1R5I	Immune System	date	Oct 10, 2003
title	Crystal Structure Of The Mam-Mhc Complex
authors	Y.Zhao, Z.Li, S.J.Drozd, Y.Guo, W.Mourad, H.Li
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain; Chain: A, E Fragment: Alpha Chain Of Class II Mhc (Residues 26-206) Synonym: Mhc Class II Antigen Dra Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain; Chain: B, F Fragment: Beta Chain Of Class II Mhc (Residues 30-219) Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
Molecule: Hemagglutinin Peptide Chain: C, G Fragment: Haemagglutinin Peptide (Residues 306-318) Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized. This Sequence Occurs Naturally In Influenza Virus.;
Molecule: Superantigen Chain: D, H Synonym: Mycoplasma Arthritidis-Derived Mitogen Engineered: Yes		Organism_scientific: Mycoplasma Arthritidis Organism_taxid: 2111 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p-1
symmetry	Space Group: I 2 2 2	R_factor 0.238 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 138.286 178.814 179.554 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	MSE, PO4	enzyme
related structures	by homologous chain: 1BX2, 1FYT, 1KG0
Primary reference	Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex., Zhao Y, Li Z, Drozd SJ, Guo Y, Mourad W, Li H, Structure (Camb) 2004 Feb;12(2):277-88. PMID:14962388

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk] Biological Unit Coordinates (1r5i.pdb1.gz) 104 Kb Biological Unit Coordinates (1r5i.pdb2.gz) 103 Kb LPC: Ligand-Protein Contacts for 1R5I CSU: Contacts of Structural Units for 1R5I Likely Quarternary Molecular Structure file(s) for 1R5I Structure Factors (635 Kb) Retrieve 1R5I in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1R5I from S2C, [Save to disk] Re-refined 1r5i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1R5I 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 1R5I

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 1R5I, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1r5ia2, region A:1-81 [Jmol] [rasmolscript] [script source]     - Domain d1r5ia1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1r5ib2, region B:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1r5ib1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1r5id_, region D [Jmol] [rasmolscript] [script source]     - Domain d1r5ie2, region E:1-81 [Jmol] [rasmolscript] [script source]     - Domain d1r5ie1, region E:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1r5if2, region F:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1r5if1, region F:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1r5ih_, region H [Jmol] [rasmolscript] [script source] Fold representative 1r5i from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1r5i_A] [1r5i_B] [1r5i_C] [1r5i_D] [1r5i_E] [1r5i_F] [1r5i_G] [1r5i_H] SWISS-PROT database: [P04229] [P01903] [P11133] [Q48898] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [HEMA_I78A9] [Q48898_MYCAT] by SWISSPFAM Domains found in 1R5I: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1R5I with the sequences similar proteins can be viewed for 1R5I's classification [2B11_HUMAN] [DRA_HUMAN] [HEMA_I78A9] [Q48898_MYCAT] 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] [HEMA_I78A9] [Q48898_MYCAT] at ProtoMap. Click on the Cluster number.

Other resources with information on 1R5I

Community annotation for 1R5I at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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