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

General features for molecule PDB_01173 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01173 Molecule name [?]: STRUCTURE OF 23S RRNA OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS IN COMPLEX WITH TH Source [?]: RCSB Protein Data Bank Source ID [?]: 2O43 Reference [?]: E.PYETAN,D.BARAM,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_01174, PDB_01175, PDB_01182, PDB_01183 Number of domains [?]: 1 Number of unpaired bases [?]: 1284 Number of paired bases [?]: 1482

Click on any header below for additional features.

Stem features Number of stems [?]: 125 Number of base pairs in stems [?]: 544 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.35 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.01 Minimum estimated free energy [?]: -20

Hairpin loop features Number of hairpin loops [?]: 56 Maximum number of free bases in hairpin loops [?]: 19 Average number of free bases in hairpin loops [?]: 6.41 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 16 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.69 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 37 Maximum number of free bases in internal loops: 12 Average number of free bases in internal loops: 3.2 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1.27 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.51 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 23 Average number of free bases in multi-loops: 4.31 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 22 Average multi-loop absolute asymmetry: 4.27 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 23 Average multi-loop relative asymmetry: 1.59 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.69 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 50 Total number of AA non-canonical base pairs: 6 Total number of AC non-canonical base pairs: 8 Total number of AG non-canonical base pairs: 26 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 3 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 17 Number of base pairs in bands: 197 Maximum band length: 38 Average band length: 11.59 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.4 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: 22 Average number of in-bands: 5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 340 Average number of unpaired bases: 81.8 Minimum number of unpaired bases: 8 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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