CDR3 loop flexibility contributes to the degeneracy of TCR recognition

Reiser, J.-B; Darnault, C; Gregoire, C; Mosser, T; Mazza, G; Kearnay, A; van der Merwe, P.A; Fontecilla-Camps, J.C; Housset, D; Malissen, B.

Structural Similarities for the Entities in PDB 1NAN

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2].

To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Currently viewing only significant results (P-value < 0.001). Show all available results.

Cluster data are up-to-date as of: Sep-27-2017

Info & Help Documentation

A detailed description of the procedure for the all vs. all alignments is available.

You can also use the structure comparison tool to compare any 2 given structures

Entity #1 | Chains H,L

Description: H-2 class I histocompatibility antigen, K-B alpha chain protein | Length: 278

No structure alignment results are available for 1NAN.H, 1NAN.L explicitly.

These chains are represented by chain 1K5N.a which has more than 70% sequence identity.

Show structure comparison results for representative 1K5N.a

Entity #2 | Chains I,P

Description: Beta-2-microglobulin protein | Length: 99

No structure alignment results are available for 1NAN.I, 1NAN.P explicitly.

These chains are represented by chain 1K5N.b which has more than 50% sequence identity.

Show structure comparison results for representative 1K5N.b

Entity #3 | Chains M,Q

Description: pBM1 peptide protein | Length: 8

This entity is too short to be considered for the all vs. all structure alignments.

References

[1] Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985
[2] The all vs. all comparisons are based on jFATCAT (a Java port of the original FATCAT algorithm Yuzhen Ye & Adam Godzik (2003))
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Bioinformatics vol.19 suppl. 2. ii246-ii255.

[3] Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2008).
Data growth and its impact on the SCOP database: new developments.
Nucl. Acids Res. 2008 36: D419-D425
[4] Alexandrov N., Shindyalov I. (2003)
PDP: protein domain parser.
Bioinformatics 2003 Feb;19(3);429-30.

139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1NAN

MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE

Structural Similarities for the Entities in PDB 1NAN

Info & Help Documentation

No structure alignment results are available for 1NAN.H, 1NAN.L explicitly.

No structure alignment results are available for 1NAN.I, 1NAN.P explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1NAN

MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE

Structural Similarities for the Entities in PDB 1NAN

Info & Help Documentation

No structure alignment results are available for 1NAN.H, 1NAN.L explicitly.

No structure alignment results are available for 1NAN.I, 1NAN.P explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References