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

General features for molecule PDB_00863 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00863 Molecule name [?]: CRYSTAL STRUCTURE OF APRAMYCIN BOUND TO A RIBOSOMAL RNA A SITE OLIGONUCLEOTIDE Source [?]: RCSB Protein Data Bank Source ID [?]: 1YRJ Reference [?]: Q.HAN,Q.ZHAO,S.FISH,K.B.SIMONSEN,D.VOURLOUMIS, J.M.FROELICH,D.WALL,T.HERMANN. MOLECULAR RECOGNITION BY GLYCOSIDE PSEUDO BASE PAIRS AND TRIPLES IN AN APRAMYCIN-RNA COMPLEX.. ANGEW.CHEM.INT.ED.ENGL. V. 44 2694 2005 ASTM ACIEAY GE ISSN 0570-0833 Type [?]: Other Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: N/A Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.70 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 45 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 9 Number of paired bases [?]: 36

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 18 Maximum length of a stem [?]: 8 Average length of a stem [?]: 6 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -5.8 Average estimated free energy [?]: -9.73 Minimum estimated free energy [?]: -17.6

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 1 Average number of free bases in hairpin loops [?]: 1 Minimum number of free bases in hairpin loop [?]: 1

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 Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of UU non-canonical base pairs: 2

Pseudoknot features

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

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