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

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General features for molecule PDB_00134
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00134
Molecule name [?]:PEMV-1 P1-P2 FRAMESHIFTING PSEUDOKNOT, 15 LOWEST ENERGY STRUCTURES
Source [?]:RCSB Protein Data Bank
Source ID [?]:1KPY
Reference [?]:P.L.NIXON,A.RANGAN,Y-.G.KIM,A.RICH,D.W.HOFFMAN, M.HENNIG,D.P.GIEDROC. SOLUTION STRUCTURE OF A LUTEOVIRAL P1-P2 FRAMESHIFTING MRNA PSEUDOKNOT. J.MOL.BIOL. V. 322 621 2002 ASTM JMOBAK UK ISSN 0022-2836
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 [?]:28
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00135
Number of domains [?]:1
Number of unpaired bases [?]:12
Number of paired bases [?]:16

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:2
Number of base pairs in bands:8
Maximum band length:5
Average band length:4
Minimum band length:3
Maximum number of bands per pseudoknot:2
Average number of bands per pseudoknot:2
Minimum number of bands per pseudoknot:2
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:11
Average number of unpaired bases:11
Minimum number of unpaired bases:11
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:3
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:3
Minimum number of base pairs to remove, per pseudoknot:3
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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