1T5X HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2 date
authors Zavala-Ruiz, Z., Strug, I., Anderson, M.W., Gorski, J., Stern, L.J.
compound source
symmetry
R_factor
R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
related structures by homologous chain: 1D5X, 1LNU, 1R5V, 2SEB
Gene
Ontology
ChainFunctionProcessComponent
A


B


D
  • toxin activity


    • 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) 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
  • 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
    • 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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