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

General features for molecule PDB_01240 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01240 Molecule name [?]: INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 2QNH, CONTAINS Source [?]: RCSB Protein Data Bank Source ID [?]: 2QNH Reference [?]: A.KOROSTELEV,S.TRAKHANOV,H.ASAHARA,M.LAURBERG, L.LANCASTER,H.F.NOLLER. INTERACTIONS AND DYNAMICS OF THE SHINE DALGARNO HELIX IN THE 70S RIBOSOME.. PROC.NATL.ACAD.SCI.USA V. 104 16840 2007 ASTM PNASA6 US ISSN 0027-8424 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 3.83 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1685 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 605 Number of paired bases [?]: 1080

Click on any header below for additional features.

Stem features Number of stems [?]: 100 Number of base pairs in stems [?]: 497 Maximum length of a stem [?]: 20 Average length of a stem [?]: 4.98 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.4 Minimum estimated free energy [?]: -32.5

Hairpin loop features Number of hairpin loops [?]: 35 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.97 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 [?]: 27 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.72 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 19 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 3.03 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: 2 Average internal loop relative asymmetry: 1.16 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 18 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.1 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 2.77 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 10 Average multi-loop relative asymmetry: 1.18 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.5 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 65 Total number of AA non-canonical base pairs: 6 Total number of AC non-canonical base pairs: 9 Total number of AG non-canonical base pairs: 41 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 2 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: 43 Maximum band length: 20 Average band length: 7.17 Minimum band length: 3 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 Minimum number of un-bands: 0 Maximum number of in-bands: 3 Average number of in-bands: 1 Minimum number of in-bands: 0 Maximum number of unpaired bases: 28 Average number of unpaired bases: 20.33 Minimum number of unpaired bases: 14 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 10 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 3.33 Minimum number of base pairs to remove, per pseudoknot: 3 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