1T5X Immune System date May 05, 2004
title Hla-Dr1 In Complex With A Synthetic Peptide (Aaysdqatplllspr) And The 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;
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 Beta Chain;
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 Mig1;
Chain: C
Fragment: Synthetic Peptide
Synonym: Regulatory Protein Cat4
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Desinged To Study The P10 Side 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 Diffractionresolution 2.50 Å
related structures by homologous chain: 1D5X, 1LNU, 1R5V, 2SEB
Gene
Ontology
ChainFunctionProcessComponent
D


Primary referenceA 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] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (1t5x.pdb1.gz) 108 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
  • 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 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]
  • Fold representative 1t5x 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: [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
  • Alignments of the sequence of 1T5X with the sequences similar proteins can be viewed for 1T5X's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [MIG1_YEAST] 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] [MIG1_YEAST] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1T5X
  • Community annotation for 1T5X at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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