Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.

Pancera, M; Majeed, S; Ban, Y.E; Chen, L; Huang, C.C; Kong, L; Kwon, Y.D; Stuckey, J; Zhou, T; Robinson, J.E; Schief, W.R; Sodroski, J; Wyatt, R; Kwong, P.D.

3JWO

Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility

Structural Similarities for the Entities in PDB 3JWO

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].

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Cluster data are up-to-date as of: Jun-20-2017

Info & Help Documentation

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

Entity #1 | Chains A

Description: HIV-1 GP120 ENVELOPE GLYCOPROTEIN protein | Length: 357

No structure alignment results are available for 3JWO.A explicitly.

It is represented by chain 4JZZ.A which has more than 70% sequence identity.

Show structure comparison results for representative 4JZZ.A

Entity #2 | Chains C

Description: T-cell surface glycoprotein CD4 protein | Length: 184

No structure alignment results are available for 3JWO.C explicitly.

It is represented by chain 4H8W.C which is 100% sequence identical.

Show structure comparison results for representative 4H8W.C

Entity #3 | Chains L

Description: FAB 48D LIGHT CHAIN protein | Length: 209

No structure alignment results are available for 3JWO.L explicitly.

It is represented by chain 4NZU.L which has more than 90% sequence identity.

Show structure comparison results for representative 4NZU.L

Entity #4 | Chains H

Description: FAB 48D Heavy CHAIN protein | Length: 220

No structure alignment results are available for 3JWO.H explicitly.

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

Show structure comparison results for representative 4NZU.L

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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