RNA STRAND molecule page

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

General features for molecule PDB_01041
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_01041
Molecule name [?]:	SOLUTION STRUCTURE OF A GAAG TETRALOOP IN SRP RNA FROM PYROCOCCUS FURIOSUS
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	2F87
Reference [?]:	K.OKADA,M.TAKAHASHI,T.SAKAMOTO,G.KAWAI,K.NAKAMURA, A.KANAI. SOLUTION STRUCTURE OF A GAAG TETRALOOP IN HELIX 6 OF SRP RNA FROM PYROCOCCUS FURIOSUS. NUCLEOSIDES NUCLEOTIDES V. 25 383 2006 NUCLEIC ACIDS US ISSN 1525-7770
Type [?]:	Signal Recognition Particle RNA	[?] 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 [?]:	12
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 [?]:	10

Click on any header below for additional features.

Stem features

Number of stems [?]:	1
Number of base pairs in stems [?]:	5
Maximum length of a stem [?]:	5
Average length of a stem [?]:	5
Minimum length of a stem [?]:	5
Maximum estimated free energy [?]:	-8.8
Average estimated free energy [?]:	-8.8
Minimum estimated free energy [?]:	-8.8

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 GG non-canonical base pairs:	1

Pseudoknot features