The Crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface

Yang, Z; Pandi, L; Doolittle, R.F.

1N73

Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE

Structural Similarities for the Entities in PDB 1N73

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,D

Description: Fibrin alpha-1 chain protein | Length: 119

No structure alignment results are available for 1N73.A, 1N73.D explicitly.

These chains are represented by chain 1LWU.a which is 100% sequence identical.

Show structure comparison results for representative 1LWU.a

Entity #2 | Chains B,E

Description: Fibrin beta chain protein | Length: 323

No structure alignment results are available for 1N73.B, 1N73.E explicitly.

These chains are represented by chain 3E1I.B which has more than 50% sequence identity.

Show structure comparison results for representative 3E1I.B

Entity #3 | Chains C,F

Description: Fibrin gamma chain protein | Length: 330

No structure alignment results are available for 1N73.C, 1N73.F explicitly.

These chains are represented by chain 3E1I.C which has more than 50% sequence identity.

Show structure comparison results for representative 3E1I.C

Entity #4 | Chains G,H,I,J

Description: peptide ligand: Gly-his-Arg-Pro-amide protein | Length: 4

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.

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