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

General features for molecule PDB_01128 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01128 Molecule name [?]: SOLUTION STRUCTURE OF THE ROUS SARCOMA VIRUS NUCLEOCAPSID PROTEIN:UPSI RNA PACKAGING SIGNAL COMPLEX Source [?]: RCSB Protein Data Bank Source ID [?]: 2IHX Reference [?]: J.ZHOU,R.L.BEAN,V.M.VOGT,M.SUMMERS. SOLUTION STRUCTURE OF THE ROUS SARCOMA VIRUS NUCLEOCAPSID PROTEIN: MUPSI RNA PACKAGING SIGNAL COMPLEX.. J.MOL.BIOL. V. 365 453 2007 ASTM JMOBAK UK ISSN 0022-2836 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 [?]: 75 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 21 Number of paired bases [?]: 54

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 27 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5.4 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -7 Average estimated free energy [?]: -10.24 Minimum estimated free energy [?]: -18.7

Hairpin loop features Number of hairpin loops [?]: 3 Maximum number of free bases in hairpin loops [?]: 5 Average number of free bases in hairpin loops [?]: 3.33 Minimum number of free bases in hairpin loop [?]: 2

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 Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 4 Average number of free bases in multi-loops: 2.5 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 4 Average multi-loop absolute asymmetry: 2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1.33 Average multi-loop relative asymmetry: 0.69 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 4 Minimum number of branches in multi-loops: 4

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

Pseudoknot features