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

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General features for molecule PDB_00185
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00185
Molecule name [?]:SOLUTION STRUCTURE OF HCV IRES DOMAIN II
Source [?]:RCSB Protein Data Bank
Source ID [?]:1P5O
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_00186
Number of domains [?]:1
Number of unpaired bases [?]:21
Number of paired bases [?]:56

Click on any header below for additional features.

Stem features

Number of stems [?]:6
Number of base pairs in stems [?]:28
Maximum length of a stem [?]:8
Average length of a stem [?]:4.67
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.78
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 [?]:3
Maximum number of free bases in bulge loops [?]:5
Average number of free bases in bulge loops [?]:1.17
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:1.75
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.5
Minimum internal loop absolute asymmetry:0
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 [?]: 3
Total number of AG non-canonical base pairs:2
Total number of CU non-canonical base pairs:1

Pseudoknot features



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