Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.

Kwong, P.D; Wyatt, R; Majeed, S; Robinson, J; Sweet, R.W; Sodroski, J; Hendrickson, W.A.

1G9M

HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

Structural Similarities for the Entities in PDB 1G9M

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 G

Description: ENVELOPE GLYCOPROTEIN GP120 protein | Length: 321

No structure alignment results are available for 1G9M.G 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: 185

No structure alignment results are available for 1G9M.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: ANTIBODY 17B, LIGHT CHAIN protein | Length: 214

No structure alignment results are available for 1G9M.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: ANTIBODY 17B, HEAVY CHAIN protein | Length: 229

No structure alignment results are available for 1G9M.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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