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

General features for molecule PDB_01090 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01090 Molecule name [?]: STRUCTURE OF THE 30S SUBUNIT OF A SECM-STALLED E. COLI RIBOSOME COMPLEX OBTAINED BY FITTING ATOMIC M Source [?]: RCSB Protein Data Bank Source ID [?]: 2GYB Reference [?]: K.MITRA,C.SCHAFFITZEL,F.FABIOLA,M.S.CHAPMAN,N.BAN, J.FRANK. ELONGATION ARREST BY SECM VIA A CASCADE OF RIBOSOMAL RNA REARRANGEMENTS. MOL.CELL V. 22 533 2006 ASTM MOCEFL US ISSN 1097-2765 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 2.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1716 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01088 Number of domains [?]: 7 Number of unpaired bases [?]: 762 Number of paired bases [?]: 954

Click on any header below for additional features.

Stem features Number of stems [?]: 96 Number of base pairs in stems [?]: 450 Maximum length of a stem [?]: 14 Average length of a stem [?]: 4.69 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.68 Minimum estimated free energy [?]: -18.7

Hairpin loop features Number of hairpin loops [?]: 36 Maximum number of free bases in hairpin loops [?]: 14 Average number of free bases in hairpin loops [?]: 5.14 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 [?]: 20 Maximum number of free bases in bulge loops [?]: 16 Average number of free bases in bulge loops [?]: 1.12 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: 29 Average number of free bases in internal loops: 3.58 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 25 Average internal loop absolute asymmetry: 1.92 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 7 Average internal loop relative asymmetry: 1.62 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 14 Maximum number of free bases in multi-loops: 18 Average number of free bases in multi-loops: 3.51 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 3.16 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 0.96 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.64 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 60 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 36 Total number of CC non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 27 Maximum band length: 9 Average band length: 4.5 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: 6 Average number of un-bands: 2.67 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 67 Average number of unpaired bases: 35.67 Minimum number of unpaired bases: 15 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 7 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.33 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 3 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