RNA STRAND molecule page

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

General features for molecule PDB_00066
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Format:

Molecule ID [?]:	PDB_00066
Molecule name [?]:	SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIIE
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1F85
Reference [?]:	P.J.LUKAVSKY,G.A.OTTO,A.M.LANCASTER,P.SARNOW, J.D.PUGLISI. STRUCTURES OF TWO RNA DOMAINS ESSENTIAL FOR HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE FUNCTION.. NAT.STRUCT.BIOL. V. 7 1105 2000 ASTM NSBIEW US ISSN 1072-8368
Type [?]:	Internal Ribosome Entry Site	[?] PS figure PDF figure Figure from original source
Organism [?]:	N/A
Validated by NMR or X-Ray [?]:	Yes
Method for secondary structure determination [?]:	NMR; ran through RNAview
Number of molecules [?]:	1
Length [?]:	14
Fragments used [?]:	Yes
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	1
Number of unpaired bases [?]:	2
Number of paired bases [?]:	12

Click on any header below for additional features.

Stem features

Number of stems [?]:	1
Number of base pairs in stems [?]:	6
Maximum length of a stem [?]:	6
Average length of a stem [?]:	6
Minimum length of a stem [?]:	6
Maximum estimated free energy [?]:	-9.4
Average estimated free energy [?]:	-9.4
Minimum estimated free energy [?]:	-9.4

Hairpin loop features

Number of hairpin loops [?]:	1
Maximum number of free bases in hairpin loops [?]:	2
Average number of free bases in hairpin loops [?]:	2
Minimum number of free bases in hairpin loop [?]:	2

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 [?]:	1
Total number of AG non-canonical base pairs:	1

Pseudoknot features