PaperBLAST – Find papers about a protein or its homologs

 

BLAST against PDB

Comparing PDB to 73 a.a. (SDKPKRPLSA...) (73 a.a., SDKPKRPLSA...)

14 hits were found against non-redundant PDB (which was clustered at 80% identity)

8r1x A Solution structure and chemical shift assignments for hmg-d y12f mutant complexed to a 14:12 da2 bulge DNA
99% identity, 100% coverage of query, 147.0 bits, E = 3e-36

1wxl A Solution structure of the hmg-box domain in the ssrp1 subunit of fact
61% identity, 95% coverage of query, 90.5 bits, E = 3e-19

9eh2 y FACT complex subunit SSRP1
53% identity, 93% coverage of query, 85.9 bits, E = 8e-18

2yqi A Solution structure of the second hmg-box domain from high mobility group protein b3
40% identity, 96% coverage of query, 60.1 bits, E = 4e-10

1cg7 A Hmg protein nhp6a from saccharomyces cerevisiae
44% identity, 82% coverage of query, 51.6 bits, E = 2e-07

2yrq A Solution structure of the tandem hmg box domain from human high mobility group protein b1
43% identity, 96% coverage of query, 50.8 bits, E = 2e-07

5jgh A Crystal structure of the mitochondrial DNA packaging protein abf2p in complex with DNA at 2.6 angstrom resolution
36% identity, 92% coverage of query, 50.1 bits, E = 5e-07

2gzk A Structure of a complex of tandem hmg boxes and DNA
43% identity, 93% coverage of query, 47.4 bits, E = 3e-06

2gzk A Structure of a complex of tandem hmg boxes and DNA
29% identity, 70% coverage of query, 40.0 bits, E = 0.0004

6t90 L Oct4-sox2-bound nucleosome - shl-6
35% identity, 63% coverage of query, 40.8 bits, E = 0.0003

6edb A Crystal structure of sry.Hcgas-21bp dsdna complex
30% identity, 68% coverage of query, 40.8 bits, E = 0.0003

6t78 A Structure of human sox11 transcription factor in complex with a short DNA fragment
37% identity, 59% coverage of query, 40.0 bits, E = 0.0004

7yho A Cryoem structure of arabidopsis ros1 in complex with tg mismatch dsdna at 3.3 angstroms resolution
30% identity, 68% coverage of query, 39.7 bits, E = 0.0005

4euw A Crystal structure of a hmg domain of transcription factor sox-9 bound to DNA (sox-9/DNA) from homo sapiens at 2.77 a resolution
35% identity, 59% coverage of query, 39.7 bits, E = 0.0006

To find additional similar structures, try the "Find Similar Assemblies" links at RCSB.

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by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory