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

General features for molecule PDB_00272 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00272 Molecule name [?]: CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE Source [?]: RCSB Protein Data Bank Source ID [?]: 462D Reference [?]: E.ENNIFAR,M.YUSUPOV,P.WALTER,R.MARQUET,B.EHRESMANN, C.EHRESMANN,P.DUMAS. THE CRYSTAL STRUCTURE OF THE DIMERIZATION INITIATION SITE OF GENOMIC HIV-1 RNA REVEALS AN EXTENDED DUPLEX WITH TWO ADENINE BULGES.. STRUCTURE FOLD.DES. V. 7 1439 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 [?]: X-RAY, RESOLUTION 2.30 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 46 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00174, PDB_00179, PDB_00803, PDB_00818, PDB_00834, PDB_00835, PDB_00836, PDB_00837, PDB_00838, PDB_00839, PDB_00951 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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