X-ray structure determination of the cytochrome c2: reaction center electron transfer complex from Rhodobacter sphaeroides.

Axelrod, H.L; Abresch, E.C; Okamura, M.Y; Yeh, A.P; Rees, D.C; Feher, G.

1L9J

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

Structural Similarities for the Entities in PDB 1L9J

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 L,R

Description: REACTION CENTER PROTEIN L CHAIN protein | Length: 281

No structure alignment results are available for 1L9J.L, 1L9J.R explicitly.

These chains are represented by chain 2WJN.L which has more than 50% sequence identity.

Show structure comparison results for representative 2WJN.L

Entity #2 | Chains M,S

Description: REACTION CENTER PROTEIN M CHAIN protein | Length: 307

No structure alignment results are available for 1L9J.M, 1L9J.S explicitly.

These chains are represented by chain 2WJN.M which has more than 50% sequence identity.

Show structure comparison results for representative 2WJN.M

Entity #3 | Chains H,T

Description: REACTION CENTER PROTEIN H CHAIN protein | Length: 260

No structure alignment results are available for 1L9J.H, 1L9J.T explicitly.

These chains are represented by chain 2WJN.H which has more than 40% sequence identity.

Show structure comparison results for representative 2WJN.H

Entity #4 | Chains C,D

Description: cytochrome c-2 protein | Length: 124

No structure alignment results are available for 1L9J.C, 1L9J.D explicitly.

These chains are represented by chain 4N0K.A which has more than 40% sequence identity.

Show structure comparison results for representative 4N0K.A

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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