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

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General features for molecule PDB_00828
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00828
Molecule name [?]:A-RIBOSWITCH-ADENINE COMPLEX
Source [?]:RCSB Protein Data Bank
Source ID [?]:1Y26
Reference [?]:A.SERGANOV,Y.R.YUAN,O.PIKOVSKAYA,A.POLONSKAIA, L.MALININA,A.T.PHAN,C.HOBARTNER,R.MICURA, R.R.BREAKER,D.J.PATEL. STRUCTURAL BASIS FOR DISCRIMINATIVE REGULATION OF GENE EXPRESSION BY ADENINE- AND GUANINE-SENSING MRNAS. CHEM.BIOL. V. 11 1729 2004 ASTM CBOLE2 UK ISSN 1074-5521
Type [?]:Other RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:VIBRIO VULNIFICUS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.10 ANGSTROMS; ran through RNAview
Number of molecules [?]:1
Length [?]:71
Fragments used [?]:Yes
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:17
Number of paired bases [?]:54

Click on any header below for additional features.

Stem features

Number of stems [?]:1
Number of base pairs in stems [?]:9
Maximum length of a stem [?]:9
Average length of a stem [?]:9
Minimum length of a stem [?]:9
Maximum estimated free energy [?]:-13.8
Average estimated free energy [?]:-13.8
Minimum estimated free energy [?]:-13.8

Hairpin loop features

Number of hairpin loops [?]:0
Maximum number of free bases in hairpin loops [?]:N/A
Average number of free bases in hairpin loops [?]:N/A
Minimum number of free bases in hairpin loop [?]:N/A

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 [?]:1
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:2.5
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:3
Number of base pairs in bands:18
Maximum band length:7
Average band length:6
Minimum band length:5
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:0
Average number of un-bands:0
Minimum number of un-bands:0
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:12
Average number of unpaired bases:12
Minimum number of unpaired bases:12
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:5
Maximum number of base pairs to remove, per pseudoknot:5
Average number of base pairs to remove, per pseudoknot:5
Minimum number of base pairs to remove, per pseudoknot:5
Minimum number of bands to remove, per molecule:1
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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