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

General features for molecule PDB_01277 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01277 Molecule name [?]: STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, Source [?]: RCSB Protein Data Bank Source ID [?]: 2V47 Reference [?]: A.WEIXLBAUMER,S.PETRY,C.M.DUNHAM,M.SELMER, A.C.KELLEY,V.RAMAKRISHNAN. CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE RIBOSOME. NAT.STRUCT.MOL.BIOL. V. 14 733 2007 ASTM NSMBCU US ISSN 1545-9993 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 3.8 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2886 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01279 Number of domains [?]: 3 Number of unpaired bases [?]: 1170 Number of paired bases [?]: 1716

Click on any header below for additional features.

Stem features Number of stems [?]: 142 Number of base pairs in stems [?]: 638 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.49 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.5 Minimum estimated free energy [?]: -27.6

Hairpin loop features Number of hairpin loops [?]: 57 Maximum number of free bases in hairpin loops [?]: 24 Average number of free bases in hairpin loops [?]: 5.77 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 31 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.74 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 39 Maximum number of free bases in internal loops: 10 Average number of free bases in internal loops: 2.31 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 9 Average internal loop absolute asymmetry: 0.82 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 10 Average internal loop relative asymmetry: 1.49 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 23 Average number of free bases in multi-loops: 3.34 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 22 Average multi-loop absolute asymmetry: 3 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 23 Average multi-loop relative asymmetry: 1.37 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 [?]: 85 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 5 Total number of AG non-canonical base pairs: 56 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 6 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 5

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 20 Number of base pairs in bands: 220 Maximum band length: 41 Average band length: 11 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.33 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 4.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 300 Average number of unpaired bases: 64.83 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: 23 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 3.83 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.33 Minimum number of bands to remove, per pseudoknot: 1

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