RNA STRAND molecule page

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

General features for molecule PDB_01337
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_01337
Molecule name [?]:	MS2 PROTEIN CAPSID/RNA COMPLEX
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	5MSF
Reference [?]:	S.ROWSELL,N.J.STONEHOUSE,M.A.CONVERY,C.J.ADAMS, A.D.ELLINGTON,I.HIRAO,D.S.PEABODY,P.G.STOCKLEY, S.E.PHILLIPS. CRYSTAL STRUCTURES OF A SERIES OF RNA APTAMERS COMPLEXED TO THE SAME PROTEIN TARGET.. NAT.STRUCT.BIOL. V. 5 970 1998 ASTM NSBIEW US ISSN 1072-8368
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 2.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:	2
Length [?]:	34
Fragments used [?]:	Yes
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	2
Number of unpaired bases [?]:	12
Number of paired bases [?]:	22

Click on any header below for additional features.

Stem features

Number of stems [?]:	4
Number of base pairs in stems [?]:	11
Maximum length of a stem [?]:	4
Average length of a stem [?]:	2.75
Minimum length of a stem [?]:	2
Maximum estimated free energy [?]:	-2.4
Average estimated free energy [?]:	-3.67
Minimum estimated free energy [?]:	-5.7

Hairpin loop features

Number of hairpin loops [?]:	2
Maximum number of free bases in hairpin loops [?]:	4
Average number of free bases in hairpin loops [?]:	4
Minimum number of free bases in hairpin loop [?]:	4

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:	2

Pseudoknot features