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

General features for molecule PDB_00854 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00854 Molecule name [?]: CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR AND TRNAS. 30S SUBUNIT. THE COORDINATES FOR THE Source [?]: RCSB Protein Data Bank Source ID [?]: 1YL4 Reference [?]: L.JENNER,P.ROMBY,B.REES,C.SCHULZE-BRIESE, M.SPRINGER,C.EHRESMANN,B.EHRESMANN,D.MORAS, G.YUSUPOVA,M.YUSUPOV. TRANSLATIONAL OPERATOR OF MRNA ON THE RIBOSOME: HOW REPRESSOR PROTEINS EXCLUDE RIBOSOME BINDING. SCIENCE V. 308 120 2005 ASTM SCIEAS US ISSN 1095-9203 Type [?]: 16S 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 [?]: 4 Length [?]: 1733 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 663 Number of paired bases [?]: 1070

Click on any header below for additional features.

Stem features Number of stems [?]: 93 Number of base pairs in stems [?]: 469 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.04 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -9.01 Minimum estimated free energy [?]: -28.2

Hairpin loop features Number of hairpin loops [?]: 36 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.89 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 18 Maximum number of free bases in bulge loops [?]: 6 Average number of free bases in bulge loops [?]: 0.94 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: 9 Average number of free bases in internal loops: 3.28 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.12 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.36 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 14 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 3.41 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 8 Average multi-loop absolute asymmetry: 2.8 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.31 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.29 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 42 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 4 Total number of AG non-canonical base pairs: 28 Total number of CC non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 66 Maximum band length: 31 Average band length: 11 Minimum band length: 2 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 4.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 68 Average number of unpaired bases: 34.67 Minimum number of unpaired bases: 7 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 10 Maximum number of base pairs to remove, per pseudoknot: 5 Average number of base pairs to remove, per pseudoknot: 3.33 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 3 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1