RNA STRAND molecule page

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

General features for molecule PDB_00101
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00101
Molecule name [?]:	CRYSTAL STRUCTURE OF A 14MER RNA CONTAINING DOUBLE UU BULGES IN TWO CRYSTAL FORMS: A NOVEL U*(AU) IN
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1IK5
Reference [?]:	J.DENG,Y.XIONG,C.SUDARSANAKUMAR,K.SHI, M.SUNDARALINGAM. CRYSTAL STRUCTURES OF TWO FORMS OF A 14-MER RNA/DNA CHIMER DUPLEX WITH DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(A X U) BASE TRIPLE.. RNA V. 7 1425 2001 ASTM RNARFU UK ISSN 1355-8382
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 1.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:	2
Length [?]:	28
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 [?]:	24

Click on any header below for additional features.

Stem features

Number of stems [?]:	3
Number of base pairs in stems [?]:	12
Maximum length of a stem [?]:	5
Average length of a stem [?]:	4
Minimum length of a stem [?]:	2
Maximum estimated free energy [?]:	-1.4
Average estimated free energy [?]:	-5.93
Minimum estimated free energy [?]:	-8.2

Hairpin loop features

Number of hairpin loops [?]:	1
Maximum number of free bases in hairpin loops [?]:	0
Average number of free bases in hairpin loops [?]:	0
Minimum number of free bases in hairpin loop [?]:	0

Bulge loop features

Number of bulge loops [?]:	2
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 [?]:

Pseudoknot features