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

General features for molecule PDB_01278 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01278 Molecule name [?]: STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, Source [?]: RCSB Protein Data Bank Source ID [?]: 2V48 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 [?]: 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 3.8 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1609 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01276 Number of domains [?]: 6 Number of unpaired bases [?]: 737 Number of paired bases [?]: 872

Click on any header below for additional features.

Stem features Number of stems [?]: 106 Number of base pairs in stems [?]: 408 Maximum length of a stem [?]: 9 Average length of a stem [?]: 3.85 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.13 Minimum estimated free energy [?]: -18

Hairpin loop features Number of hairpin loops [?]: 32 Maximum number of free bases in hairpin loops [?]: 28 Average number of free bases in hairpin loops [?]: 6.09 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 [?]: 20 Maximum number of free bases in bulge loops [?]: 16 Average number of free bases in bulge loops [?]: 1.1 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: 8 Average number of free bases in internal loops: 2.18 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.82 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.33 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 14 Average number of free bases in multi-loops: 4.19 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 11 Average multi-loop absolute asymmetry: 3.19 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 12 Average multi-loop relative asymmetry: 1.16 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.53 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 49 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 27 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 5

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 28 Maximum band length: 8 Average band length: 4.67 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: 1.67 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 35 Average number of unpaired bases: 23.67 Minimum number of unpaired bases: 17 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 8 Maximum number of base pairs to remove, per pseudoknot: 4 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: 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