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

General features for molecule PDB_01028 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01028 Molecule name [?]: COMPLEX BETWEEN LIVIDOMYCIN A AND THE 16S-RRNA A SITE Source [?]: RCSB Protein Data Bank Source ID [?]: 2ESJ Reference [?]: B.FRANCOIS,R.J.M.RUSSEL,J.B.MURRAY,F.ABOUL-ELA, B.MASQUIDA,Q.VICENS,E.WESTHOF. CRYSTAL STRUCTURES OF COMPLEXES BETWEEN AMINOGLYCOSIDES AND DECODING A SITE OLIGONUCLEOTIDES: ROLE OF THE NUMBER OF RINGS AND POSITIVE CHARGES IN THE SPECIFIC BINDING LEADING TO MISCODING. NUCLEIC ACIDS RES. V. 33 5677 2005 ASTM NARHAD UK ISSN 0305-1048 Type [?]: Other RNA [?]     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 2.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 42 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00479, PDB_00543, PDB_00166, PDB_00624, PDB_00958, PDB_00959, PDB_01029, PDB_01030, PDB_01031, PDB_01032, PDB_01036, PDB_01038, PDB_01063, PDB_01171, PDB_01207 Number of domains [?]: 1 Number of unpaired bases [?]: 6 Number of paired bases [?]: 36

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 18 Maximum length of a stem [?]: 8 Average length of a stem [?]: 6 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -5.8 Average estimated free energy [?]: -9.73 Minimum estimated free energy [?]: -17.6

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 [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

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

Pseudoknot features

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