2IPK

Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2

Structural Biology Knowledgebase: 2IPK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2IPK

Classification: IMMUNE SYSTEM

Total Structure Weight: 72849.55

Macromolecule Entities
Molecule Chains Length Organism Details
HLA class II histocompatibility antigen, DR alpha chain A 183 Homo sapiens Fragment: Extracellular domain, residues 26-207
Gene Name(s): HLA-DRA Gene View HLA-DRA1
HLA class II histocompatibility antigen, DRB1-1 beta chain B 190 Homo sapiens Fragment: Extracellular domain, residues 30-219
Gene Name(s): HLA-DRB1 Gene View
HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) C 14 Influenza a virus Gene Name(s):
Enterotoxin type C-3 D 240 Staphylococcus aureus Fragment: Residues 28-266
Mutation: K43S, L45F, A46K, H47W
Gene Name(s): entC3

Small Molecules
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
C NON-POLYMER C2 H4 O --
4DP
Query on 4DP
C L-PEPTIDE LINKING C13 H15 N3 O4 TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.203
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 171.98 α = 90.00
b = 171.98 β = 90.00
c = 121.13 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-12
  • Released Date: 2007-03-13
  • Deposition author(s): Nguyen, T.T., Stern, L.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4