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

General features for molecule PDB_00933 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00933 Molecule name [?]: CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI AT 3.5 A RESOLUTION. THIS FILE CON Source [?]: RCSB Protein Data Bank Source ID [?]: 2AVY Reference [?]: B.S.SCHUWIRTH,M.A.BOROVINSKAYA,C.W.HAU,W.ZHANG, A.VILA-SANJURJO,J.M.HOLTON,J.H.CATE. STRUCTURES OF THE BACTERIAL RIBOSOME AT 3.5 A RESOLUTION.. SCIENCE V. 310 827 2005 ASTM SCIEAS US ISSN 0036-8075 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 3.46 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_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, PDB_01284 Number of domains [?]: 4 Number of unpaired bases [?]: 480 Number of paired bases [?]: 1050

Click on any header below for additional features.

Stem features Number of stems [?]: 89 Number of base pairs in stems [?]: 461 Maximum length of a stem [?]: 24 Average length of a stem [?]: 5.19 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.02 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 [?]: 4.29 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 [?]: 34 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.69 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 15 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.6 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1.2 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.6 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.86 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.38 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.14 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 [?]: 74 Total number of AA non-canonical base pairs: 11 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 38 Total number of CC non-canonical base pairs: 1 Total number of CU 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: 64 Average number of unpaired bases: 29 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