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

General features for molecule PDB_00954 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00954 Molecule name [?]: 30S RIBOSOMAL SUBUNIT, TRNAS AND MRNA FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX WITH A Source [?]: RCSB Protein Data Bank Source ID [?]: 2B9O Reference [?]: S.PETRY,D.E.BRODERSEN,F.V.MURPHY IV,C.M.DUNHAM, M.SELMER,M.J.TARRY,A.C.KELLEY,V.RAMAKRISHNAN. CRYSTAL STRUCTURES OF THE RIBOSOME IN COMPLEX WITH RELEASE FACTORS RF1 AND RF2 BOUND TO A COGNATE STOP CODON.. CELL (CAMBRIDGE,MASS.) V. 123 1255 2005 ASTM CELLB5 US ISSN 0092-8674 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 6.46 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1673 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00946 Number of domains [?]: 8 Number of unpaired bases [?]: 675 Number of paired bases [?]: 998

Click on any header below for additional features.

Stem features Number of stems [?]: 101 Number of base pairs in stems [?]: 471 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.67 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.95 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 35 Maximum number of free bases in hairpin loops [?]: 13 Average number of free bases in hairpin loops [?]: 4.97 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 18 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.81 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 31 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.42 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.97 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.48 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 3.14 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.52 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.09 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.5 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 52 Total number of AA non-canonical base pairs: 7 Total number of AC non-canonical base pairs: 8 Total number of AG non-canonical base pairs: 30 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 28 Maximum band length: 8 Average band length: 4.67 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: 1.67 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: 33 Average number of unpaired bases: 23.33 Minimum number of unpaired bases: 16 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