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

    [ Home | Search | Analyse | Submit structures | News | Help ]



General features for molecule PDB_00856
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00856
Molecule name [?]:CRYSTAL STRUCTURE OF SELENIUM-MODIFIED DIELS-ALDER RIBOZYME COMPLEXED WITH THE PRODUCT OF THE REACTI
Source [?]:RCSB Protein Data Bank
Source ID [?]:1YLS
Reference [?]:A.SERGANOV,S.KEIPER,L.MALININA,V.TERESHKO, E.SKRIPKIN,C.HOBARTNER,A.POLONSKAIA,A.T.PHAN, R.WOMBACHER,R.MICURA,Z.DAUTER,A.JASCHKE,D.J.PATEL. STRUCTURAL BASIS FOR DIELS-ALDER RIBOZYME-CATALYZED CARBON-CARBON BOND FORMATION.. NAT.STRUCT.MOL.BIOL. V. 12 218 2005 US ISSN 1545-9993
Type [?]:Other 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 3.00 ANGSTROMS; ran through RNAview
Number of molecules [?]:4
Length [?]:98
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:2
Number of unpaired bases [?]:14
Number of paired bases [?]:84

Click on any header below for additional features.

Stem features

Number of stems [?]:4
Number of base pairs in stems [?]:26
Maximum length of a stem [?]:7
Average length of a stem [?]:6.5
Minimum length of a stem [?]:6
Maximum estimated free energy [?]:-10
Average estimated free energy [?]:-13.45
Minimum estimated free energy [?]:-16.9

Hairpin loop features

Number of hairpin loops [?]:4
Maximum number of free bases in hairpin loops [?]:2
Average number of free bases in hairpin loops [?]:1
Minimum number of free bases in hairpin loop [?]:0

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

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 2
Total number of AG non-canonical base pairs:2

Pseudoknot features
Number of pseudoknots [?]:2
Number of bands:6
Number of base pairs in bands:16
Maximum band length:4
Average band length:2.67
Minimum band length:2
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:3
Minimum number of bands per pseudoknot:3
Maximum number of un-bands:2
Average number of un-bands:2
Minimum number of un-bands:2
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:5
Average number of unpaired bases:5
Minimum number of unpaired bases:5
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:8
Maximum number of base pairs to remove, per pseudoknot:4
Average number of base pairs to remove, per pseudoknot:4
Minimum number of base pairs to remove, per pseudoknot:4
Minimum number of bands to remove, per molecule:4
Maximum number of bands to remove, per pseudoknot:2
Average number of bands to remove, per pseudoknot:2
Minimum number of bands to remove, per pseudoknot:2



    [ Home | Search | Analyse | Submit structures | News | Help ]

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

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