Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01.

Zhou, T; Georgiev, I; Wu, X; Yang, Z.Y; Dai, K; Finzi, A; Do Kwon, Y; Scheid, J.F; Shi, W; Xu, L; Yang, Y; Zhu, J; Nussenzweig, M.C; Sodroski, J; Shapiro, L; Nabel, G.J; Mascola, J.R; Kwong, P.D.

3NGB

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

Structural Similarities for the Entities in PDB 3NGB

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

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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 A,D,G,I

Description: Envelope glycoprotein gp160 protein | Length: 353

No structure alignment results are available for 3NGB.A, 3NGB.D, 3NGB.G, 3NGB.I explicitly.

These chains are represented by chain 4JZZ.A which has more than 70% sequence identity.

Show structure comparison results for representative 4JZZ.A

Entity #2 | Chains B,E,H,J

Description: Antigen binding fragment of heavy chain: Antibody VRC01 protein | Length: 224

No structure alignment results are available for 3NGB.B, 3NGB.E, 3NGB.H, 3NGB.J explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

Show structure comparison results for representative XXXX.null

Entity #3 | Chains C,F,K,L

Description: Antigen binding fragment of light chain: Antibody VRC01 protein | Length: 210

No structure alignment results are available for 3NGB.C, 3NGB.F, 3NGB.K, 3NGB.L explicitly.

These chains are represented by chain XXXX.null which has more than 70% 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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