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 Diffraction	resolution	2.30 Å
ligand	4DP, ACE	enzyme
Gene Ontology	Chain Function Process Component D pathogenesis extracellular region
Primary reference	Fluorogenic 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2ipk_B] [2ipk_C] [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 Alignments of the sequence of 2IPK with the sequences similar proteins can be viewed for 2IPK's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] at ProtoMap. Click on the Cluster number.

Other resources with information on 2IPK

Community annotation for 2IPK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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