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

General features for molecule PDB_01133 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01133 Molecule name [?]: SOLUTION STRUCTURE OF THE APICAL STEM-LOOP OF THE HUMAN HEPATITIS B VIRUS ENCAPSIDATION SIGNAL Source [?]: RCSB Protein Data Bank Source ID [?]: 2IXY Reference [?]: S.FLODELL,M.PETERSEN,F.GIRARD,J.ZDUNEK, K.KIDD-LJUNGGREN,J.SCHLEUCHER,S.WIJMENGA. SOLUTION STRUCTURE OF THE APICAL STEM-LOOP OF THE HUMAN HEPATITIS B VIRUS ENCAPSIDATION SIGNAL.. NUCLEIC ACIDS RES. V. 34 4449 2006 ASTM NARHAD UK ISSN 0305-1048 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 [?]: 27 Fragments used [?]: Yes 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 [?]: 20

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 10 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -9.9 Average estimated free energy [?]: -9.95 Minimum estimated free energy [?]: -10

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 6 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 6

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

Multi-loop features

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

Pseudoknot features