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

General features for molecule PDB_01107 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01107 Molecule name [?]: CRYSTAL STRUCTURE OF KASUGAMYCIN BOUND TO THE 30S RIBOSOMAL SUBUNIT Source [?]: RCSB Protein Data Bank Source ID [?]: 2HHH Reference [?]: F.SCHLUENZEN,C.TAKEMOTO,D.N.WILSON,T.KAMINISHI, J.M.HARMS,K.HANAWA-SUETSUGU,W.SZAFLARSKI,M.KAWAZOE, M.SHIROUZO,K.H.NIERHAUS,S.YOKOYAMA,P.FUCINI. THE ANTIBIOTIC KASUGAMYCIN MIMICS MRNA NUCLEOTIDES TO DESTABILIZE TRNA BINDING AND INHIBIT CANONICAL TRANSLATION INITIATION.. NAT.STRUCT.MOL.BIOL. V. 13 871 2006 US ISSN 1545-9985 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 3.35 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1505 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 481 Number of paired bases [?]: 1024

Click on any header below for additional features.

Stem features Number of stems [?]: 88 Number of base pairs in stems [?]: 482 Maximum length of a stem [?]: 23 Average length of a stem [?]: 5.49 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.98 Minimum estimated free energy [?]: -39.2

Hairpin loop features Number of hairpin loops [?]: 29 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.34 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 [?]: 27 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.78 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 16 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.59 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1.19 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.69 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.94 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.53 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.47 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: 10 Total number of AC non-canonical base pairs: 10 Total number of AG non-canonical base pairs: 44 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 30 Maximum band length: 8 Average band length: 5 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: 1.67 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 27 Average number of unpaired bases: 20 Minimum number of unpaired bases: 14 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: 4 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 3 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