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

General features for molecule PDB_00465 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00465 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT Source [?]: RCSB Protein Data Bank Source ID [?]: 1IBM Reference [?]: J.M.OGLE,D.E.BRODERSEN,W.M.CLEMONS JR.,M.J.TARRY, A.P.CARTER,V.RAMAKRISHNAN. RECOGNITION OF COGNATE TRANSFER RNA BY THE 30S RIBOSOMAL SUBUNIT.. SCIENCE V. 292 897 2001 ASTM SCIEAS US ISSN 0036-8075 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 3.31 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1528 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 496 Number of paired bases [?]: 1032

Click on any header below for additional features.

Stem features Number of stems [?]: 81 Number of base pairs in stems [?]: 448 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.54 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 [?]: 27 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.3 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 [?]: 24 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.77 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: 20 Average number of free bases in internal loops: 2.79 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 15 Average internal loop absolute asymmetry: 1.79 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.74 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 10 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.97 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.42 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.13 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.2 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 74 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 11 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: 5 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 10 Number of base pairs in bands: 68 Maximum band length: 32 Average band length: 6.8 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 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 60 Average number of unpaired bases: 23.2 Minimum number of unpaired bases: 4 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 13 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.6 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 5 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