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

General features for molecule PDB_00378 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00378 Molecule name [?]: CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE Source [?]: RCSB Protein Data Bank Source ID [?]: 1F1T Reference [?]: C.BAUGH,D.GRATE,C.WILSON. 2.8 A CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER.. J.MOL.BIOL. V. 301 117 2000 ASTM JMOBAK UK ISSN 0022-2836 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 2.80 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 38 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00655 Number of domains [?]: 1 Number of unpaired bases [?]: 10 Number of paired bases [?]: 28

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 14 Maximum length of a stem [?]: 6 Average length of a stem [?]: 4.67 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.4 Average estimated free energy [?]: -8.6 Minimum estimated free energy [?]: -12.5

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 [?]: 3 Average number of free bases in bulge loops [?]: 1.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 4 Average number of free bases in internal loops: 2.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 3 Minimum internal loop absolute asymmetry: 3 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 4 Minimum internal loop relative asymmetry: 4

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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