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

General features for molecule PDB_00149 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00149 Molecule name [?]: STRUCTURE OF WILD-TYPE AND MUTANT INTERNAL LOOPS FROM THE SL-1 DOMAIN OF THE HIV-1 PACKAGING SIGNAL Source [?]: RCSB Protein Data Bank Source ID [?]: 1M5L Reference [?]: J.GREATOREX,J.GALLEGO,G.VARANI,A.LEVER. STRUCTURE AND STABILITY OF WILD-TYPE AND MUTANT RNA INTERNAL LOOPS FROM THE SL-1 DOMAIN OF THE HIV-1 PACKAGING SIGNAL. J.MOL.BIOL. V. 322 543 2002 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 [?]: 38 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 8 Number of paired bases [?]: 30

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 15 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -6.9 Average estimated free energy [?]: -7.87 Minimum estimated free energy [?]: -9.2

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 2 Average number of free bases in hairpin loops [?]: 2 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 [?]: 2 Average number of free bases in bulge loops [?]: 1 Minimum number of free bases in bulge loop [?]: 0

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

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

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