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

General features for molecule PDB_00609 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00609 Molecule name [?]: CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS Source [?]: RCSB Protein Data Bank Source ID [?]: 1NKW Reference [?]: J.M.HARMS,F.SCHLUENZEN,R.ZARIVACH,A.BASHAN,S.GAT, I.AGMON,H.BARTELS,F.FRANCESCHI,A.YONATH. HIGH RESOLUTION STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM A MESOPHILIC EUBACTERIUM. CELL (CAMBRIDGE,MASS.) V. 107 679 2001 ASTM CELLB5 US ISSN 0092-8674 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 3.10 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2884 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00615, PDB_00616, PDB_00719, PDB_00808, PDB_00833 Number of domains [?]: 2 Number of unpaired bases [?]: 1304 Number of paired bases [?]: 1580

Click on any header below for additional features.

Stem features Number of stems [?]: 147 Number of base pairs in stems [?]: 598 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.07 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.47 Minimum estimated free energy [?]: -20

Hairpin loop features Number of hairpin loops [?]: 59 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.76 Minimum number of free bases in hairpin loop [?]: 0

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 [?]: 0.71 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 48 Maximum number of free bases in internal loops: 11 Average number of free bases in internal loops: 2.94 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 0.96 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.42 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 15 Average number of free bases in multi-loops: 3.67 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 3.06 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.15 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.81 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 54 Total number of AA non-canonical base pairs: 5 Total number of AC non-canonical base pairs: 7 Total number of AG non-canonical base pairs: 32 Total number of CU non-canonical base pairs: 6 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 192 Maximum band length: 31 Average band length: 10.67 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.6 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.8 Minimum number of un-bands: 0 Maximum number of in-bands: 22 Average number of in-bands: 4.8 Minimum number of in-bands: 0 Maximum number of unpaired bases: 324 Average number of unpaired bases: 84.2 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: 22 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 4.4 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 7 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.4 Minimum number of bands to remove, per pseudoknot: 1

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