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

General features for molecule PDB_01182 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01182 Molecule name [?]: THE CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE Source [?]: RCSB Protein Data Bank Source ID [?]: 2OGM Reference [?]: C.DAVIDOVICH,A.BASHAN,T.AUERBACH-NEVO,R.D.YAGGIE, R.R.GONTAREK,A.YONATH. INDUCED-FIT TIGHTENS PLEUROMUTILINS BINDING TO RIBOSOMES AND REMOTE INTERACTIONS ENABLE THEIR SELECTIVITY.. PROC.NATL.ACAD.SCI.USA V. 104 4291 2007 ASTM PNASA6 US ISSN 0027-8424 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: DEINOCOCCUS RADIODURANS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2766 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00606, PDB_00880, PDB_00922, PDB_01173, PDB_01174, PDB_01175, PDB_01183 Number of domains [?]: 1 Number of unpaired bases [?]: 1148 Number of paired bases [?]: 1618

Click on any header below for additional features.

Stem features Number of stems [?]: 136 Number of base pairs in stems [?]: 603 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.43 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.77 Minimum estimated free energy [?]: -20

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 13 Average number of free bases in hairpin loops [?]: 5.41 Minimum number of free bases in hairpin loop [?]: 0 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 22 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.8 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 41 Maximum number of free bases in internal loops: 11 Average number of free bases in internal loops: 2.67 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 0.95 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.44 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 15 Average number of free bases in multi-loops: 3.21 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 2.95 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.11 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.87 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 79 Total number of AA non-canonical base pairs: 6 Total number of AC non-canonical base pairs: 7 Total number of AG non-canonical base pairs: 46 Total number of CC non-canonical base pairs: 3 Total number of CU non-canonical base pairs: 7 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 206 Maximum band length: 36 Average band length: 11.44 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.6 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.6 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 5.2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 307 Average number of unpaired bases: 78.6 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: 21 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 4.2 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 7 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.4 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