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

General features for molecule PDB_00618 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00618 Molecule name [?]: CROSSLINKED HAMMERHEAD RIBOZYME INITIAL STATE Source [?]: RCSB Protein Data Bank Source ID [?]: 1NYI Reference [?]: C.M.DUNHAM,J.B.MURRAY,W.G.SCOTT. A HELICAL TWIST-INDUCED CONFORMATIONAL SWITCH ACTIVATES CLEAVAGE IN THE HAMMERHEAD RIBOZYME.. J.MOL.BIOL. V. 332 327 2003 ASTM JMOBAK UK ISSN 0022-2836 Type [?]: Hammerhead Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: N/A Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.85 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 40 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 6 Number of paired bases [?]: 34

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 17 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5.67 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -6.7 Average estimated free energy [?]: -7.73 Minimum estimated free energy [?]: -9.8

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 2 Average number of free bases in hairpin loops [?]: 1.5 Minimum number of free bases in hairpin loop [?]: 1

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

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 3 Average number of free bases in multi-loops: 1 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 3 Average multi-loop absolute asymmetry: 2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 0 Average multi-loop relative asymmetry: 0 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 [?]: 4 Total number of AG non-canonical base pairs: 3 Total number of CC non-canonical base pairs: 1

Pseudoknot features

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