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

General features for molecule PDB_00997 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00997 Molecule name [?]: AN ALTERNATING SHEARED AA PAIR IN 5'GGUGAAGGCU/3'PCCGAAGCCG: II. THE MINOR CONFORMATION WITH A6/A5/A Source [?]: RCSB Protein Data Bank Source ID [?]: 2DD3 Reference [?]: G.CHEN,S.D.KENNEDY,J.QIAO,T.R.KRUGH,D.H.TURNER. AN ALTERNATING SHEARED AA PAIR AND ELEMENTS OF STABILITY FOR A SINGLE SHEARED PURINE-PURINE PAIR FLANKED BY SHEARED GA PAIRS IN RNA. BIOCHEMISTRY V. 45 6889 2006 ASTM BICHAW US ISSN 0006-2960 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 [?]: 2 Length [?]: 20 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00996 Number of domains [?]: 1 Number of unpaired bases [?]: 4 Number of paired bases [?]: 16

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 8 Maximum length of a stem [?]: 4 Average length of a stem [?]: 4 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -5.8 Average estimated free energy [?]: -6.25 Minimum estimated free energy [?]: -6.7

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 1 Average number of free bases in hairpin loops [?]: 1 Minimum number of free bases in hairpin loop [?]: 1

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: 1 Average number of free bases in internal loops: 1 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 0 Average internal loop absolute asymmetry: 0 Minimum internal loop absolute asymmetry: 0 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