1D5M	Immune System	date	Oct 07, 1999
title	X-Ray Crystal Structure Of Hla-Dr4 Complexed With Peptide And Seb
authors	A.L.Swain, R.Crowther, U.Kammlott
compound		source
Molecule: Hla Class II Histocompatibility Antigen Chain: A Fragment: Dr Alpha Chain, Extracellular Domain Synonym: Hla-Dr4 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly
Molecule: Hla Class II Histocompatibility Antigen Chain: B Fragment: Dr-4 Beta Chain, Extracellular Domain Synonym: Hla-Dr4 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Expression_system: Drosophila Melanogaster Expression_system_common: Fruit Fly
Molecule: Enterotoxin Type B Chain: C Synonym: Seb, Superantigen		Organism_scientific: Staphylococcus Aureus Organism_common: Bacteria
Molecule: Peptide Inhibitor Chain: D Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized.
symmetry	Space Group: P 21 21 21	R_factor	0.236
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.380 93.340 99.680 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	ACE, ALC, CLE, CY1, NAG	enzyme
related structures	by homologous chain: 1CQV, 1D5Z, 1PYW
similarity	Belongs to the mhc class ii family. Belongs to the staphylococcal/streptococcal toxin family. Contains 1 ig-like c1-type (immunoglobulin-like) domain.[MHC_II_alpha]
subunit	Heterodimer of an alpha chain and a beta chain.
polymorphism	The sequence shown is that of drb1*0401. The sequence shown is that of dra*0101. The following alleles of drb1-4 are known: drb1*0401, drb1*0402, drb1*0403, drb1*0404 and drb1*0411. The following alleles of dra are known dra*0102.
subcellular loc.	Secreted protein. Membrane; single-pass type i membrane protein.
Genes	ENTB (S. aureus); HLA-DRA1, HLA-DRA, HLA-DRB1 (H. sapiens)
function	The illness characterized by high fever, hypotension, diarrhea, shock, and in some cases death. Staphylococcal enterotoxins cause the intoxication staphylococcal food poisoning syndrome.
Gene Ontology	Chain Function Process Component A MHC class II receptor activi... antigen processing and prese... immune response antigen processing and prese... lysosome plasma membrane integral to plasma membrane membrane integral to membrane MHC class II protein complex... B MHC class II receptor activi... antigen processing and prese... immune response signal transduction pathogenesis antigen processing and prese... integral to plasma membrane membrane integral to membrane MHC class II protein complex... C pathogenesis extracellular region
Primary reference	Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures., Bolin DR, Swain AL, Sarabu R, Berthel SJ, Gillespie P, Huby NJ, Makofske R, Orzechowski L, Perrotta A, Toth K, Cooper JP, Jiang N, Falcioni F, Campbell R, Cox D, Gaizband D, Belunis CJ, Vidovic D, Ito K, Crowther R, Kammlott U, Zhang X, Palermo R, Weber D, Guenot J, Nagy Z, Olson GL, J Med Chem 2000 Jun 1;43(11):2135-48. PMID:10841792

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk] Biological Unit Coordinates (1d5m.pdb1.gz) 104 Kb CSU: Contacts of Structural Units for 1D5M Likely Quarternary Molecular Structure file(s) for 1D5M Structure Factors (475 Kb) Retrieve 1D5M in mmCIF format [Save to disk]

View 1D5M in 3D

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Visual 3D analysis of 1D5M

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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 1D5M, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d5ma2, region A:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1d5ma1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1d5mb2, region B:2-92 [Jmol] [rasmolscript] [script source]     - Domain d1d5mb1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1d5mc2, region C:122-237 [Jmol] [rasmolscript] [script source]     - Domain d1d5mc1, region C:2-121 [Jmol] [rasmolscript] [script source] Fold representative 1d5m 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: [1d5m_C] [1d5m_A] [1d5m_D] [1d5m_B]

Other resources with information on 1D5M

InterPro: IPR001003 , IPR007110 , IPR006173 , IPR003006 , IPR006177 , IPR000353 , IPR006126 , IPR006123 , IPR003597 PDBREPORT (protein verification by WHAT_CHECK procedures) MMDB (Entrez's Structure Database)

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