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

General features for molecule PDB_01154 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01154 Molecule name [?]: STRUCTURE OF A HIGH AFFINITY ANTI-NFKB RNA APTAMER Source [?]: RCSB Protein Data Bank Source ID [?]: 2JWV Reference [?]: N.J.REITER,L.J.MAHER III,S.E.BUTCHER. DNA MIMICRY BY A HIGH-AFFINITY ANTI-NF-{KAPPA}B RNA APTAMER. NUCLEIC ACIDS RES. 2007 ASTM NARHAD UK ESSN 1362-4962 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 [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 29 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 7 Number of paired bases [?]: 22

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 11 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5.5 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -5.2 Average estimated free energy [?]: -6.1 Minimum estimated free energy [?]: -7

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 [?]: 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 [?]: 1 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 [?]: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features