2ipk Summary

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Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2

The structure was published by Venkatraman, P., Nguyen, T.T., Sainlos, M., et al., Chitta, S., Imperiali, B., and Stern, L.J., in 2007 in a paper entitled "Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.3 Å and deposited in 2006.

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 (26-207) (DRA_HUMAN)search Homo sapienssearch < 90% 183 97%
B HLA class II histocompatibility antigen, DRB1-1 beta chain P04229 (30-219) (2B11_HUMAN)search Homo sapienssearch < 90% 190 100%
C HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) A8CDU0 (59-71) (A8CDU0_9INFA)search Influenza A virus (A/mallard/Sweden/S90391/2005(H3N8))search < 90% 14 100%
D Enterotoxin type C-3 P0A0L5 (28-266) (ENTC3_STAAU)search Staphylococcus aureussearch 99% 240 96%


This entry contains 4 unique UniProt proteins:

UniProt accession Name Organism PDB
P01903 (26 - 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
A8CDU0 (59 - 71) HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine)
P0A0L5 (28 - 266) Enterotoxin type C-3 Staphylococcus aureus subsp. aureus Mu50

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 Haemagglutininsearch
D (P0A0L5) Superantigen toxins, N-terminal domainsearch, Superantigen toxins, C-terminal domainsearch Ubiquitin-like (UB roll)search, OB fold (Dihydrolipoamide Acetyltransferase, E2P)search PF01123: Staphylococcal/Streptococcal toxin, OB-fold domainsearch, PF02876: Staphylococcal/Streptococcal toxin, beta-grasp domainsearch

Chain ID Biological process (GO) Cellular component (GO)
A (P01903) immune responsesearch antigen processing and presentationsearch MHC class II protein complexsearch membranesearch
B (P04229) antigen processing and presentationsearch immune responsesearch membranesearch MHC class II protein complexsearch
D (P0A0L5) pathogenesissearch extracellular regionsearch

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