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

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General features for molecule PDB_00988
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00988
Molecule name [?]:SOLUTION RNA STRUCTURE OF LOOP REGION OF THE HIV-1 DIMERIZATION INITIATION SITE IN THE KISSING-LOOP
Source [?]:RCSB Protein Data Bank
Source ID [?]:2D19
Reference [?]:S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI, N.YAMAMOTO,G.KAWAI. SOLUTION RNA STRUCTURES OF THE HIV-1 DIMERIZATION INITIATION SITE IN THE KISSING-LOOP AND EXTENDED-DUPLEX DIMERS.. J.BIOCHEM.(TOKYO) V. 138 583 2005 ASTM JOBIAO JA ISSN 0021-924X
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 [?]:2
Length [?]:34
Fragments used [?]:Yes
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00987
Number of domains [?]:1
Number of unpaired bases [?]:6
Number of paired bases [?]:28

Click on any header below for additional features.

Stem features


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

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:14
Maximum band length:6
Average band length:4.67
Minimum band length:4
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:6
Average number of unpaired bases:6
Minimum number of unpaired bases:6
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:6
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:6
Minimum number of base pairs to remove, per pseudoknot:6
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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