RNA STRAND molecule page

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

General features for molecule PDB_00337
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00337
Molecule name [?]:	SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1D0U
Reference [?]:	J.S.SMITH,E.P.NIKONOWICZ. PHOSPHOROTHIOATE SUBSTITUTION CAN SUBSTANTIALLY ALTER RNA CONFORMATION.. BIOCHEMISTRY V. 39 5642 2000 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 [?]:	21
Fragments used [?]:	No
Duplicated sequence [?]:	Molecules in the database with the same sequence: PDB_00035
Number of domains [?]:	1
Number of unpaired bases [?]:	3
Number of paired bases [?]:	18

Click on any header below for additional features.

Stem features

Number of stems [?]:	2
Number of base pairs in stems [?]:	9
Maximum length of a stem [?]:	6
Average length of a stem [?]:	4.5
Minimum length of a stem [?]:	3
Maximum estimated free energy [?]:	-3.3
Average estimated free energy [?]:	-6.4
Minimum estimated free energy [?]:	-9.5

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

Pseudoknot features