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

General features for molecule PDB_00587 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00587 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CODON AND CRYSTALLOGR Source [?]: RCSB Protein Data Bank Source ID [?]: 1N34 Reference [?]: J.M.OGLE,F.V.MURPHY IV,M.J.TARRY,V.RAMAKRISHNAN. SELECTION OF TRNA BY THE RIBOSOME REQUIRES A TRANSITION FROM AN OPEN TO A CLOSED FORM. CELL (CAMBRIDGE,MASS.) V. 111 721 2002 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 3.80 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 1517 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 727 Number of paired bases [?]: 790

Click on any header below for additional features.

Stem features Number of stems [?]: 88 Number of base pairs in stems [?]: 342 Maximum length of a stem [?]: 10 Average length of a stem [?]: 3.89 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.15 Minimum estimated free energy [?]: -18.1

Hairpin loop features Number of hairpin loops [?]: 27 Maximum number of free bases in hairpin loops [?]: 30 Average number of free bases in hairpin loops [?]: 8.04 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 [?]: 19 Maximum number of free bases in bulge loops [?]: 12 Average number of free bases in bulge loops [?]: 0.92 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 31 Maximum number of free bases in internal loops: 10 Average number of free bases in internal loops: 2.71 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 0.9 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.32 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.51 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.06 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.18 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 43 Total number of AA non-canonical base pairs: 6 Total number of AC non-canonical base pairs: 6 Total number of AG non-canonical base pairs: 23 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 5

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 53 Maximum band length: 28 Average band length: 6.62 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: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 8 Average number of in-bands: 2.25 Minimum number of in-bands: 0 Maximum number of unpaired bases: 101 Average number of unpaired bases: 38.25 Minimum number of unpaired bases: 11 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 9 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.25 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 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