Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.

Basore, K; Kim, A.S; Nelson, C.A; Zhang, R; Smith, B.K; Uranga, C; Vang, L; Cheng, M; Gross, M.L; Smith, J; Diamond, M.S; Fremont, D.H.

6NK6

Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor

Structural Similarities for the Entities in PDB 6NK6

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

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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 M,N,O,P

Description: Matrix remodeling-associated protein 8 protein | Length: 269

No structure alignment results are available for 6NK6.M, 6NK6.N, 6NK6.O, 6NK6.P explicitly.

These chains are represented by chain XXXX.null which is 100% sequence identical.

Show structure comparison results for representative XXXX.null

Entity #2 | Chains A,B,C,D

Description: E1 glycoprotein protein | Length: 439

No structure alignment results are available for 6NK6.A, 6NK6.B, 6NK6.C, 6NK6.D explicitly.

These chains are represented by chain 3N44.F which has more than 90% sequence identity.

Show structure comparison results for representative 3N44.F

Entity #3 | Chains E,F,G,H

Description: E2 glycoprotein protein | Length: 419

No structure alignment results are available for 6NK6.E, 6NK6.F, 6NK6.G, 6NK6.H explicitly.

These chains are represented by chain XXXX.null which is 100% sequence identical.

Show structure comparison results for representative XXXX.null

Entity #4 | Chains I,J,K,L

Description: Capsid protein protein | Length: 151

No structure alignment results are available for 6NK6.I, 6NK6.J, 6NK6.K, 6NK6.L explicitly.

These chains are represented by chain 4AGK.A which has more than 50% sequence identity.

Show structure comparison results for representative 4AGK.A

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.

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