RNA STRAND molecule page

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

General features for molecule PDB_00170
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00170
Molecule name [?]:	SOLUTION STRUCTURE OF HIV-1 STEM LOOP SL1
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1N8X
Reference [?]:	D.C.LAWRENCE,C.C.STOVER,J.NOZNITSKY,Z.WU, M.F.SUMMERS. STRUCTURE OF THE INTACT STEM AND BULGE OF HIV-1 PSI-RNA STEM-LOOP SL1. J.MOL.BIOL. V. 326 529 2003 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 [?]:	36
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 [?]:	32

Click on any header below for additional features.

Stem features

Number of stems [?]:	2
Number of base pairs in stems [?]:	16
Maximum length of a stem [?]:	9
Average length of a stem [?]:	8
Minimum length of a stem [?]:	7
Maximum estimated free energy [?]:	-12
Average estimated free energy [?]:	-13.4
Minimum estimated free energy [?]:	-14.8

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 [?]:	1
Maximum number of free bases in bulge loops [?]:	2
Average number of free bases in bulge loops [?]:	1
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