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

General features for molecule PDB_01139 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01139 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 1 Source [?]: RCSB Protein Data Bank Source ID [?]: 2J00 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 [?]: 16S 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 [?]: 5 Length [?]: 1687 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01141 Number of domains [?]: 6 Number of unpaired bases [?]: 619 Number of paired bases [?]: 1068

Click on any header below for additional features.

Stem features Number of stems [?]: 95 Number of base pairs in stems [?]: 448 Maximum length of a stem [?]: 25 Average length of a stem [?]: 4.73 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.45 Minimum estimated free energy [?]: -41.6

Hairpin loop features Number of hairpin loops [?]: 32 Maximum number of free bases in hairpin loops [?]: 26 Average number of free bases in hairpin loops [?]: 5.69 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 [?]: 24 Maximum number of free bases in bulge loops [?]: 26 Average number of free bases in bulge loops [?]: 1.27 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 27 Maximum number of free bases in internal loops: 9 Average number of free bases in internal loops: 2.2 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.78 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.37 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: 2.67 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.23 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 0.96 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.27 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 69 Total number of AA non-canonical base pairs: 7 Total number of AC non-canonical base pairs: 10 Total number of AG non-canonical base pairs: 40 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 5 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 12 Number of base pairs in bands: 86 Maximum band length: 32 Average band length: 7.17 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 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 62 Average number of unpaired bases: 23.33 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: 16 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.67 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 6 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