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

General features for molecule PDB_01038 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01038 Molecule name [?]: ASITE RNA + DESIGNER ANTIBIOTIC Source [?]: RCSB Protein Data Bank Source ID [?]: 2F4U Reference [?]: J.B.MURRAY,S.O.MEROUEH,R.J.RUSSELL,G.LENTZEN, J.HADDAD,S.MOBASHERY. INTERACTIONS OF DESIGNER ANTIBIOTICS AND THE BACTERIAL RIBOSOMAL AMINOACYL-TRNA SITE. CHEM.BIOL. V. 13 129 2006 ASTM CBOLE2 UK ISSN 1074-5521 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SYNTHETIC Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.60 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_01028, PDB_01029, PDB_01030, PDB_01031, PDB_01032, PDB_01036, PDB_01063, PDB_01171, PDB_01207 Number of domains [?]: 1 Number of unpaired bases [?]: 8 Number of paired bases [?]: 34

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 17 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5.67 Minimum length of a stem [?]: 3 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 [?]: 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 Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 4 Average number of free bases in internal loops: 3.5 Minimum number of free bases in internal loop: 3 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of AA non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 1

Pseudoknot features

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