1T5X	Immune System	date	May 05, 2004
title	Hla-Dr1 In Complex With A Synthetic Peptide (Aaysdqatplllspr Superantigen Sec3-3b2
authors	Z.Zavala-Ruiz, I.Strug, M.W.Anderson, J.Gorski, L.J.Stern
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain: A Fragment: Extracellular Domain Synonym: Mhc Class II Antigen Dra Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Dra0101 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Polymeraselac Expression_system_plasmid: Plm1
Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B Chain: B Fragment: Extracellular Domain Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Drb10101 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Polymerase Lac Expression_system_plasmid: Plm1
Molecule: 15-Mer Peptide Fragment Of Regulatory Protein Mig Chain: C Fragment: Synthetic Peptide Synonym: Regulatory Protein Cat4 Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide Desinged To Study The P10 Chain Specificity Of Hla-Dr1;
Molecule: Enterotoxin Type C-3 Chain: D Fragment: Sec3 Variant 3b2 Synonym: Sec3; Enterotoxin Typec3 Engineered: Yes Mutation: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Gene: Sec3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Hb 2151 Expression_system_vector_type: Lac
symmetry	Space Group: H 3	R_factor 0.208 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 173.208 173.208 121.543 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.50 Å
related structures	by homologous chain: 1D5X, 1LNU, 1R5V, 2SEB
Gene Ontology	Chain Function Process Component A B D toxin activity
Primary reference	A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins., Zavala-Ruiz Z, Strug I, Anderson MW, Gorski J, Stern LJ, Chem Biol 2004 Oct;11(10):1395-402. PMID:15489166

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk] Biological Unit Coordinates (1t5x.pdb1.gz) 106 Kb CSU: Contacts of Structural Units for 1T5X Likely Quarternary Molecular Structure file(s) for 1T5X Structure Factors (454 Kb) Retrieve 1T5X in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1T5X from S2C, [Save to disk] Re-refined 1t5x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1T5X 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 1T5X

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 3D motif for 1T5X, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1t5xa2, region A:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1t5xa1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1t5xb2, region B:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1t5xb1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1t5xd1, region D:1-121 [Jmol] [rasmolscript] [script source]     - Domain d1t5xd2, region D:122-239 [Jmol] [rasmolscript] [script source] 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: [1t5x_D] [1t5x] [1t5x_B] [1t5x_A] [1t5x_C] SWISS-PROT database: [P04229] [P01903] [P0A0L5] [P27705] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [MIG1_YEAST] by SWISSPFAM Domains found in 1T5X: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART

Other resources with information on 1T5X

Community annotation for 1T5X at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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