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

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General features for molecule PDB_00174
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00174
Molecule name [?]:HIV-1 DIS(MAL) DUPLEX ZN-SOAKED
Source [?]:RCSB Protein Data Bank
Source ID [?]:1NLC
Reference [?]:E.ENNIFAR,P.WALTER,P.DUMAS. A CRYSTALLOGRAPHIC STUDY OF THE BINDING OF 13 METAL IONS TO TWO RELATED RNA DUPLEXES.. NUCLEIC ACIDS RES. V. 31 2671 2003 ASTM NARHAD UK ISSN 0305-1048
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 1.85 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:46
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00179, PDB_00803, PDB_00818, PDB_00834, PDB_00835, PDB_00836, PDB_00837, PDB_00838, PDB_00839, PDB_00951, PDB_00272
Number of domains [?]:1
Number of unpaired bases [?]:2
Number of paired bases [?]:44

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:22
Maximum length of a stem [?]:8
Average length of a stem [?]:7.33
Minimum length of a stem [?]:7
Maximum estimated free energy [?]:-12
Average estimated free energy [?]:-12.47
Minimum estimated free energy [?]:-12.7

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 [?]:2
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 [?]: 2
Total number of AG non-canonical base pairs:2

Pseudoknot features



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