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

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



General features for molecule PDB_00178
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00178
Molecule name [?]:THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT W
Source [?]:RCSB Protein Data Bank
Source ID [?]:1O15
Reference [?]:G.M.CLORE,J.KUSZEWSKI. IMPROVING THE ACCURACY OF NMR STRUCTURES OF RNA BY MEANS OF CONFORMATIONAL DATABASE POTENTIALS OF MEAN FORCE AS ASSESSED BY COMPLETE DIPOLAR COUPLING CROSS-VALIDATION. J.AM.CHEM.SOC. V. 125 1518 2003 ASTM JACSAT US ISSN 0002-7863
Type [?]:Synthetic RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:SYNTHETIC
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:NMR; ran through RNAview
Number of molecules [?]:1
Length [?]:33
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00359
Number of domains [?]:1
Number of unpaired bases [?]:11
Number of paired bases [?]:22

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:11
Maximum length of a stem [?]:5
Average length of a stem [?]:3.67
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-3.3
Average estimated free energy [?]:-5.47
Minimum estimated free energy [?]:-6.7

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:2
Average number of free bases in hairpin loops [?]:2
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 [?]:2
Maximum number of free bases in internal loops:4
Average number of free bases in internal loops:2.25
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.5
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:2.5
Minimum internal loop relative asymmetry:1

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



    [ 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