Bypassing pan-enterovirus host factor PLA2G16.

Baggen, J; Liu, Y; Lyoo, H; van Vliet, A.L.W; Wahedi, M; de Bruin, J.W; Roberts, R.W; Overduin, P; Meijer, A; Rossmann, M.G; Thibaut, H.J; van Kuppeveld, F.J.M.

6CVB

CryoEM structure of human enterovirus D68 in complex with 6'-sialyl-N-acetyllactosamine

Structural Similarities for the Entities in PDB 6CVB

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: viral protein 1 protein | Length: 297

No structure alignment results are available for 6CVB.A explicitly.

It is represented by chain 4Q4W.1 which has more than 40% sequence identity.

Show structure comparison results for representative 4Q4W.1

Entity #2 | Chains B

Description: viral protein 3 protein | Length: 247

No structure alignment results are available for 6CVB.B explicitly.

It is represented by chain 4Q4W.3 which has more than 50% sequence identity.

Show structure comparison results for representative 4Q4W.3

Entity #3 | Chains C

Description: viral protein 2 protein | Length: 248

No structure alignment results are available for 6CVB.C explicitly.

It is represented by chain 4Q4W.2 which has more than 50% sequence identity.

Show structure comparison results for representative 4Q4W.2

Entity #4 | Chains D

Description: viral protein 4 protein | Length: 68

No structure alignment results are available for 6CVB.D explicitly.

It is represented by chain 4Q4W.4 which has more than 50% sequence identity.

Show structure comparison results for representative 4Q4W.4

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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