1SEB Complex (Mhc Ii Peptide Toxin) date Nov 26, 1995
title Complex Of The Human Mhc Class II Glycoprotein Hla-Dr1 And The Bacterial Superantigen Seb
authors T.S.Jardetzky, J.H.Brown, J.C.Gorga, L.J.Stern, R.G.Urban, Y.I.Chi, C.Stauffacher, J.L.Strominger, D.C.Wiley
compound source
Molecule: Hla Class II Histocompatibility Antigen
Chain: A, E
Fragment: Extracellular Domain
Synonym: Hla-Dr1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Lg-2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Lg-2 Cells

Molecule: Hla Class II Histocompatibility Antigen
Chain: B, F
Fragment: Extracellular Domain
Synonym: Hla-Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Lg-2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Lg-2 Cells

Molecule: Endogenous Peptide Model, Poly-Ala
Chain: C, G
Other_details: Superposition Of Many Different Peptides

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Enterotoxin Type B
Chain: D, H
Synonym: Seb

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Cell_line: Lg-2
symmetry Space Group: P 21 21 21
R_factor 0.257 R_Free 0.327
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.000 114.700 149.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1A6A, 1IEB, 1SE2
Gene
Ontology
ChainFunctionProcessComponent
H, D


Primary referenceThree-dimensional structure of a human class II histocompatibility molecule complexed with superantigen., Jardetzky TS, Brown JH, Gorga JC, Stern LJ, Urban RG, Chi YI, Stauffacher C, Strominger JL, Wiley DC, Nature 1994 Apr 21;368(6473):711-8. PMID:8152483
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (197 Kb) [Save to disk]
  • Biological Unit Coordinates (1seb.pdb1.gz) 191 Kb
  • CSU: Contacts of Structural Units for 1SEB
  • Likely Quarternary Molecular Structure file(s) for 1SEB
  • Retrieve 1SEB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SEB from S2C, [Save to disk]
  • View 1SEB 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 1SEB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1SEB, from MSDmotif at EBI
  • Genome occurence of 1SEB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1seba2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1seba1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1sebb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1sebb1, region B:93-192 [Jmol] [rasmolscript] [script source]
        - Domain d1sebd2, region D:127-235 [Jmol] [rasmolscript] [script source]
        - Domain d1sebd1, region D:2-121 [Jmol] [rasmolscript] [script source]
        - Domain d1sebe2, region E:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1sebe1, region E:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1sebf2, region F:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1sebf1, region F:93-192 [Jmol] [rasmolscript] [script source]
        - Domain d1sebh2, region H:127-235 [Jmol] [rasmolscript] [script source]
        - Domain d1sebh1, region H:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 1seb 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: [1seb_D] [1seb_A] [1seb] [1seb_G] [1seb_H] [1seb_B] [1seb_C] [1seb_F] [1seb_E]
  • SWISS-PROT database: [P04229] [P01903] [P01552]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ETXB_STAAU] by SWISSPFAM
  • Domains found in 1SEB: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1SEB
  • Community annotation for 1SEB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1SEB from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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