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

General features for molecule PDB_01166 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01166 Molecule name [?]: STRUCTURAL INVESTIGATION OF THE GLMS RIBOZYME BOUND TO ITS CATALYTIC COFACTOR Source [?]: RCSB Protein Data Bank Source ID [?]: 2NZ4 Reference [?]: J.C.COCHRANE,S.V.LIPCHOCK,S.A.STROBEL. STRUCTURAL INVESTIGATION OF THE GLMS RIBOZYME BOUND TO ITS CATALYTIC COFACTOR. CHEM.BIOL. V. 14 97 2007 ASTM CBOLE2 UK ISSN 1074-5521 Type [?]: Other Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: HOMO SAPIENS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 8 Length [?]: 604 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 8 Number of unpaired bases [?]: 180 Number of paired bases [?]: 424

Click on any header below for additional features.

Stem features Number of stems [?]: 14 Number of base pairs in stems [?]: 116 Maximum length of a stem [?]: 11 Average length of a stem [?]: 8.29 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.1 Average estimated free energy [?]: -12.19 Minimum estimated free energy [?]: -21.6

Hairpin loop features Number of hairpin loops [?]: 8 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 5.62 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features Number of internal loops [?]: 6 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 2.08 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 0.83 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.17 Minimum internal loop relative asymmetry: 1

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 12 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 4 Total number of AG non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 8 Number of bands: 16 Number of base pairs in bands: 96 Maximum band length: 8 Average band length: 6 Minimum band length: 4 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: 1 Average number of un-bands: 0.5 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 19 Average number of unpaired bases: 12.13 Minimum number of unpaired bases: 4 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 44 Maximum number of base pairs to remove, per pseudoknot: 6 Average number of base pairs to remove, per pseudoknot: 5.5 Minimum number of base pairs to remove, per pseudoknot: 4 Minimum number of bands to remove, per molecule: 8 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

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