3pdo Summary

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Crystal Structure of HLA-DR1 with CLIP102-120

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 1.95 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.

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 heterotrimers.

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 95%
B HLA class II histocompatibility antigen, DRB1-1 beta chain P04229 (30-227) (2B11_HUMAN)search Homo sapienssearch < 90% 199 95%
C HLA class II histocompatibility antigen gamma chain P04233 (102-120) (HG2A_HUMAN)search Homo sapienssearch < 90% 19 89%


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 (102 - 120) HLA class II histocompatibility antigen gamma chain Homo sapiens

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

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

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