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

General features for molecule PDB_01039 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01039 Molecule name [?]: 30S RIBOSOME + DESIGNER ANTIBIOTIC Source [?]: RCSB Protein Data Bank Source ID [?]: 2F4V Reference [?]: J.B.MURRAY,S.O.MEROUEH,R.J.RUSSELL,G.LENTZEN, J.HADDAD,S.MOBASHERY. INTERACTIONS OF DESIGNER ANTIBIOTICS AND THE BACTERIAL RIBOSOME AMINOACYL-TRNA SITE. CHEM.BIOL. V. 13 129 2006 ASTM CBOLE2 UK ISSN 1074-5521 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 [?]: 1511 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 579 Number of paired bases [?]: 932

Click on any header below for additional features.

Stem features Number of stems [?]: 89 Number of base pairs in stems [?]: 400 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.51 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.38 Minimum estimated free energy [?]: -22.5

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 30 Average number of free bases in hairpin loops [?]: 5.93 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 [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 27 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.33 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.89 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.48 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 12 Average number of free bases in multi-loops: 3.34 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 2.8 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.16 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 [?]: 52 Total number of AA non-canonical base pairs: 8 Total number of AC non-canonical base pairs: 8 Total number of AG non-canonical base pairs: 25 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: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 66 Maximum band length: 35 Average band length: 8.25 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: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 60 Average number of unpaired bases: 28.5 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.75 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