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

General features for molecule PDB_01142 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01142 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 4 Source [?]: RCSB Protein Data Bank Source ID [?]: 2J03 Reference [?]: M.SELMER,C.M.DUNHAM,F.V.MURPHY,A.WEIXLBAUMER, S.PETRY,A.C.KELLEY,J.R.WEIR,V.RAMAKRISHNAN. STRUCTURE OF THE 70S RIBOSOME COMPLEXED WITH MRNA AND TRNA.. SCIENCE V. 313 1935 2006 ASTM SCIEAS US ISSN 0036-8075 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.80 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2891 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01140 Number of domains [?]: 2 Number of unpaired bases [?]: 1039 Number of paired bases [?]: 1852

Click on any header below for additional features.

Stem features Number of stems [?]: 138 Number of base pairs in stems [?]: 697 Maximum length of a stem [?]: 13 Average length of a stem [?]: 5.05 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.61 Minimum estimated free energy [?]: -27.6

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 20 Average number of free bases in hairpin loops [?]: 5.88 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 40 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 0.86 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 24 Maximum number of free bases in internal loops: 5 Average number of free bases in internal loops: 2.12 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.67 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.42 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.15 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.19 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.14 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.69 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 98 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: 64 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: 3 Total number of UU non-canonical base pairs: 5

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 20 Number of base pairs in bands: 229 Maximum band length: 43 Average band length: 11.45 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.33 Minimum number of un-bands: 0 Maximum number of in-bands: 24 Average number of in-bands: 4.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 258 Average number of unpaired bases: 56.33 Minimum number of unpaired bases: 8 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 23 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 3.83 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.33 Minimum number of bands to remove, per pseudoknot: 1

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