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

General features for molecule PDB_00409 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00409 Molecule name [?]: STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION Source [?]: RCSB Protein Data Bank Source ID [?]: 1FKA Reference [?]: F.SCHLUENZEN,A.TOCILJ,R.ZARIVACH,J.HARMS, M.GLUEHMANN,D.JANELL,A.BASHAN,H.BARTELS,I.AGMON, F.FRANCESCHI,A.YONATH. STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 ANGSTROMS RESOLUTION.. CELL V. 102 615 2000 ASTM CELLB5 US ISSN 0092-8674 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 3.30 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1174 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 684 Number of paired bases [?]: 490

Click on any header below for additional features.

Stem features Number of stems [?]: 73 Number of base pairs in stems [?]: 236 Maximum length of a stem [?]: 9 Average length of a stem [?]: 3.23 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -5.34 Minimum estimated free energy [?]: -14.8

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.46 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 4 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 26 Maximum number of free bases in internal loops: 16 Average number of free bases in internal loops: 3.27 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 13 Average internal loop absolute asymmetry: 1.62 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 5 Average internal loop relative asymmetry: 1.54 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 16 Average number of free bases in multi-loops: 5.11 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 14 Average multi-loop absolute asymmetry: 4.22 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 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: 3.53 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 14 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 7 Total number of GG non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 9 Maximum band length: 3 Average band length: 2.25 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: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 21 Average number of unpaired bases: 17.5 Minimum number of unpaired bases: 14 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 4 Maximum number of base pairs to remove, per pseudoknot: 2 Average number of base pairs to remove, per pseudoknot: 2 Minimum number of base pairs to remove, per pseudoknot: 2 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