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

General features for molecule PDB_01088 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01088 Molecule name [?]: STRUCTURE OF THE 30S SUBUNIT OF A PRE-TRANSLOCATIONAL E. COLI RIBOSOME OBTAINED BY FITTING ATOMIC MO Source [?]: RCSB Protein Data Bank Source ID [?]: 2GY9 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_01090 Number of domains [?]: 7 Number of unpaired bases [?]: 622 Number of paired bases [?]: 1094

Click on any header below for additional features.

Stem features Number of stems [?]: 104 Number of base pairs in stems [?]: 528 Maximum length of a stem [?]: 16 Average length of a stem [?]: 5.08 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.42 Minimum estimated free energy [?]: -18.7

Hairpin loop features Number of hairpin loops [?]: 39 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.79 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 [?]: 27 Maximum number of free bases in bulge loops [?]: 6 Average number of free bases in bulge loops [?]: 0.83 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: 7 Average number of free bases in internal loops: 2.8 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.2 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.3 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 18 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.16 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.77 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.04 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.56 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: 8 Total number of AC non-canonical base pairs: 12 Total number of AG non-canonical base pairs: 39 Total number of GG non-canonical base pairs: 5 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 19 Maximum band length: 9 Average band length: 4.75 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: 2.5 Minimum number of un-bands: 2 Maximum number of in-bands: 1 Average number of in-bands: 0.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 24 Average number of unpaired bases: 22.5 Minimum number of unpaired bases: 21 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 6 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 2 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