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

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General features for molecule PDB_01188
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01188
Molecule name [?]:CRYSTAL STRUCTURE OF THE DUPLEX FORM OF THE HIV-1(LAI) RNA DIMERIZATION INITIATION SITE
Source [?]:RCSB Protein Data Bank
Source ID [?]:2OIY
Reference [?]:E.ENNIFAR,P.WALTER,P.DUMAS. SELF-CLEAVING ACTIVITY IN THE DUPLEX FORM OF THE HIV-1(LAI) RNA DIMERIZATION INITIATION SITE. TO BE PUBLISHED
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 1.60 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:46
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00112, PDB_00817, PDB_00950, PDB_01186, PDB_01189
Number of domains [?]:1
Number of unpaired bases [?]:6
Number of paired bases [?]:40

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:20
Maximum length of a stem [?]:7
Average length of a stem [?]:6.67
Minimum length of a stem [?]:6
Maximum estimated free energy [?]:-12
Average estimated free energy [?]:-13
Minimum estimated free energy [?]:-15

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 [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:2
Average number of free bases in internal loops:1.5
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:2
Minimum internal loop relative asymmetry:2

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features



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