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

General features for molecule PDB_00794 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00794 Molecule name [?]: CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH THE ANTIBIOTIC KAS Source [?]: RCSB Protein Data Bank Source ID [?]: 1VS8 Reference [?]: B.S.SCHUWIRTH,J.M.DAY,C.W.HAU,G.R.JANSSEN, A.E.DAHLBERG,J.H.D.CATE,A.VILA-SANJURJO. STRUCTURAL ANALYSIS OF KASUGAMYCIN INHIBITION OF TRANSLATION.. NAT.STRUCT.MOL.BIOL. V. 13 879 2006 US ISSN 1545-9993 Type [?]: 23S 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 3.46 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2958 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00792, PDB_00934, PDB_00936, PDB_01121, PDB_01123, PDB_01221, PDB_01223, PDB_01225, PDB_01227, PDB_01229, PDB_01231, PDB_01233, PDB_01235, PDB_01242, PDB_01244, PDB_01246, PDB_01248, PDB_01283, PDB_01285 Number of domains [?]: 2 Number of unpaired bases [?]: 990 Number of paired bases [?]: 1968

Click on any header below for additional features.

Stem features Number of stems [?]: 142 Number of base pairs in stems [?]: 750 Maximum length of a stem [?]: 17 Average length of a stem [?]: 5.29 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.51 Minimum estimated free energy [?]: -21.1

Hairpin loop features Number of hairpin loops [?]: 57 Maximum number of free bases in hairpin loops [?]: 13 Average number of free bases in hairpin loops [?]: 4.79 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 39 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 [?]: 29 Maximum number of free bases in internal loops: 5 Average number of free bases in internal loops: 2.02 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 0.79 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.45 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.17 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.21 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.35 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.75 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 114 Total number of AA non-canonical base pairs: 21 Total number of AC non-canonical base pairs: 5 Total number of AG non-canonical base pairs: 70 Total number of CC non-canonical base pairs: 3 Total number of CU non-canonical base pairs: 4 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 8

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 22 Number of base pairs in bands: 234 Maximum band length: 39 Average band length: 10.64 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.67 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.33 Minimum number of un-bands: 0 Maximum number of in-bands: 22 Average number of in-bands: 4.17 Minimum number of in-bands: 0 Maximum number of unpaired bases: 266 Average number of unpaired bases: 58.67 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: 25 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 4.17 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 9 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.5 Minimum number of bands to remove, per pseudoknot: 1

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