Structural definition of a conserved neutralization epitope on HIV-1 gp120.

Zhou, T; Xu, L; Dey, B; Hessell, A.J; Van Ryk, D; Xiang, S.H; Yang, X; Zhang, M.Y; Zwick, M.B; Arthos, J; Burton, D.R; Dimitrov, D.S; Sodroski, J; Wyatt, R; Nabel, G.J; Kwong, P.D.

2NY4

HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, S334A, S375W) Complexed with CD4 and Antibody 17b

Structural Similarities for the Entities in PDB 2NY4

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: 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: ENVELOPE GLYCOPROTEIN GP120 protein | Length: 317

No structure alignment results are available for 2NY4.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 B

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

No structure alignment results are available for 2NY4.B explicitly.

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

Show structure comparison results for representative 4H8W.C

Entity #3 | Chains C

Description: ANTIBODY 17B, LIGHT CHAIN protein | Length: 214

No structure alignment results are available for 2NY4.C 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 D

Description: ANTIBODY 17B, HEAVY CHAIN protein | Length: 229

No structure alignment results are available for 2NY4.D 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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