2SEB Complex (Mhc Class Ii Superantigen) date Oct 16, 1997
title X-Ray Crystal Structure Of Hla-Dr4 Complexed With A Peptide Collagen II
authors A.Dessen, C.M.Lawrence, S.Cupo, D.M.Zaller, D.C.Wiley
compound source
Molecule: Hla Class II Histocompatibility Antigen
Chain: A
Fragment: Extracellular Domain
Synonym: Hla-Dr4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila
Expression_system_common: Fruit Flies
Expression_system_taxid: 7215
Expression_system_cellular_location: S2
Expression_system_vector: Prmha-3

Molecule: Hla Class II Histocompatibility Antigen
Chain: B
Fragment: Extracellular Domain
Synonym: Hla-Dr4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila
Expression_system_common: Fruit Flies
Expression_system_taxid: 7215
Expression_system_cellular_location: S2
Expression_system_vector: Prmha-3

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

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280

Molecule: Peptide From Collagen II
Chain: E

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.530 100.280 100.870 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAG enzyme
related structures by homologous chain: 1CK1, 1JWS, 1R5V, 1T5X
Gene
Ontology
ChainFunctionProcessComponent
A


B


D


Primary referenceX-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II., Dessen A, Lawrence CM, Cupo S, Zaller DM, Wiley DC, Immunity 1997 Oct;7(4):473-81. PMID:9354468
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (2seb.pdb1.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 2SEB
  • CSU: Contacts of Structural Units for 2SEB
  • Likely Quarternary Molecular Structure file(s) for 2SEB
  • Structure Factors (217 Kb)
  • Retrieve 2SEB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2SEB from S2C, [Save to disk]
  • Re-refined 2seb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2SEB 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 2SEB
  • 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 2SEB, from MSDmotif at EBI
  • Genome occurence of 2SEB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2seba2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d2seba1, region A:82-180 [Jmol] [rasmolscript] [script source]
        - Domain d2sebb2, region B:2-92 [Jmol] [rasmolscript] [script source]
        - Domain d2sebb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d2sebd2, region D:122-236 [Jmol] [rasmolscript] [script source]
        - Domain d2sebd1, region D:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 2seb 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: [2seb_A] [2seb_E] [2seb_D] [2seb_B] [2seb]
  • SWISS-PROT database: [P13760] [P02458] [P01903] [P01552]
  • Domain organization of [2B14_HUMAN] [CO2A1_HUMAN] [DRA_HUMAN] [ETXB_STAAU] by SWISSPFAM
  • Domains found in 2SEB: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 2SEB with the sequences similar proteins can be viewed for 2SEB's classification [2B14_HUMAN] [CO2A1_HUMAN] [DRA_HUMAN] [ETXB_STAAU] 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 [2B14_HUMAN] [CO2A1_HUMAN] [DRA_HUMAN] [ETXB_STAAU] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2SEB
  • Community annotation for 2SEB 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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