3e3q Summary

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Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9

The structure was published by Jones, L.L., Colf, L.A., Stone, J.D., Garcia, K.C., and Kranz, D.M., in 2008 in a paper entitled "Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.95 Å and deposited in 2008.

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

This entry contains 32 copies of 4 unique biopolymers (complete list).

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 H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
B H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
c H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
H H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
L H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
P H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
U H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
Y H-2 class I histocompatibility antigen, L-D alpha chain P01897 (25-199) (HA1L_MOUSE)search Mus musculussearch < 90% 175 100%
Q QL9 peptide Not available
Synthetic Not available 9 100%
G QL9 peptide Not available
Synthetic Not available 9 100%
f QL9 peptide Not available
Synthetic Not available 9 100%
K QL9 peptide Not available
Synthetic Not available 9 100%
O QL9 peptide Not available
Synthetic Not available 9 100%
T QL9 peptide Not available
Synthetic Not available 9 100%
X QL9 peptide Not available
Synthetic Not available 9 100%
b QL9 peptide Not available
Synthetic Not available 9 100%
D T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
C T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
d T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
I T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
M T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
R T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
V T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
Z T-cell receptor alpha chain V region PHDS58 Q5R1C2 (22-113) (Q5R1C2_MOUSE)search Mus musculussearch < 90% 109 100%
E TCR beta chain Not available
Mus musculussearch Not available 111 100%
F TCR beta chain Not available
Mus musculussearch Not available 111 100%
e TCR beta chain Not available
Mus musculussearch Not available 111 100%
J TCR beta chain Not available
Mus musculussearch Not available 111 100%
N TCR beta chain Not available
Mus musculussearch Not available 111 100%
S TCR beta chain Not available
Mus musculussearch Not available 111 100%
W TCR beta chain Not available
Mus musculussearch Not available 111 100%
a TCR beta chain Not available
Mus musculussearch Not available 111 100%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P01897 (25 - 199) H-2 class I histocompatibility antigen, L-D alpha chain Mus musculus
Q5R1C2 (22 - 113) T-cell receptor alpha chain V region PHDS58 Mus musculus

Chain Structural classification (CATH) Sequence family (Pfam)
A, B, c, H, L, P, U, Y Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1search Class I Histocompatibility antigen, domains alpha 1 and 2search
Q, G, f, K, O, T, X, b
D, C, d, I, M, R, V, Z Immunoglobulinssearch Immunoglobulin V-set domainsearch
E, F, e, J, N, S, W, a Immunoglobulinssearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A, B, c, H, L, P, U, Y (P01897) immune responsesearch antigen processing and presentationsearch positive regulation of T cell mediated cytotoxicitysearch antigen processing and presentation of peptide antigen via MHC class Isearch peptide antigen bindingsearch membranesearch MHC class I protein complexsearch
D, C, d, I, M, R, V, Z (Q5R1C2) positive regulation of T cell mediated cytotoxicitysearch antigen processing and presentationsearch immune responsesearch antigen processing and presentation of peptide antigen via MHC class Isearch peptide antigen bindingsearch MHC class I protein complexsearch membranesearch

Chain InterPro annotation
A, B, c, H, L, P, U, Y MHC class I alpha chain, alpha1 alpha2 domainssearch MHC class I-like antigen recognitionsearch MHC classes I/II-like antigen recognition proteinsearch MHC class I alpha chainsearch
Q, G, f, K, O, T, X, b
D, C, d, I, M, R, V, Z Immunoglobulin V-set, subgroupsearch Immunoglobulin-like domainsearch Immunoglobulin V-set domainsearch Immunoglobulin-like foldsearch
E, F, e, J, N, S, W, a Immunoglobulin V-set, subgroupsearch Immunoglobulin-like domainsearch Immunoglobulin V-set domainsearch Immunoglobulin-like foldsearch