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

General features for molecule PDB_00953 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00953 Molecule name [?]: 50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF2, TRNAS AND MRNA BOUND TO THE RI Source [?]: RCSB Protein Data Bank Source ID [?]: 2B9N Reference [?]: S.PETRY,D.E.BRODERSEN,F.V.MURPHY IV,C.M.DUNHAM, M.SELMER,M.J.TARRY,A.C.KELLEY,V.RAMAKRISHNAN. CRYSTAL STRUCTURES OF THE RIBOSOME IN COMPLEX WITH RELEASE FACTORS RF1 AND RF2 BOUND TO A COGNATE STOP CODON.. CELL (CAMBRIDGE,MASS.) V. 123 1255 2005 ASTM CELLB5 US ISSN 0092-8674 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 6.76 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2937 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00947, PDB_00955 Number of domains [?]: 2 Number of unpaired bases [?]: 1443 Number of paired bases [?]: 1494

Click on any header below for additional features.

Stem features Number of stems [?]: 153 Number of base pairs in stems [?]: 638 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.17 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.57 Minimum estimated free energy [?]: -27.6

Hairpin loop features Number of hairpin loops [?]: 57 Maximum number of free bases in hairpin loops [?]: 17 Average number of free bases in hairpin loops [?]: 6.61 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 24 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.79 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 49 Maximum number of free bases in internal loops: 23 Average number of free bases in internal loops: 3.77 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 21 Average internal loop absolute asymmetry: 1.53 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 22 Average internal loop relative asymmetry: 1.69 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 23 Maximum number of free bases in multi-loops: 29 Average number of free bases in multi-loops: 4.53 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 28 Average multi-loop absolute asymmetry: 4.52 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 29 Average multi-loop relative asymmetry: 1.62 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 6 Average number of branches in multi-loops: 3.61 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: 7 Total number of AC non-canonical base pairs: 6 Total number of AG non-canonical base pairs: 32 Total number of CC non-canonical base pairs: 1 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: 1

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 14 Number of base pairs in bands: 109 Maximum band length: 34 Average band length: 7.79 Minimum band length: 2 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 2.33 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: 15 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 201 Average number of unpaired bases: 46.33 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: 15 Maximum number of base pairs to remove, per pseudoknot: 5 Average number of base pairs to remove, per pseudoknot: 2.5 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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