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

General features for molecule PDB_01186 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01186 Molecule name [?]: HIV-1 SUBTYPE B DIS RNA EXTENDED DUPLEX AUCL3 SOAKED Source [?]: RCSB Protein Data Bank Source ID [?]: 2OIJ 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 2.31 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_01188, PDB_01189 Number of domains [?]: 1 Number of unpaired bases [?]: 10 Number of paired bases [?]: 36

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 18 Maximum length of a stem [?]: 6 Average length of a stem [?]: 6 Minimum length of a stem [?]: 6 Maximum estimated free energy [?]: -10.6 Average estimated free energy [?]: -12.07 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: 3 Average number of free bases in internal loops: 2.5 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features

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

Pseudoknot features

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