1t5x Summary

pdbe.org/1t5x
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HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2

The structure was published by Zavala-Ruiz, Z., Strug, I., Anderson, M.W., Gorski, J., and Stern, L.J., in 2004 in a paper entitled "A Polymorphic Pocket at the P10 Position Contributes to Peptide Binding Specificity in Class II MHC Proteins" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.5 Å and deposited in 2004.

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

This entry contains 8 copies of 4 unique biopolymers (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, DR alpha chain P01903 (27-207) (DRA_HUMAN)search Homo sapienssearch < 90% 181 98%
B HLA class II histocompatibility antigen, DRB1-1 beta chain P04229 (30-219) (2B11_HUMAN)search Homo sapienssearch < 90% 190 100%
C 15-mer peptide fragment of Regulatory protein MIG1 P27705 (455-462) (MIG1_YEAST)search Saccharomyces cerevisiae S288csearch < 90% 15 86%
D Enterotoxin type C-3 P0A0L5 (28-266) (ENTC3_STAAU)search Staphylococcus aureussearch 99% 239 96%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P01903 (27 - 207) HLA class II histocompatibility antigen, DR alpha chain Homo sapiens
P04229 (30 - 219) HLA class II histocompatibility antigen, DRB1-1 beta chain Homo sapiens
P27705 (455 - 462) 15-mer peptide fragment of Regulatory protein MIG1
P0A0L5 (28 - 266) Enterotoxin type C-3 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
D (P0A0L5) 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 antigen processing and presentationsearch immune responsesearch
B (P04229) MHC class II protein complexsearch membranesearch antigen processing and presentationsearch immune responsesearch
D (P0A0L5) 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
D 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