MHC class II HLA-DR molecules have been elucidated through a combination of peptide structure-activity studies and structure-based drug design, resulting in analogues with nanomolar affinity in binding assays. Stabilization of lead compounds against cathepsin B cleavage by N-methylation of noncritical backbone NH groups or by dipeptide mimetic substitutions has generated analogues that compete effectively against protein antigens in cellular assays, resulting in inhibition of T-cell proliferation. Crystal structures of four ternary complexes of different peptide mimetics with the rheumatoid arthritis-linked MHC DRB10401 and the bacterial superantigen SEB have been obtained. Peptide-sugar hybrids have also been identified using a structure-based design approach in which the sugar residue replaces a dipeptide. These studies illustrate the complementary roles played by phage display library methods, peptide analogue SAR, peptide mimetics substitutions, and structure-based drug design in the discovery of inhibitors of antigen presentation by MHC class II HLA-DR molecules.


    Organizational Affiliation

    Roche Research Center, Hoffmann-La Roche Inc., Nutley, New Jersey 07110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
A
181Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
B
192Homo sapiensGene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P13760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ENTEROTOXIN TYPE B
C
239Staphylococcus aureusGene Names: entB
Find proteins for P01552 (Staphylococcus aureus)
Go to UniProtKB:  P01552
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DIPEPTIDE MIMETIC INHIBITOR
D
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000395
Query on PRD_000395
DACE-HAC-ARG-MAA-HAQ-SELPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.838α = 90.00
b = 104.252β = 90.00
c = 107.818γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other