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

General features for molecule PDB_01207 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01207 Molecule name [?]: CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE COMPLEXED WITH AMINOGLYCOSIDE CONTAINING Source [?]: RCSB Protein Data Bank Source ID [?]: 2PWT Reference [?]: J.KONDO,K.PACHAMUTHU,B.FRANCOIS,J.SZYCHOWSKI, S.HANESSIAN,E.WESTHOF. CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE COMPLEXED WITH A SYNTHETIC DOUBLY FUNCTIONALIZED PAROMOMYCIN DERIVATIVE: A NEW SPECIFIC BINDING MODE TO AN A-MINOR MOTIF ENHANCES IN VITRO ANTIBACTERIAL ACTIVITY. CHEMMEDCHEM V. 2 1631 2007 DE ISSN 1860-7179 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 1.80 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_01038, PDB_01063, PDB_01171 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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