1LO5	Immune System Toxin	date	May 06, 2002
title	Crystal Structure Of The D227a Variant Of Staphylococcal Enterotoxin A In Complex With Human Mhc Class II
authors	K.Petersson, M.Thunnissen, G.Forsberg, B.Walse
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain; Chain: A Fragment: Extracellular Domain Synonym: Mhc Class II (Hla-Dr1, Dra 0101)-Chain A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
Molecule: Hla Class II Histocompatibility Antigen, Dr-1 Beta Chain; Chain: B Fragment: Extracellular Domain Synonym: Mhc Class II (Hla-Dr1, Drb1 0101)-Chain B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
Molecule: Hemagglutinin Peptide Chain: C Engineered: Yes		Synthetic: Yes Other_details: This Sequence Is Peptide From Influenza Virus, Hemagglutinin Peptide;
Molecule: Enterotoxin A Chain: D Engineered: Yes Mutation: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Ul635 Expression_system_vector_type: Plasmid Expression_system_plasmid: Plr16 Expression_system_gene: K12
symmetry	Space Group: P 21 21 21	R_factor 0.245 R_Free 0.339
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.008 75.792 198.082 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.20 Å
Gene Ontology	Chain Function Process Component D MHC class II protein binding... metal ion binding pathogenesis extracellular region
Primary reference	Crystal structure of a SEA variant in complex with MHC class II reveals the ability of SEA to crosslink MHC molecules., Petersson K, Thunnissen M, Forsberg G, Walse B, Structure (Camb) 2002 Dec;10(12):1619-26. PMID:12467569

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk] Biological Unit Coordinates (1lo5.pdb1.gz) 96 Kb CSU: Contacts of Structural Units for 1LO5 Likely Quarternary Molecular Structure file(s) for 1LO5 Structure Factors (129 Kb) Retrieve 1LO5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1LO5 from S2C, [Save to disk] Re-refined 1lo5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1LO5 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 1LO5

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 1LO5, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1lo5a2, region A:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1lo5a1, region A:82-182 [Jmol] [rasmolscript] [script source]     - Domain d1lo5b2, region B:3-92 [Jmol] [rasmolscript] [script source]     - Domain d1lo5b1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1lo5d1, region D:1-120 [Jmol] [rasmolscript] [script source]     - Domain d1lo5d2, region D:121-233 [Jmol] [rasmolscript] [script source] Fold representative 1lo5 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: [1lo5_A] [1lo5_B] [1lo5_C] [1lo5_D] SWISS-PROT database: [P04229] [P01903] [P0A0L2] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ETXA_STAAU] by SWISSPFAM Domains found in 1LO5: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1LO5 with the sequences similar proteins can be viewed for 1LO5's classification [2B11_HUMAN] [DRA_HUMAN] [ETXA_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] [ETXA_STAAU] at ProtoMap. Click on the Cluster number.

Other resources with information on 1LO5

Community annotation for 1LO5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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