OCA Atlas for 1SEB
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, B, E, F
Fragment: Extracellular Domain
Synonym: Hla-Dr1
 Organism_scientific: Homo Sapiens
Organism_common: Human
Cell_line: Lg-2

Molecule: Endogenous Peptide Model, Poly-Ala
Chain: C, G
Other_details: Superposition Of Many Different Peptides
Organism_scientific: Homo Sapiens
Organism_common: Human

Molecule: Enterotoxin Type B
Chain: D, H
Synonym: Seb
Organism_scientific: Staphylococcus Aureus
symmetry Space Group: P 21 21 21
R_factor 0.257
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 2.7 Å
related structures by homologous chain: 1A6A, 1AQD, 1BX2, 1DLH
similarity Belongs to the staphylococcal/streptococcal toxin family.[MHC_II_alpha]
gene HLA-DRA (H. sapiens); ENTB (S. aureus)
disease Staphylococcal enterotoxins cause the intoxication staphylococcal food poisoning syndrome.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (216 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1SEB
  • Likely Quarternary Molecular Structure file(s) for 1SEB
  • Retrieve 1SEB in mmCIF format [Save to disk]
    • View 1SEB in 3D
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • FirstGlance in Chemscape Chime (Install Chime freeware) This is good for easiest viewing of basic structure.
  • RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1SEB
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • GRASS (Graphical Representation and Analysis of Structure Server)
    • View 1SEB in 2D
  • Topology of domains/folds: Chain: A, Chain: B, Chain: D, Chain: E, Chain: F, Chain: H from TOPS (The Atlas of protein topology cartoons )
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Genome occurence of 1SEB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1seba2, region A:1-81 [rasmolscript] [script source]
        - Domain d1seba1, region A:82-181 [rasmolscript] [script source]
        - Domain d1sebb2, region B:1-92 [rasmolscript] [script source]
        - Domain d1sebb1, region B:93-192 [rasmolscript] [script source]
        - Domain d1sebd2, region D:127-235 [rasmolscript] [script source]
        - Domain d1sebd1, region D:2-121 [rasmolscript] [script source]
        - Domain d1sebe2, region E:1-81 [rasmolscript] [script source]
        - Domain d1sebe1, region E:82-181 [rasmolscript] [script source]
        - Domain d1sebf2, region F:1-92 [rasmolscript] [script source]
        - Domain d1sebf1, region F:93-192 [rasmolscript] [script source]
        - Domain d1sebh2, region H:127-235 [rasmolscript] [script source]
        - Domain d1sebh1, region H:2-121 [rasmolscript] [script source]
  • Fold representative 1seb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Domain Definition for 1seb from 3Dee ( The Database of Protein Domain Definitions )
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily: CATH
  • Summaries and structural analyses of PDB data files: PDBSum
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1seb_A] [1seb_B] [1seb_C] [1seb_D] [1seb_E] [1seb_F] [1seb_G] [1seb_H]
  • SWISS-PROT database: [HA2R_HUMAN] [ETXB_STAAU] [HB2F_HUMAN]
  • Domain organization of [HA2R_HUMAN] [ETXB_STAAU] [HB2F_HUMAN] by SWISSPFAM
  • Domain found in 1SEB: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_II_alpha (PF00993) of Pfam.
  • Alignments of the sequence of 1SEB with the sequences similar proteins can be viewed for classification [HA2R_HUMAN] [ETXB_STAAU] [HB2F_HUMAN] 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 [HA2R_HUMAN] [ETXB_STAAU] [HB2F_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1SEB
  • InterPro: IPR003006 , IPR001961 , IPR003597 , IPR000353 , IPR001003
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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