RNA STRAND molecule page

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

General features for molecule PDB_00257
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Format:

Molecule ID [?]:	PDB_00257
Molecule name [?]:	A 1.3 A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS- ACTIVATION RESPONSE REGION RNA STEM REVEALS
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	397D
Reference [?]:	J.A.IPPOLITO,T.A.STEITZ. A 1.3-A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS-ACTIVATION RESPONSE REGION RNA STEM REVEALS A METAL ION-DEPENDENT BULGE CONFORMATION.. PROC.NATL.ACAD.SCI.USA V. 95 9819 1998 ASTM PNASA6 US ISSN 0027-8424
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 1.30 ANGSTROMS; ran through RNAview
Number of molecules [?]:	2
Length [?]:	27
Fragments used [?]:	No
Duplicated sequence [?]:	No other molecule in the database has the same sequence
Number of domains [?]:	1
Number of unpaired bases [?]:	5
Number of paired bases [?]:	22

Click on any header below for additional features.

Stem features

Number of stems [?]:	2
Number of base pairs in stems [?]:	11
Maximum length of a stem [?]:	7
Average length of a stem [?]:	5.5
Minimum length of a stem [?]:	4
Maximum estimated free energy [?]:	-7.9
Average estimated free energy [?]:	-12.25
Minimum estimated free energy [?]:	-16.6

Hairpin loop features

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

Bulge loop features

Number of bulge loops [?]:	1
Maximum number of free bases in bulge loops [?]:	3
Average number of free bases in bulge loops [?]:	1.5
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