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

General features for molecule PDB_01267 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01267 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE-ASL WITH CMO5U I Source [?]: RCSB Protein Data Bank Source ID [?]: 2UUA Reference [?]: A.WEIXLBAUMER,F.V.MURPHY,A.DZIERGOWSKA, A.MALKIEWICZ,F.A.P.VENDEIX,P.F.AGRIS,V.RAMAKRISHNAN. MECHANISM FOR EXPANDING THE DECODING CAPACITY OF TRANSFER RNAS BY MODIFICATION OF URIDINES. NAT.STRUCT.MOL.BIOL. V. 14 498 2007 ASTM NSMBCU US ISSN 1545-9993 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 2.9 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 1530 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 508 Number of paired bases [?]: 1022

Click on any header below for additional features.

Stem features Number of stems [?]: 81 Number of base pairs in stems [?]: 442 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.47 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -9.12 Minimum estimated free energy [?]: -28.2

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.29 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 [?]: 3 Average number of free bases in bulge loops [?]: 0.79 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 17 Maximum number of free bases in internal loops: 10 Average number of free bases in internal loops: 2.88 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1.06 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.65 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: 3.03 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.38 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.14 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.18 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 63 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: 37 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 10 Number of base pairs in bands: 69 Maximum band length: 32 Average band length: 6.9 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: 24.4 Minimum number of unpaired bases: 6 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 13 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.6 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 5 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