1d5m Summary

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X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE AND SEB

The structure was published by Bolin, D.R., Swain, A.L., Sarabu, R., et al., Guenot, J., Nagy, Z., and Olson, G.L., in 2000 in a paper entitled "Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.0 Å and deposited in 1999.

The experimental data on which the structure is based was also deposited.

This entry contains 9 copies of 4 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotetramers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A HLA CLASS II HISTOCOMPATIBILITY ANTIGEN P01903 (26-206) (DRA_HUMAN)search Homo sapienssearch < 90% 181 98%
B HLA CLASS II HISTOCOMPATIBILITY ANTIGEN P13760 (30-221) (2B14_HUMAN)search Homo sapienssearch < 90% 192 94%
C ENTEROTOXIN TYPE B P01552 (28-266) (ETXB_STAAU)search Staphylococcus aureussearch 98% 239 94%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
P01903 (26 - 206) HLA CLASS II HISTOCOMPATIBILITY ANTIGEN Homo sapiens
P13760 (30 - 221) HLA CLASS II HISTOCOMPATIBILITY ANTIGEN Homo sapiens
P01552 (28 - 266) ENTEROTOXIN TYPE B Staphylococcus aureus

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A C1 set domains (antibody constant domain-like)search, MHC antigen-recognition domainsearch Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1search, Immunoglobulinssearch Class II histocompatibility antigen, alpha domainsearch, Immunoglobulin C1-set domainsearch
B C1 set domains (antibody constant domain-like)search, MHC antigen-recognition domainsearch Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1search, Immunoglobulinssearch Class II histocompatibility antigen, beta domainsearch, Immunoglobulin C1-set domainsearch
C (P01552) Superantigen toxins, N-terminal domainsearch, Superantigen toxins, C-terminal domainsearch OB fold (Dihydrolipoamide Acetyltransferase, E2P)search, Ubiquitin-like (UB roll)search PF01123: Staphylococcal/Streptococcal toxin, OB-fold domainsearch, PF02876: Staphylococcal/Streptococcal toxin, beta-grasp domainsearch

Chain ID Cellular component (GO) Biological process (GO)
A (P01903) membranesearch MHC class II protein complexsearch immune responsesearch antigen processing and presentationsearch
B (P13760) membranesearch MHC class II protein complexsearch immune responsesearch antigen processing and presentationsearch
C (P01552) extracellular regionsearch pathogenesissearch

Chain InterPro annotation
A MHC class II, alpha chain, N-terminalsearch Immunoglobulin/major histocompatibility complex, conserved sitesearch Immunoglobulin C1-setsearch Immunoglobulin-like domainsearch MHC classes I/II-like antigen recognition proteinsearch Immunoglobulin-like foldsearch MHC class II, alpha/beta chain, N-terminalsearch
B MHC class II, beta chain, N-terminalsearch Immunoglobulin/major histocompatibility complex, conserved sitesearch Immunoglobulin C1-setsearch Immunoglobulin-like domainsearch MHC classes I/II-like antigen recognition proteinsearch Immunoglobulin-like foldsearch MHC class II, alpha/beta chain, N-terminalsearch
C Staphylococcal/Streptococcal toxin, beta-grasp domainsearch Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved sitesearch Staphylococcal/Streptococcal toxin, OB-foldsearch Staphylococcal/streptococcal toxin, bacterialsearch Enterotoxinsearch Superantigen, staphylococcal/streptococcal toxin, bacterialsearch Superantigen toxin, C-terminalsearch