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

General features for molecule PDB_00488 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00488 Molecule name [?]: FULLY REFINED CRYSTAL STRUCTURE OF THE HALOARCULA MARISMORTUI LARGE RIBOSOMAL SUBUNIT AT 2.4 ANGSTRO Source [?]: RCSB Protein Data Bank Source ID [?]: 1JJ2 Reference [?]: D.J.KLEIN,T.M.SCHMEING,P.B.MOORE,T.A.STEITZ. THE KINK-TURN: A NEW RNA SECONDARY STRUCTURE MOTIF.. EMBO J. V. 20 4214 2001 ASTM EMJODG UK ISSN 0261-4189 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 2.40 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2876 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00510, PDB_00511, PDB_00514, PDB_00518, PDB_00554, PDB_00595, PDB_00604, PDB_00797 Number of domains [?]: 3 Number of unpaired bases [?]: 938 Number of paired bases [?]: 1938

Click on any header below for additional features.

Stem features Number of stems [?]: 142 Number of base pairs in stems [?]: 734 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.17 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.5 Minimum estimated free energy [?]: -25.2

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 4.24 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 42 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.74 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: 6 Average number of free bases in internal loops: 2.31 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1.22 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.78 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.16 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.13 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.24 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.73 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 136 Total number of AA non-canonical base pairs: 18 Total number of AC non-canonical base pairs: 18 Total number of AG non-canonical base pairs: 67 Total number of CC non-canonical base pairs: 13 Total number of CU non-canonical base pairs: 9 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 10

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 22 Number of base pairs in bands: 235 Maximum band length: 38 Average band length: 10.68 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.67 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: 231 Average number of unpaired bases: 52.83 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: 27 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 4.5 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 9 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.5 Minimum number of bands to remove, per pseudoknot: 1

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