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

General features for molecule PDB_00853 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00853 Molecule name [?]: CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR AND TRNAS. LARGE SUBUNIT. THE COORDINATES FOR T Source [?]: RCSB Protein Data Bank Source ID [?]: 1YL3 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 0036-8075 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 [?]: 2995 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 1435 Number of paired bases [?]: 1560

Click on any header below for additional features.

Stem features Number of stems [?]: 153 Number of base pairs in stems [?]: 669 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.37 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0.3 Average estimated free energy [?]: -8.08 Minimum estimated free energy [?]: -27.6

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 [?]: 6.65 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 [?]: 21 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.76 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 52 Maximum number of free bases in internal loops: 28 Average number of free bases in internal loops: 4.35 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 21 Average internal loop absolute asymmetry: 1.92 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 22 Average internal loop relative asymmetry: 1.73 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 20 Maximum number of free bases in multi-loops: 26 Average number of free bases in multi-loops: 3.52 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 26 Average multi-loop absolute asymmetry: 3.22 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.45 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 6 Average number of branches in multi-loops: 3.65 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: 3 Total number of AG non-canonical base pairs: 36 Total number of CC non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 13 Number of base pairs in bands: 111 Maximum band length: 33 Average band length: 8.54 Minimum band length: 2 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 2.17 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 5 Average number of un-bands: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 19 Average number of in-bands: 3.67 Minimum number of in-bands: 0 Maximum number of unpaired bases: 215 Average number of unpaired bases: 48.33 Minimum number of unpaired bases: 4 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: 5 Average number of base pairs to remove, per pseudoknot: 2.67 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: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1

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