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

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General features for molecule PDB_00186
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00186
Molecule name [?]:SOLUTION STRUCTURE OF HCV IRES DOMAIN II (MINIMIZED AVERAGE STRUCTURE)
Source [?]:RCSB Protein Data Bank
Source ID [?]:1P5P
Reference [?]:P.J.LUKAVSKY,I.KIM,G.A.OTTO,J.D.PUGLISI. STRUCTURE OF HCV IRES DOMAIN II DETERMINED BY NMR.. NAT.STRUCT.BIOL. V. 10 1033 2003 ASTM NSBIEW US ISSN 1072-8368
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 [?]:77
Fragments used [?]:Yes
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00185
Number of domains [?]:1
Number of unpaired bases [?]:15
Number of paired bases [?]:62

Click on any header below for additional features.

Stem features

Number of stems [?]:5
Number of base pairs in stems [?]:31
Maximum length of a stem [?]:11
Average length of a stem [?]:6.2
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-6.4
Average estimated free energy [?]:-8.26
Minimum estimated free energy [?]:-10.9

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:7
Minimum number of free bases in hairpin loop [?]:7

Bulge loop features
Number of bulge loops [?]:4
Maximum number of free bases in bulge loops [?]:5
Average number of free bases in bulge loops [?]:1
Minimum number of free bases in bulge loop [?]:0

Internal loop features

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 5
Total number of AA non-canonical base pairs:1
Total number of AG non-canonical base pairs:2
Total number of CU non-canonical base pairs:1
Total number of UU non-canonical base pairs:1

Pseudoknot features



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