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

General features for molecule PDB_00783 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00783 Molecule name [?]: THE STRUCTURE OF CCDA-PHE-CAP-BIO AND THE ANTIBIOTIC SPARSOMYCIN BOUND TO THE LARGE RIBOSOMAL SUBUNI Source [?]: RCSB Protein Data Bank Source ID [?]: 1VQ8 Reference [?]: T.M.SCHMEING,K.S.HUANG,D.E.KITCHEN,S.A.STROBEL, T.A.STEITZ. STRUCTURAL INSIGHTS INTO THE ROLES OF WATER AND THE 2' HYDROXYL OF THE P SITE TRNA IN THE PEPTIDYL TRANSFERASE REACTION.. MOL.CELL V. 20 437 2005 ASTM MOCEFL US ISSN 1097-2765 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 2.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 2879 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00784, PDB_00785, PDB_00789 Number of domains [?]: 1 Number of unpaired bases [?]: 947 Number of paired bases [?]: 1932

Click on any header below for additional features.

Stem features Number of stems [?]: 141 Number of base pairs in stems [?]: 727 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.16 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.52 Minimum estimated free energy [?]: -25.2

Hairpin loop features Number of hairpin loops [?]: 57 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 4.19 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 [?]: 28 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.3 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.11 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.64 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: 3.16 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.17 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.27 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.73 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 134 Total number of AA non-canonical base pairs: 18 Total number of AC non-canonical base pairs: 15 Total number of AG non-canonical base pairs: 69 Total number of CC non-canonical base pairs: 13 Total number of CU non-canonical base pairs: 8 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 10

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 25 Number of base pairs in bands: 239 Maximum band length: 38 Average band length: 9.56 Minimum band length: 2 Maximum number of bands per pseudoknot: 12 Average number of bands per pseudoknot: 4.17 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 12 Average number of un-bands: 2.17 Minimum number of un-bands: 0 Maximum number of in-bands: 20 Average number of in-bands: 3.83 Minimum number of in-bands: 0 Maximum number of unpaired bases: 250 Average number of unpaired bases: 56 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: 29 Maximum number of base pairs to remove, per pseudoknot: 12 Average number of base pairs to remove, per pseudoknot: 4.83 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 10 Maximum number of bands to remove, per pseudoknot: 4 Average number of bands to remove, per pseudoknot: 1.67 Minimum number of bands to remove, per pseudoknot: 1

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