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

General features for molecule PDB_00340 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00340 Molecule name [?]: MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER Source [?]: RCSB Protein Data Bank Source ID [?]: 1DDY Reference [?]: D.SUSSMAN,J.C.NIX,C.WILSON. THE STRUCTURAL BASIS FOR MOLECULAR RECOGNITION BY THE VITAMIN B 12 RNA APTAMER.. NAT.STRUCT.BIOL. V. 7 53 2000 ASTM NSBIEW US ISSN 1072-8368 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 3.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 140 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 100 Number of paired bases [?]: 40

Click on any header below for additional features.

Stem features

Hairpin loop features Number of hairpin loops [?]: 0 Maximum number of free bases in hairpin loops [?]: N/A Average number of free bases in hairpin loops [?]: N/A Minimum number of free bases in hairpin loop [?]: N/A

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

Multi-loop features

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

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 20 Maximum band length: 3 Average band length: 2.5 Minimum band length: 2 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 0 Average number of un-bands: 0 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 17 Average number of unpaired bases: 17 Minimum number of unpaired bases: 17 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 8 Maximum number of base pairs to remove, per pseudoknot: 2 Average number of base pairs to remove, per pseudoknot: 2 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1

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