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].

Currently viewing ALL results. Show only significant 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.

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 XXXX.null which has more than 70% sequence identity.

Show structure comparison results for representative XXXX.null

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 XXXX.null which is 100% sequence identical.

Show structure comparison results for representative XXXX.null

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 XXXX.null which has more than 90% sequence identity.

Show structure comparison results for representative XXXX.null

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 XXXX.null which has more than 50% sequence identity.

Show structure comparison results for representative XXXX.null

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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134436 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

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

Info & Help Documentation

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

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

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

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

References