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

General features for molecule PDB_00676 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00676 Molecule name [?]: STRUCTURE OF CCA OLIGONUCLEOTIDE BOUND TO THE TRNA BINDING SITES OF THE LARGE RIBOSOMAL SUBUNIT OF H Source [?]: RCSB Protein Data Bank Source ID [?]: 1QVG Reference [?]: T.M.SCHMEING,P.B.MOORE,T.A.STEITZ. STRUCTURES OF DEACYLATED TRNA MIMICS BOUND TO THE E SITE OF THE LARGE RIBOSOMAL SUBUNIT. RNA V. 9 1345 2003 ASTM RNARFU UK ISSN 1355-8382 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: HALOARCULA MARISMORTUI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.90 ANGSTROMS; ran through RNAview Number of molecules [?]: 5 Length [?]: 2885 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 945 Number of paired bases [?]: 1940

Click on any header below for additional features.

Stem features Number of stems [?]: 136 Number of base pairs in stems [?]: 714 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.25 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.63 Minimum estimated free energy [?]: -25.2

Hairpin loop features Number of hairpin loops [?]: 56 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 4.21 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 41 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.77 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 25 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.42 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.08 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.6 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 14 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.19 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.16 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.21 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.79 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 132 Total number of AA non-canonical base pairs: 18 Total number of AC non-canonical base pairs: 16 Total number of AG non-canonical base pairs: 67 Total number of CC non-canonical base pairs: 12 Total number of CU non-canonical base pairs: 9 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 9

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 28 Number of base pairs in bands: 256 Maximum band length: 37 Average band length: 9.14 Minimum band length: 2 Maximum number of bands per pseudoknot: 15 Average number of bands per pseudoknot: 4.67 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 14 Average number of un-bands: 2.5 Minimum number of un-bands: 0 Maximum number of in-bands: 18 Average number of in-bands: 3.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 267 Average number of unpaired bases: 58.83 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: 31 Maximum number of base pairs to remove, per pseudoknot: 14 Average number of base pairs to remove, per pseudoknot: 5.17 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 11 Maximum number of bands to remove, per pseudoknot: 5 Average number of bands to remove, per pseudoknot: 1.83 Minimum number of bands to remove, per pseudoknot: 1

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