RNA STRAND molecule page

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

General features for molecule PDB_00104
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00104
Molecule name [?]:	CRYSTAL STRUCTURE OF AN RNA DUPLEX WITH URIDINE BULGES
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1J9H
Reference [?]:	Y.XIONG,J.DENG,C.SUDARSANAKUMAR,M.SUNDARALINGAM. CRYSTAL STRUCTURE OF AN RNA DUPLEX R(GUGUCGCAC)(2) WITH URIDINE BULGES.. J.MOL.BIOL. V. 313 573 2001 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 [?]:	X-RAY, RESOLUTION 1.40 ANGSTROMS; ran through RNAview
Number of molecules [?]:	4
Length [?]:	36
Fragments used [?]:	No
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	2
Number of unpaired bases [?]:	4
Number of paired bases [?]:	32

Click on any header below for additional features.

Stem features

Number of stems [?]:	6
Number of base pairs in stems [?]:	16
Maximum length of a stem [?]:	3
Average length of a stem [?]:	2.67
Minimum length of a stem [?]:	2
Maximum estimated free energy [?]:	-2.4
Average estimated free energy [?]:	-3.67
Minimum estimated free energy [?]:	-4.3

Hairpin loop features

Number of hairpin loops [?]:	2
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 [?]:	4
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 [?]:

Pseudoknot features