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

General features for molecule PDB_00645 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00645 Molecule name [?]: CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI, 30S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1P Source [?]: RCSB Protein Data Bank Source ID [?]: 1PNX Reference [?]: A.VILA-SANJURJO,W.K.RIDGEWAY,V.SEYMANER,W.ZHANG, S.SANTOSO,K.YU,J.H.D.CATE. X-RAY CRYSTAL STRUCTURES OF THE WT AND A HYPER-ACCURATE RIBOSOME FROM ESCHERICHIA COLI. PROC.NATL.ACAD.SCI.USA V. 100 8682 2003 ASTM PNASA6 US ISSN 0027-8424 Type [?]: 16S 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 9.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1533 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 499 Number of paired bases [?]: 1034

Click on any header below for additional features.

Stem features Number of stems [?]: 92 Number of base pairs in stems [?]: 501 Maximum length of a stem [?]: 23 Average length of a stem [?]: 5.46 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.88 Minimum estimated free energy [?]: -39.2

Hairpin loop features Number of hairpin loops [?]: 30 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 2

Bulge loop features Number of bulge loops [?]: 26 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.73 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 18 Maximum number of free bases in internal loops: 8 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: 1.17 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.78 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 17 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.1 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 8 Average multi-loop absolute asymmetry: 2.52 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.13 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.47 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 80 Total number of AA non-canonical base pairs: 11 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 44 Total number of CC non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 7

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 16 Maximum band length: 7 Average band length: 4 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: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 23 Average number of unpaired bases: 19.5 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: 5 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.5 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 2 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