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

General features for molecule PDB_01091 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01091 Molecule name [?]: STRUCTURE OF THE 50S SUBUNIT OF A SECM-STALLED E. COLI RIBOSOME COMPLEX OBTAINED BY FITTING ATOMIC M Source [?]: RCSB Protein Data Bank Source ID [?]: 2GYC Reference [?]: K.MITRA,C.SCHAFFITZEL,F.FABIOLA,M.S.CHAPMAN,N.BAN, J.FRANK. ELONGATION ARREST BY SECM VIA A CASCADE OF RIBOSOMAL RNA REARRANGEMENTS. MOL.CELL V. 22 533 2006 ASTM MOCEFL US ISSN 1097-2765 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: ESCHERICHIA COLI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2848 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01089 Number of domains [?]: 3 Number of unpaired bases [?]: 1650 Number of paired bases [?]: 1198

Click on any header below for additional features.

Stem features Number of stems [?]: 112 Number of base pairs in stems [?]: 448 Maximum length of a stem [?]: 10 Average length of a stem [?]: 4 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -5.22 Minimum estimated free energy [?]: -16.7

Hairpin loop features Number of hairpin loops [?]: 55 Maximum number of free bases in hairpin loops [?]: 78 Average number of free bases in hairpin loops [?]: 7.78 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 7 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 0.64 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 38 Maximum number of free bases in internal loops: 12 Average number of free bases in internal loops: 2.97 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 0.95 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.45 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 12 Maximum number of free bases in multi-loops: 29 Average number of free bases in multi-loops: 6.98 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 29 Average multi-loop absolute asymmetry: 5.34 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 14 Average multi-loop relative asymmetry: 1.62 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.92 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 70 Total number of AA non-canonical base pairs: 13 Total number of AC non-canonical base pairs: 5 Total number of AG non-canonical base pairs: 40 Total number of CC non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 7 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 15 Number of base pairs in bands: 151 Maximum band length: 35 Average band length: 10.07 Minimum band length: 2 Maximum number of bands per pseudoknot: 6 Average number of bands per pseudoknot: 3 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 0.8 Minimum number of un-bands: 0 Maximum number of in-bands: 28 Average number of in-bands: 6 Minimum number of in-bands: 0 Maximum number of unpaired bases: 531 Average number of unpaired bases: 127.8 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 13 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.6 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 6 Maximum number of bands to remove, per pseudoknot: 2 Average number of bands to remove, per pseudoknot: 1.2 Minimum number of bands to remove, per pseudoknot: 1

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