Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design.

Baldwin, E.T; Bhat, T.N; Gulnik, S; Hosur, M.V; Sowder 2nd; R.C; Cachau, R.E; Collins, J; Silva, A.M; Erickson, J.W.

Structural Similarities for the Entities in PDB 1LYB

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

Info & Help Documentation

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,C

Description: CATHEPSIN D protein | Length: 97

No structure alignment results are available for 1LYB.A, 1LYB.C explicitly.

These chains are represented by chain 4OD9.A which is 100% sequence identical.

Show structure comparison results for representative 4OD9.A

Entity #2 | Chains B,D

Description: CATHEPSIN D protein | Length: 241

No structure alignment results are available for 1LYB.B, 1LYB.D explicitly.

These chains are represented by chain 4OD9.B which is 100% sequence identical.

Show structure comparison results for representative 4OD9.B

Entity #3 | Chains I,J

Description: PEPSTATIN protein | Length: 6

This entity is too short to be considered for the all vs. all structure alignments.

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.

139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1LYB

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Structural Similarities for the Entities in PDB 1LYB

Info & Help Documentation

No structure alignment results are available for 1LYB.A, 1LYB.C explicitly.

No structure alignment results are available for 1LYB.B, 1LYB.D explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1LYB

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Structural Similarities for the Entities in PDB 1LYB

Info & Help Documentation

No structure alignment results are available for 1LYB.A, 1LYB.C explicitly.

No structure alignment results are available for 1LYB.B, 1LYB.D explicitly.

This entity is too short to be considered for the all vs. all structure alignments.

References