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

General features for molecule PDB_01077 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01077 Molecule name [?]: THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME Source [?]: RCSB Protein Data Bank Source ID [?]: 2GOZ Reference [?]: M.MARTICK,W.G.SCOTT. TERTIARY CONTACTS DISTANT FROM THE ACTIVE SITE PRIME A RIBOZYME FOR CATALYSIS.. CELL V. 126 309 2006 ASTM CELLB5 US ISSN 0092-8674 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 2.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 63 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01181 Number of domains [?]: 1 Number of unpaired bases [?]: 25 Number of paired bases [?]: 38

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 19 Maximum length of a stem [?]: 6 Average length of a stem [?]: 3.8 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.52 Minimum estimated free energy [?]: -11.3

Hairpin loop features Number of hairpin loops [?]: 2 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 [?]: 8

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 1 Minimum number of free bases in bulge loop [?]: 0

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

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 7 Average number of free bases in multi-loops: 3.67 Minimum number of free bases in multi-loop: 1 Maximum multi-loop absolute asymmetry: 6 Average multi-loop absolute asymmetry: 4 Minimum multi-loop absolute asymmetry: 2 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 2.21 Minimum multi-loop relative asymmetry: 0.14 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 [?]: 1 Total number of CU non-canonical base pairs: 1

Pseudoknot features

For questions, comments, suggestions and bug reports, please contact:

Copyright © 2004-2008 BETA LAB - University of British Columbia