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

General features for molecule PDB_00079 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00079 Molecule name [?]: A PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAHYMENA RIBOZYME Source [?]: RCSB Protein Data Bank Source ID [?]: 1GRZ Reference [?]: B.L.GOLDEN,A.R.GOODING,E.R.PODELL,T.R.CECH. A PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAHYMENA RIBOZYME.. SCIENCE V. 282 259 1998 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Other Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: TETRAHYMENA THERMOPHILA Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 5.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 494 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 210 Number of paired bases [?]: 284

Click on any header below for additional features.

Stem features Number of stems [?]: 26 Number of base pairs in stems [?]: 115 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.42 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -5.73 Minimum estimated free energy [?]: -13.6

Hairpin loop features Number of hairpin loops [?]: 10 Maximum number of free bases in hairpin loops [?]: 8 Average number of free bases in hairpin loops [?]: 4 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 5 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 9 Maximum number of free bases in internal loops: 8 Average number of free bases in internal loops: 2.89 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 5 Average internal loop absolute asymmetry: 1.56 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 6 Average internal loop relative asymmetry: 1.67 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 17 Average number of free bases in multi-loops: 5.67 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 17 Average multi-loop absolute asymmetry: 6.33 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 2 Average multi-loop relative asymmetry: 0.88 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 3 Average number of branches in multi-loops: 3 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 19 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 3 Total number of AG non-canonical base pairs: 11 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 27 Maximum band length: 9 Average band length: 6.75 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: 3 Average number of un-bands: 3 Minimum number of un-bands: 3 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 30 Average number of unpaired bases: 29.5 Minimum number of unpaired bases: 29 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 7 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: 2 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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