Toward a Hepatitis C Virus Vaccine: the Structural Basis of Hepatitis C Virus Neutralization by AP33, a Broadly Neutralizing Antibody.

Potter, J.A; Owsianka, A.M; Jeffery, N; Matthews, D.J; Keck, Z.Y; Lau, P; Foung, S.K; Taylor, G.L; Patel, A.H.

Structural Similarities for the Entities in PDB 4GAJ

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: Dec-31-1969

Info & Help Documentation

A detailed description of the procedure for the all vs. all alignments is available.

Entity #1 | Chains H

Description: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN protein | Length: 218

No structure alignment results are available for 4GAJ.H explicitly.

It is represented by chain XXXX.null which has more than 50% sequence identity.

Show structure comparison results for representative XXXX.null

Entity #2 | Chains L

Description: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN protein | Length: 218

No structure alignment results are available for 4GAJ.L explicitly.

It is represented by chain XXXX.null which has more than 70% sequence identity.

Show structure comparison results for representative XXXX.null

Entity #3 | Chains P

Description: Genome polyprotein 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.

134436 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

4GAJ

Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 411-424)

Structural Similarities for the Entities in PDB 4GAJ

Info & Help Documentation

No structure alignment results are available for 4GAJ.H explicitly.

No structure alignment results are available for 4GAJ.L explicitly.

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

References

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Deposition Help & Resources

134436 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

4GAJ

Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 411-424)

Structural Similarities for the Entities in PDB 4GAJ

Info & Help Documentation

No structure alignment results are available for 4GAJ.H explicitly.

No structure alignment results are available for 4GAJ.L explicitly.

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

References