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

General features for molecule PDB_01104 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01104 Molecule name [?]: CRYSTAL STRUCTURE OF THE 70S THERMUS THERMOPHILUS RIBOSOME WITH TRANSLOCATED AND ROTATED SHINE-DALGA Source [?]: RCSB Protein Data Bank Source ID [?]: 2HGQ Reference [?]: G.YUSUPOVA,L.JENNER,B.REES,D.MORAS,M.YUSUPOV. STRUCTURAL BASIS FOR MESSENGER RNA MOVEMENT ON THE RIBOSOME.. NATURE V. 444 391 2006 ASTM NATUAS UK ISSN 0028-0836 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 5.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 3012 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01102, PDB_01106 Number of domains [?]: 2 Number of unpaired bases [?]: 1270 Number of paired bases [?]: 1742

Click on any header below for additional features.

Stem features Number of stems [?]: 140 Number of base pairs in stems [?]: 671 Maximum length of a stem [?]: 18 Average length of a stem [?]: 4.79 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -9.04 Minimum estimated free energy [?]: -33.6

Hairpin loop features Number of hairpin loops [?]: 60 Maximum number of free bases in hairpin loops [?]: 19 Average number of free bases in hairpin loops [?]: 5.98 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 [?]: 22 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 1 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: 23 Average number of free bases in internal loops: 3.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 21 Average internal loop absolute asymmetry: 2.07 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 11 Average internal loop relative asymmetry: 1.91 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.47 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.39 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.48 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.67 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 47 Total number of AA non-canonical base pairs: 3 Total number of AC non-canonical base pairs: 3 Total number of AG non-canonical base pairs: 32 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 16 Number of base pairs in bands: 200 Maximum band length: 39 Average band length: 12.5 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 4 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.75 Minimum number of un-bands: 0 Maximum number of in-bands: 27 Average number of in-bands: 7.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 326 Average number of unpaired bases: 93 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: 16 Maximum number of base pairs to remove, per pseudoknot: 7 Average number of base pairs to remove, per pseudoknot: 4 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: 3 Average number of bands to remove, per pseudoknot: 1.5 Minimum number of bands to remove, per pseudoknot: 1

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