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

General features for molecule PDB_00629 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00629 Molecule name [?]: CRYSTAL STRUCTURE OF NF-KB(P50)2 COMPLEXED TO A HIGH- AFFINITY RNA APTAMER Source [?]: RCSB Protein Data Bank Source ID [?]: 1OOA Reference [?]: D.B.HUANG,D.VU,L.A.CASSIDAY,J.M.ZIMMERMAN, L.J.MAHER III,G.GHOSH. CRYSTAL STRUCTURE OF NF-KAPPAB (P50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER.. PROC.NATL.ACAD.SCI.USA V. 100 9268 2003 ASTM PNASA6 US ISSN 0027-8424 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 2.45 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 58 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 12 Number of paired bases [?]: 46

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 23 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5.75 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -5.2 Average estimated free energy [?]: -5.95 Minimum estimated free energy [?]: -6.7

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 4 Average number of free bases in hairpin loops [?]: 3 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 [?]: 2 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 5 Total number of AG non-canonical base pairs: 3 Total number of CU non-canonical base pairs: 2

Pseudoknot features

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