RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule PDB_00278 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00278 Molecule name [?]: X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES Source [?]: RCSB Protein Data Bank Source ID [?]: 486D Reference [?]: J.H.CATE,M.M.YUSUPOV,G.Z.YUSUPOVA,T.N.EARNEST, H.F.NOLLER. X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES.. SCIENCE V. 285 2095 1999 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 7.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 5 Length [?]: 224 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 3 Number of unpaired bases [?]: 80 Number of paired bases [?]: 144

Click on any header below for additional features.

Stem features Number of stems [?]: 10 Number of base pairs in stems [?]: 56 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5.6 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -3.6 Average estimated free energy [?]: -9.75 Minimum estimated free energy [?]: -14.4

Hairpin loop features Number of hairpin loops [?]: 8 Maximum number of free bases in hairpin loops [?]: 8 Average number of free bases in hairpin loops [?]: 6.62 Minimum number of free bases in hairpin loop [?]: 5

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 3 Average number of free bases in multi-loops: 1.25 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 3 Average multi-loop absolute asymmetry: 1.83 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1.5 Average multi-loop relative asymmetry: 0.36 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 4 Minimum number of branches in multi-loops: 4

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 4 Total number of AA non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features Number of pseudoknots [?]: 1 Number of bands: 2 Number of base pairs in bands: 16 Maximum band length: 13 Average band length: 8 Minimum band length: 3 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 0 Average number of un-bands: 0 Minimum number of un-bands: 0 Maximum number of in-bands: 2 Average number of in-bands: 2 Minimum number of in-bands: 2 Maximum number of unpaired bases: 10 Average number of unpaired bases: 10 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 3 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 3 Minimum number of bands to remove, per molecule: 1 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1

For questions, comments, suggestions and bug reports, please contact:

Copyright © 2004-2008 BETA LAB - University of British Columbia