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

General features for molecule PDB_00922 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00922 Molecule name [?]: STRUCTURE OF TRIGGER FACTOR BINDING DOMAIN IN BIOLOGICALLY HOMOLOGOUS COMPLEX WITH EUBACTERIAL RIBOS Source [?]: RCSB Protein Data Bank Source ID [?]: 2AAR Reference [?]: D.BARAM,E.PYETAN,A.SITTNER,T.AUERBACH-NEVO, A.BASHAN,A.YONATH. STRUCTURE OF TRIGGER FACTOR BINDING DOMAIN IN BIOLOGICALLY HOMOLOGOUS COMPLEX WITH EUBACTERIAL RIBOSOME REVEALS ITS CHAPERONE ACTION. PROC.NATL.ACAD.SCI.USA V. 102 12017 2005 ASTM PNASA6 US ISSN 0027-8424 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: DEINOCOCCUS RADIODURANS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2766 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00606, PDB_00880, PDB_01173, PDB_01174, PDB_01175, PDB_01182, PDB_01183 Number of domains [?]: 1 Number of unpaired bases [?]: 1166 Number of paired bases [?]: 1600

Click on any header below for additional features.

Stem features Number of stems [?]: 133 Number of base pairs in stems [?]: 583 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.38 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.74 Minimum estimated free energy [?]: -20

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 [?]: 5.58 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 25 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.74 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 36 Maximum number of free bases in internal loops: 13 Average number of free bases in internal loops: 2.92 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 0.89 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.31 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 22 Average number of free bases in multi-loops: 3.62 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 21 Average multi-loop absolute asymmetry: 3.36 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 22 Average multi-loop relative asymmetry: 1.34 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.87 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: 6 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 35 Total number of CC non-canonical base pairs: 3 Total number of CU non-canonical base pairs: 6 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 20 Number of base pairs in bands: 217 Maximum band length: 39 Average band length: 10.85 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.33 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: 23 Average number of in-bands: 4.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 295 Average number of unpaired bases: 65 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: 22 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 3.67 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.33 Minimum number of bands to remove, per pseudoknot: 1

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