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

General features for molecule PDB_01158 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01158 Molecule name [?]: CRYSTAL STRUCTURE OF A JUNCTIONED HAIRPIN RIBOZYME INCORPORATING 9ATOM LINKER AND 2'-DEOXY 2'-AMINO Source [?]: RCSB Protein Data Bank Source ID [?]: 2NPY Reference [?]: C.MACELREVEY,R.C.SPITALE,J.KRUCINSKA,J.E.WEDEKIND. A POSTERIORI DESIGN OF CRYSTAL CONTACTS TO IMPROVE THE X-RAY DIFFRACTION PROPERTIES OF A SMALL RNA ENZYME.. ACTA CRYSTALLOGR.,SECT.D V. 63 812 2007 ASTM ABCRE6 DK ISSN 0907-4449 Type [?]: Hairpin Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: N/A Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.65 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 61 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 11 Number of paired bases [?]: 50

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 25 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.32 Minimum estimated free energy [?]: -10.9

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 0 Average number of free bases in hairpin loops [?]: 0 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 2.25 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 0.5 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 [?]: 5 Total number of AA non-canonical base pairs: 1 Total number of AC non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features