RNA STRAND molecule page

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

General features for molecule PDB_00034
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00034
Molecule name [?]:	CRYSTAL STRUCTURE OF THE RRE HIGH AFFINITY SITE
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1CSL
Reference [?]:	J.A.IPPOLITO,T.A.STEITZ. THE STRUCTURE OF THE HIV-1 RRE HIGH AFFINITY REV BINDING SITE AT 1.6 A RESOLUTION.. J.MOL.BIOL. V. 295 711 2000 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 [?]:	X-RAY, RESOLUTION 1.60 ANGSTROMS; ran through RNAview
Number of molecules [?]:	2
Length [?]:	28
Fragments used [?]:	Yes
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 [?]:	24

Click on any header below for additional features.

Stem features

Number of stems [?]:	3
Number of base pairs in stems [?]:	12
Maximum length of a stem [?]:	5
Average length of a stem [?]:	4
Minimum length of a stem [?]:	3
Maximum estimated free energy [?]:	-2.4
Average estimated free energy [?]:	-4.83
Minimum estimated free energy [?]:	-6.6

Hairpin loop features

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

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