RNA STRAND molecule page

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

General features for molecule PDB_00377
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00377
Molecule name [?]:	SOLUTION STRUCTURE OF HTLV-1 PEPTIDE BOUND TO ITS RNA APTAMER TARGET
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1EXY
Reference [?]:	F.JIANG,A.GORIN,W.HU,A.MAJUMDAR,S.BASKERVILLE,W.XU, A.ELLINGTON,D.J.PATEL. ANCHORING AN EXTENDED HTLV-1 REX PEPTIDE WITHIN AN RNA MAJOR GROOVE CONTAINING JUNCTIONAL BASE TRIPLES.. STRUCTURE FOLD.DES. V. 7 1461 1999 ASTM FODEFH UK ISSN 1359-0278
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 [?]:	33
Fragments used [?]:	No
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 [?]:	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 [?]:	3
Maximum estimated free energy [?]:	-5.7
Average estimated free energy [?]:	-6.93
Minimum estimated free energy [?]:	-9.4

Hairpin loop features

Number of hairpin loops [?]:	1
Maximum number of free bases in hairpin loops [?]:	4
Average number of free bases in hairpin loops [?]:	4
Minimum number of free bases in hairpin loop [?]:	4

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