2IPK Immune System date Oct 12, 2006
title 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
authors T.T.Nguyen, L.J.Stern
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A
Fragment: Extracellular Domain, Residues 26-207
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: T7 Polymeraselac
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain;
Chain: B
Fragment: Extracellular Domain, Residues 30-219
Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: T7 Polymeraselac
Expression_system_plasmid: Plm1

Molecule: Ha Related Fluorogenic Peptide, Acpkxvkqntlklat (X=3-[5-(Dimethylamino)-1,3-Dioxo-1,3-Dihydro-2h-Isoindol- 2-Yl]-L-Alanine);
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Peptide Naturally Found In Influenza A Virus;

Molecule: Enterotoxin Type C-3
Chain: D
Fragment: Residues 28-266
Synonym: Sec3
Engineered: Yes
Mutation: Yes

Organism_scientific: Staphylococcus Aureus Subsp. Aureus Mu50;
Organism_taxid: 158878
Strain: Mu50atcc 700699
Gene: Entc3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb 2151
Expression_system_vector: Lac
symmetry Space Group: H 3
R_factor 0.203 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.980 171.980 121.129 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 4DP, ACE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


D


Primary referenceFluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells., Venkatraman P, Nguyen TT, Sainlos M, Bilsel O, Chitta S, Imperiali B, Stern LJ, Nat Chem Biol. 2007 Apr;3(4):222-8. Epub 2007 Mar 11. PMID:17351628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (2ipk.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 2IPK
  • CSU: Contacts of Structural Units for 2IPK
  • Likely Quarternary Molecular Structure file(s) for 2IPK
  • Structure Factors (583 Kb)
  • Retrieve 2IPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IPK from S2C, [Save to disk]
  • Re-refined 2ipk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IPK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2IPK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2IPK, from MSDmotif at EBI
  • Fold representative 2ipk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ipk_C] [2ipk_A] [2ipk] [2ipk_B] [2ipk_D]
  • SWISS-PROT database: [P04229] [P01903] [P0A0L5]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] by SWISSPFAM
  • Domains found in 2IPK: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 2IPK
  • Community annotation for 2IPK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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