RNA STRAND molecule page

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

General features for molecule PDB_00043
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00043
Molecule name [?]:	STRUCTURE OF RNA (5'-GGUGGGCGCAGCUUCGGCUGCGGUACCAC-3'), NMR, 5 STRUCTURES
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1EBR
Reference [?]:	R.D.PETERSON,J.FEIGON. STRUCTURAL CHANGE IN REV RESPONSIVE ELEMENT RNA OF HIV-1 ON BINDING REV PEPTIDE.. J.MOL.BIOL. V. 264 863 1996 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 [?]:	30
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 [?]:	26

Click on any header below for additional features.

Stem features

Number of stems [?]:	3
Number of base pairs in stems [?]:	13
Maximum length of a stem [?]:	5
Average length of a stem [?]:	4.33
Minimum length of a stem [?]:	3
Maximum estimated free energy [?]:	-2.4
Average estimated free energy [?]:	-6.57
Minimum estimated free energy [?]:	-9.7

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 [?]:	2
Maximum number of free bases in bulge loops [?]:	1
Average number of free bases in bulge loops [?]:	0.5
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 [?]:	2
Total number of AG non-canonical base pairs:	1
Total number of GG non-canonical base pairs:	1

Pseudoknot features