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

General features for molecule PDB_01122 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01122 Molecule name [?]: CRYSTAL STRUCTURE OF RIBOSOME WITH MESSENGER RNA AND THE ANTICODON STEM-LOOP OF P-SITE TRNA. THIS FI Source [?]: RCSB Protein Data Bank Source ID [?]: 2I2U Reference [?]: V.BERK,W.ZHANG,R.D.PAI,J.H.D.CATE. STRUCTURAL BASIS FOR MRNA AND TRNA POSITIONING ON THE RIBOSOME.. PROC.NATL.ACAD.SCI.USA V. 103 15830 2006 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 3.22 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 1553 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_01120 Number of domains [?]: 5 Number of unpaired bases [?]: 491 Number of paired bases [?]: 1062

Click on any header below for additional features.

Stem features Number of stems [?]: 98 Number of base pairs in stems [?]: 491 Maximum length of a stem [?]: 26 Average length of a stem [?]: 5.02 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.99 Minimum estimated free energy [?]: -23.7

Hairpin loop features Number of hairpin loops [?]: 29 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.38 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 3

Bulge loop features Number of bulge loops [?]: 35 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.7 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: 6 Average number of free bases in internal loops: 2.58 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.28 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 [?]: 15 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 2.65 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.28 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 0.99 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 [?]: 71 Total number of AA non-canonical base pairs: 10 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 37 Total number of CC non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 6 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 40 Maximum band length: 10 Average band length: 5 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: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.25 Minimum number of in-bands: 0 Maximum number of unpaired bases: 25 Average number of unpaired bases: 15.5 Minimum number of unpaired bases: 2 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 12 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 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