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

General features for molecule PDB_01175 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01175 Molecule name [?]: STRUCTURE OF THE 23S RRNA OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS IN COMPLEX WIT Source [?]: RCSB Protein Data Bank Source ID [?]: 2O45 Reference [?]: D.BARAM,E.PYETAN,T.AUERBACH-NEVO,A.YONATH. CHEMICAL PARAMETERS INFLUENCING FINE TUNING IN THE BINDING OF MACROLIDE ANTIBIOTICS TO THE RIBOSOMAL TUNNEL. TO BE PUBLISHED 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 3.60 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_01182, PDB_01183 Number of domains [?]: 1 Number of unpaired bases [?]: 1260 Number of paired bases [?]: 1506

Click on any header below for additional features.

Stem features Number of stems [?]: 136 Number of base pairs in stems [?]: 553 Maximum length of a stem [?]: 10 Average length of a stem [?]: 4.07 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.23 Minimum estimated free energy [?]: -20

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.95 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 20 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 43 Maximum number of free bases in internal loops: 17 Average number of free bases in internal loops: 3.17 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 7 Average internal loop absolute asymmetry: 1.05 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.33 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 16 Average number of free bases in multi-loops: 3.59 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 2.83 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 16 Average multi-loop relative asymmetry: 1.35 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 [?]: 67 Total number of AA non-canonical base pairs: 6 Total number of AC non-canonical base pairs: 9 Total number of AG non-canonical base pairs: 31 Total number of CC non-canonical base pairs: 4 Total number of CU non-canonical base pairs: 7 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 7

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 200 Maximum band length: 36 Average band length: 11.11 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: 308 Average number of unpaired bases: 80.2 Minimum number of unpaired bases: 11 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 19 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 3.8 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

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