Structure of a viral procapsid with molecular scaffolding.

Dokland, T; McKenna, R; Ilag, L.L; Bowman, B.R; Incardona, N.L; Fane, B.A; Rossmann, M.G.

1AL0

PROCAPSID OF BACTERIOPHAGE PHIX174

Structural Similarities for the Entities in PDB 1AL0

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 1,2,3,4

Description: SCAFFOLDING PROTEIN GPD protein | Length: 152

No structure alignment results are available for 1AL0.1, 1AL0.2, 1AL0.3, 1AL0.4 explicitly.

These chains are represented by chain 1TX9.a which is 100% sequence identical.

Show structure comparison results for representative 1TX9.a

Entity #2 | Chains F

Description: CAPSID PROTEIN GPF protein | Length: 426

No structure alignment results are available for 1AL0.F explicitly.

It is represented by chain 2BPA.1 which is 100% sequence identical.

Show structure comparison results for representative 2BPA.1

Entity #3 | Chains G

Description: SPIKE PROTEIN GPG protein | Length: 175

No structure alignment results are available for 1AL0.G explicitly.

It is represented by chain 2BPA.2 which is 100% sequence identical.

Show structure comparison results for representative 2BPA.2

Entity #4 | Chains B

Description: SCAFFOLDING PROTEIN GPB protein | Length: 120

No structure alignment results are available for 1AL0.B explicitly.

It is represented by chain 1CD3.B which is 100% sequence identical.

Show structure comparison results for representative 1CD3.B

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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