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

General features for molecule PDB_00485 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00485 Molecule name [?]: THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE, 1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, Source [?]: RCSB Protein Data Bank Source ID [?]: 1JGP Reference [?]: G.Z.YUSUPOVA,M.M.YUSUPOV,J.H.CATE,H.F.NOLLER. THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME.. CELL V. 106 233 2001 ASTM CELLB5 US ISSN 0092-8674 Type [?]: Other 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 7.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 232 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00423, PDB_00484 Number of domains [?]: 1 Number of unpaired bases [?]: 84 Number of paired bases [?]: 148

Click on any header below for additional features.

Stem features Number of stems [?]: 8 Number of base pairs in stems [?]: 41 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5.12 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -4.3 Average estimated free energy [?]: -9.4 Minimum estimated free energy [?]: -14.4

Hairpin loop features Number of hairpin loops [?]: 7 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 7 Minimum number of free bases in hairpin loop [?]: 3

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 3 Average number of free bases in multi-loops: 1.25 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 3 Average multi-loop absolute asymmetry: 1.83 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1.5 Average multi-loop relative asymmetry: 0.36 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 4 Minimum number of branches in multi-loops: 4

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of AC non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 33 Maximum band length: 14 Average band length: 8.25 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: 1 Average number of un-bands: 1 Minimum number of un-bands: 1 Maximum number of in-bands: 2 Average number of in-bands: 2 Minimum number of in-bands: 2 Maximum number of unpaired bases: 17 Average number of unpaired bases: 15 Minimum number of unpaired bases: 13 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 6 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 3 Minimum number of bands to remove, per molecule: 2 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