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

General features for molecule PDB_00187 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00187 Molecule name [?]: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH Source [?]: RCSB Protein Data Bank Source ID [?]: 1P9X Reference [?]: R.BERISIO,J.HARMS,F.SCHLUENZEN,R.ZARIVACH, H.A.HANSEN,P.FUCINI,A.YONATH. STRUCTURAL INSIGHT INTO THE ANTIBIOTIC ACTION OF TELITHROMYCIN AGAINST RESISTANT MUTANTS. J.BACTERIOL. V. 185 4276 2003 ASTM JOBAAY US ISSN 0021-9193 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: DEINOCOCCUS RADIODURANS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.40 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2738 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 1306 Number of paired bases [?]: 1432

Click on any header below for additional features.

Stem features Number of stems [?]: 151 Number of base pairs in stems [?]: 598 Maximum length of a stem [?]: 12 Average length of a stem [?]: 3.96 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.05 Minimum estimated free energy [?]: -22.2

Hairpin loop features Number of hairpin loops [?]: 56 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.84 Minimum number of free bases in hairpin loop [?]: 0 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 [?]: 0.69 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 52 Maximum number of free bases in internal loops: 22 Average number of free bases in internal loops: 3.46 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 21 Average internal loop absolute asymmetry: 1.58 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 22 Average internal loop relative asymmetry: 1.83 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 19 Maximum number of free bases in multi-loops: 37 Average number of free bases in multi-loops: 4.75 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 37 Average multi-loop absolute asymmetry: 4.2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 18.5 Average multi-loop relative asymmetry: 1.47 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 4.26 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 66 Total number of AA non-canonical base pairs: 5 Total number of AC non-canonical base pairs: 6 Total number of AG non-canonical base pairs: 40 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 7 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 2

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 13 Number of base pairs in bands: 118 Maximum band length: 34 Average band length: 9.08 Minimum band length: 2 Maximum number of bands per pseudoknot: 6 Average number of bands per pseudoknot: 3.25 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 5 Average number of un-bands: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 8 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 137 Average number of unpaired bases: 50 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: 13 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 3.25 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: 2 Average number of bands to remove, per pseudoknot: 1.25 Minimum number of bands to remove, per pseudoknot: 1

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