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

General features for molecule PDB_01075 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01075 Molecule name [?]: LINEAR DIMER OF STEMLOOP SL1 FROM HIV-1 Source [?]: RCSB Protein Data Bank Source ID [?]: 2GM0 Reference [?]: N.B.ULYANOV,A.MUJEEB,Z.DU,M.TONELLI,T.G.PARSLOW, T.L.JAMES. NMR STRUCTURE OF THE FULL-LENGTH LINEAR DIMER OF STEM-LOOP-1 RNA IN THE HIV-1 DIMER INITIATION SITE.. J.BIOL.CHEM. V. 281 16168 2006 ASTM JBCHA3 US ISSN 0021-9258 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 [?]: 70 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 6 Number of paired bases [?]: 64

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 32 Maximum length of a stem [?]: 8 Average length of a stem [?]: 6.4 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -7 Average estimated free energy [?]: -10.6 Minimum estimated free energy [?]: -15

Hairpin loop features Number of hairpin loops [?]: 1 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 [?]: 4 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 0.75 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 [?]: 4 Total number of AA non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features