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

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General features for molecule PDB_00181
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Format:
Molecule ID [?]:PDB_00181
Molecule name [?]:THE STEM OF SL1 RNA IN HIV-1: STRUCTURE AND NUCLEOCAPSID PROTEIN BINDING FOR A 1X3 INTERNAL LOOP
Source [?]:RCSB Protein Data Bank
Source ID [?]:1OSW
Reference [?]:Y.YUAN,D.J.KERWOOD,A.C.PAOLETTI,M.F.SHUBSDA, P.N.BORER. STEM OF SL1 RNA IN HIV-1: STRUCTURE AND NUCLEOCAPSID PROTEIN BINDING FOR A 1X3 INTERNAL LOOP. BIOCHEMISTRY V. 42 5259 2003 ASTM BICHAW US ISSN 0006-2960
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 [?]:22
Fragments used [?]:No
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 [?]:18

Click on any header below for additional features.

Stem features

Number of stems [?]:2
Number of base pairs in stems [?]:9
Maximum length of a stem [?]:5
Average length of a stem [?]:4.5
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-7.8
Average estimated free energy [?]:-7.85
Minimum estimated free energy [?]:-7.9

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 [?]:1
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 [?]: 1
Total number of AG non-canonical base pairs:1

Pseudoknot features



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