RNA STRAND molecule page

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

General features for molecule PDB_00111
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00111
Molecule name [?]:	STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING SIGNAL
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1JTW
Reference [?]:	D.J.KERWOOD,M.J.CAVALUZZI,P.N.BORER. STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING SIGNAL.. BIOCHEMISTRY V. 40 14518 2001 ASTM BICHAW US ISSN 0006-2960
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 [?]:	16
Fragments used [?]:	No
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	1
Number of unpaired bases [?]:	4
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 [?]:	-5
Average estimated free energy [?]:	-5
Minimum estimated free energy [?]:	-5

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