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

General features for molecule PDB_01284 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01284 Molecule name [?]: CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH PAROMOMYCIN AND RI Source [?]: RCSB Protein Data Bank Source ID [?]: 2Z4M 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 [?]: 16S 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 4.45 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1530 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00791, PDB_00793, PDB_00933, PDB_00935, PDB_01220, PDB_01222, PDB_01224, PDB_01226, PDB_01228, PDB_01230, PDB_01232, PDB_01234, PDB_01241, PDB_01243, PDB_01245, PDB_01247, PDB_01282 Number of domains [?]: 4 Number of unpaired bases [?]: 496 Number of paired bases [?]: 1034

Click on any header below for additional features.

Stem features Number of stems [?]: 92 Number of base pairs in stems [?]: 453 Maximum length of a stem [?]: 22 Average length of a stem [?]: 4.93 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.84 Minimum estimated free energy [?]: -23.7

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.54 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 3

Bulge loop features Number of bulge loops [?]: 32 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.7 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 20 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.23 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 0.95 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.5 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 2.8 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.11 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.18 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 67 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 8 Total number of AG non-canonical base pairs: 37 Total number of CC non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 6 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 64 Maximum band length: 32 Average band length: 8 Minimum band length: 2 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 66 Average number of unpaired bases: 29.5 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.75 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1