A Functional and Structural Basis for Tcr Cross-Reactivity in Multiple Sclerosis

Lang, H; Jacobsen, H; Ikemizu, S; Andersson, C; Harlos, K; Madsen, L; Hjorth, P; Sondergaard, L; Svejgaard, A; Wucherpfennig, K; Stuart, D.I; Bell, J.I; Jones, E.Y; Fugger, L.

Structural Similarities for the Entities in PDB 1H15

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 A,D

Description: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN protein | Length: 182

No structure alignment results are available for 1H15.A, 1H15.D explicitly.

These chains are represented by chain 4X5W.A which is 100% sequence identical.

Show structure comparison results for representative 4X5W.A

Entity #2 | Chains B,E

Description: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR BETA 1 CHAIN protein | Length: 190

No structure alignment results are available for 1H15.B, 1H15.E explicitly.

These chains are represented by chain 4X5W.B which has more than 90% sequence identity.

Show structure comparison results for representative 4X5W.B

Entity #3 | Chains C,F

Description: DNA POLYMERASE protein | Length: 14

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

1H15

X-ray crystal structure of HLA-DRA10101/DRB50101 complexed with a peptide from Epstein Barr Virus DNA polymerase

Structural Similarities for the Entities in PDB 1H15

Info & Help Documentation

No structure alignment results are available for 1H15.A, 1H15.D explicitly.

No structure alignment results are available for 1H15.B, 1H15.E explicitly.

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

References

Prepare Data

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Deposit Data

Deposition Help & Resources

139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1H15

X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with a peptide from Epstein Barr Virus DNA polymerase

Structural Similarities for the Entities in PDB 1H15

Info & Help Documentation

No structure alignment results are available for 1H15.A, 1H15.D explicitly.

No structure alignment results are available for 1H15.B, 1H15.E explicitly.

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

References

X-ray crystal structure of HLA-DRA10101/DRB50101 complexed with a peptide from Epstein Barr Virus DNA polymerase