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

General features for molecule PDB_01225 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01225 Molecule name [?]: CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH GENTAMICIN. THIS F Source [?]: RCSB Protein Data Bank Source ID [?]: 2QBA Reference [?]: M.A.BOROVINSKAYA,R.D.PAI,W.ZHANG,B.S.SCHUWIRTH, J.M.HOLTON,G.HIROKAWA,H.KAJI,A.KAJI,J.H.CATE. STRUCTURAL BASIS FOR AMINOGLYCOSIDE INHIBITION OF BACTERIAL RIBOSOME RECYCLING.. NAT.STRUCT.MOL.BIOL. V. 14 727 2007 US ISSN 1545-9993 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: ESCHERICHIA COLI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.54 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2958 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00792, PDB_00794, PDB_00934, PDB_00936, PDB_01121, PDB_01123, PDB_01221, PDB_01223, PDB_01227, PDB_01229, PDB_01231, PDB_01233, PDB_01235, PDB_01242, PDB_01244, PDB_01246, PDB_01248, PDB_01283, PDB_01285 Number of domains [?]: 2 Number of unpaired bases [?]: 952 Number of paired bases [?]: 2006

Click on any header below for additional features.

Stem features Number of stems [?]: 145 Number of base pairs in stems [?]: 763 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.27 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.39 Minimum estimated free energy [?]: -21.1

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 11 Average number of free bases in hairpin loops [?]: 4.81 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 44 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 26 Maximum number of free bases in internal loops: 5 Average number of free bases in internal loops: 1.81 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.69 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.54 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.08 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.26 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.26 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.75 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 122 Total number of AA non-canonical base pairs: 20 Total number of AC non-canonical base pairs: 5 Total number of AG non-canonical base pairs: 76 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 5 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 10

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 22 Number of base pairs in bands: 240 Maximum band length: 40 Average band length: 10.91 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.67 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.33 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 4.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 248 Average number of unpaired bases: 54.5 Minimum number of unpaired bases: 8 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 27 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 4.5 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 9 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.5 Minimum number of bands to remove, per pseudoknot: 1