3pgd Summary

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Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation

The structure was published by Gunther, S., Schlundt, A., Sticht, J., et al., Falk, K., Rotzschke, O., and Freund, C., in 2010 in a paper entitled "Bidirectional binding of invariant chain peptides to an MHC class II molecule." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.72 Å and deposited in 2010.

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

This PDB entry contains a complex of 3 biomacromolecules, namely HLA class II histocompatibility antigen, DR alpha chain, HLA class II histocompatibility antigen, DRB1-1 beta chain, and HLA class II histocompatibility antigen gamma chain.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

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 (26-217) (DRA_HUMAN)search Homo sapienssearch < 90% 193 92%
D HLA class II histocompatibility antigen, DR alpha chain P01903 (26-217) (DRA_HUMAN)search Homo sapienssearch < 90% 193 92%
B HLA class II histocompatibility antigen, DRB1-1 beta chain P04229 (30-227) (2B11_HUMAN)search Homo sapienssearch < 90% 199 92%
E HLA class II histocompatibility antigen, DRB1-1 beta chain P04229 (30-227) (2B11_HUMAN)search Homo sapienssearch < 90% 199 92%
C HLA class II histocompatibility antigen gamma chain P04233 (106-120) (HG2A_HUMAN)search Homo sapienssearch < 90% 15 100%
F HLA class II histocompatibility antigen gamma chain P04233 (106-120) (HG2A_HUMAN)search Homo sapienssearch < 90% 15 100%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
P01903 (26 - 217) HLA class II histocompatibility antigen, DR alpha chain Homo sapiens
P04229 (30 - 227) HLA class II histocompatibility antigen, DRB1-1 beta chain Homo sapiens
P04233 (106 - 120) HLA class II histocompatibility antigen gamma chain Homo sapiens

Chain Structural classification (CATH) Sequence family (Pfam)
A, D Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1search, Immunoglobulinssearch Class II histocompatibility antigen, alpha domainsearch, Immunoglobulin C1-set domainsearch
B, E Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1search, Immunoglobulinssearch Class II histocompatibility antigen, beta domainsearch, Immunoglobulin C1-set domainsearch
C, F CLIP, MHC2 interactingsearch

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

Chain InterPro annotation
A, D 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, E 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, F