Nonstandard Peptide Binding Revealed by Crystal Structures of Hla-B5101 Complexed with HIV Immunodominant Epitopes

Maenaka, K; Maenaka, T; Tomiyama, H; Takiguchi, M; Stuart, D.I; Jones, E.Y.

Structural Similarities for the Entities in PDB 1E27

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

Description: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN HEAVY CHAIN protein | Length: 276

No structure alignment results are available for 1E27.A explicitly.

It is represented by chain 1K5N.a which has more than 90% sequence identity.

Show structure comparison results for representative 1K5N.a

Entity #2 | Chains B

Description: BETA-2 MICROGLOBULIN LIGHT CHAIN protein | Length: 99

No structure alignment results are available for 1E27.B explicitly.

It is represented by chain 1K5N.b which is 100% sequence identical.

Show structure comparison results for representative 1K5N.b

Entity #3 | Chains C

Description: HIV-1 PEPTIDE (LPPVVAKEI) protein | Length: 9

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

1E27

Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM1(LPPVVAKEI)

Structural Similarities for the Entities in PDB 1E27

Info & Help Documentation

No structure alignment results are available for 1E27.A explicitly.

No structure alignment results are available for 1E27.B 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

1E27

Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM1(LPPVVAKEI)

Structural Similarities for the Entities in PDB 1E27

Info & Help Documentation

No structure alignment results are available for 1E27.A explicitly.

No structure alignment results are available for 1E27.B explicitly.

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

References