RNA STRAND molecule page

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

General features for molecule PDB_00183
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00183
Molecule name [?]:	SOLUTION STRUCTURE OF HCV IRES DOMAIN IIA
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1P5M
Reference [?]:	P.J.LUKAVSKY,I.KIM,G.A.OTTO,J.D.PUGLISI. STRUCTURE OF HCV IRES DOMAIN II DETERMINED BY NMR.. NAT.STRUCT.BIOL. V. 10 1033 2003 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 [?]:	NMR; ran through RNAview
Number of molecules [?]:	1
Length [?]:	55
Fragments used [?]:	Yes
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	1
Number of unpaired bases [?]:	9
Number of paired bases [?]:	46

Click on any header below for additional features.

Stem features

Number of stems [?]:	4
Number of base pairs in stems [?]:	23
Maximum length of a stem [?]:	10
Average length of a stem [?]:	5.75
Minimum length of a stem [?]:	4
Maximum estimated free energy [?]:	-6.7
Average estimated free energy [?]:	-8.77
Minimum estimated free energy [?]:	-10.9

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 [?]:	3
Maximum number of free bases in bulge loops [?]:	5
Average number of free bases in bulge loops [?]:	1.17
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 [?]:	3
Total number of AG non-canonical base pairs:	1
Total number of CU non-canonical base pairs:	1
Total number of UU non-canonical base pairs:	1

Pseudoknot features