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

General features for molecule PDB_01103 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01103 Molecule name [?]: CRYSTAL STRUCTURE OF THE 70S THERMUS THERMOPHILUS RIBOSOME WITH TRANSLOCATED AND ROTATED SHINE-DALGA Source [?]: RCSB Protein Data Bank Source ID [?]: 2HGP Reference [?]: G.YUSUPOVA,L.JENNER,B.REES,D.MORAS,M.YUSUPOV. STRUCTURAL BASIS FOR MESSENGER RNA MOVEMENT ON THE RIBOSOME.. NATURE V. 444 391 2006 ASTM NATUAS UK ISSN 0028-0836 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 5.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 5 Length [?]: 1793 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 6 Number of unpaired bases [?]: 669 Number of paired bases [?]: 1124

Click on any header below for additional features.

Stem features Number of stems [?]: 98 Number of base pairs in stems [?]: 486 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.97 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.9 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 36 Maximum number of free bases in hairpin loops [?]: 21 Average number of free bases in hairpin loops [?]: 5.72 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 [?]: 22 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.84 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 24 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.79 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.5 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.9 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.55 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.07 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.47 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 40 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 27 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 12 Number of base pairs in bands: 76 Maximum band length: 14 Average band length: 6.33 Minimum band length: 2 Maximum number of bands per pseudoknot: 6 Average number of bands per pseudoknot: 3 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 6 Average number of in-bands: 1.75 Minimum number of in-bands: 0 Maximum number of unpaired bases: 47 Average number of unpaired bases: 27.75 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: 16 Maximum number of base pairs to remove, per pseudoknot: 8 Average number of base pairs to remove, per pseudoknot: 4 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: 3 Average number of bands to remove, per pseudoknot: 1.5 Minimum number of bands to remove, per pseudoknot: 1