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

General features for molecule PDB_00848 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00848 Molecule name [?]: CRYSTAL STRUCTURE OF THE MUTANT 50S RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI CONTAINING A THREE R Source [?]: RCSB Protein Data Bank Source ID [?]: 1YJ9 Reference [?]: D.TU,G.BLAHA,P.B.MOORE,T.A.STEITZ. STRUCTURES OF MLSBK ANTIBIOTICS BOUND TO MUTATED LARGE RIBOSOMAL SUBUNITS PROVIDE A STRUCTURAL EXPLANATION FOR RESISTANCE.. CELL V. 121 257 2005 ISSN 0092-8674 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: HALOARCULA MARISMORTUI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.90 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2876 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00847 Number of domains [?]: 3 Number of unpaired bases [?]: 948 Number of paired bases [?]: 1928

Click on any header below for additional features.

Stem features Number of stems [?]: 144 Number of base pairs in stems [?]: 733 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.09 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.41 Minimum estimated free energy [?]: -21.2

Hairpin loop features Number of hairpin loops [?]: 59 Maximum number of free bases in hairpin loops [?]: 13 Average number of free bases in hairpin loops [?]: 4.42 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 43 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.76 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 26 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.21 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.96 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.62 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.08 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.1 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.23 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.69 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 130 Total number of AA non-canonical base pairs: 17 Total number of AC non-canonical base pairs: 15 Total number of AG non-canonical base pairs: 67 Total number of CC non-canonical base pairs: 12 Total number of CU non-canonical base pairs: 7 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 10

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 20 Number of base pairs in bands: 231 Maximum band length: 39 Average band length: 11.55 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.33 Minimum number of un-bands: 0 Maximum number of in-bands: 24 Average number of in-bands: 4.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 229 Average number of unpaired bases: 52 Minimum number of unpaired bases: 8 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 25 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 4.17 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.33 Minimum number of bands to remove, per pseudoknot: 1

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