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

General features for molecule PDB_01089 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01089 Molecule name [?]: STRUCTURE OF THE 50S SUBUNIT OF A PRE-TRANSLOCATIONAL E. COLI RIBOSOME OBTAINED BY FITTING ATOMIC MO Source [?]: RCSB Protein Data Bank Source ID [?]: 2GYA 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 [?]: 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 2.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2848 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01091 Number of domains [?]: 4 Number of unpaired bases [?]: 1330 Number of paired bases [?]: 1518

Click on any header below for additional features.

Stem features Number of stems [?]: 153 Number of base pairs in stems [?]: 644 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.21 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -5.79 Minimum estimated free energy [?]: -17.9

Hairpin loop features Number of hairpin loops [?]: 59 Maximum number of free bases in hairpin loops [?]: 74 Average number of free bases in hairpin loops [?]: 6.29 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 19 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 0.63 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 54 Maximum number of free bases in internal loops: 13 Average number of free bases in internal loops: 2.98 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 5 Average internal loop absolute asymmetry: 1.11 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.43 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 21 Maximum number of free bases in multi-loops: 15 Average number of free bases in multi-loops: 3.73 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 2.86 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.23 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.71 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 88 Total number of AA non-canonical base pairs: 14 Total number of AC non-canonical base pairs: 6 Total number of AG non-canonical base pairs: 52 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 4 Total number of GG non-canonical base pairs: 7 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 7 Number of bands: 16 Number of base pairs in bands: 115 Maximum band length: 33 Average band length: 7.19 Minimum band length: 2 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 2.29 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 4 Average number of un-bands: 1.14 Minimum number of un-bands: 0 Maximum number of in-bands: 15 Average number of in-bands: 2.57 Minimum number of in-bands: 0 Maximum number of unpaired bases: 197 Average number of unpaired bases: 42.29 Minimum number of unpaired bases: 5 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 16 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.29 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 7 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

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