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

General features for molecule PDB_00993 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00993 Molecule name [?]: STRUCTURE OF RIBOSOME BINDING DOMAIN OF THE TRIGGER FACTOR ON THE 50S RIBOSOMAL SUBUNIT FROM D. RADI Source [?]: RCSB Protein Data Bank Source ID [?]: 2D3O Reference [?]: F.SCHLUNZEN,D.N.WILSON,P.TIAN,J.M.HARMS, S.J.MCINNES,H.A.HANSEN,R.ALBRECHT,J.BUERGER, S.M.WILBANKS,P.FUCINI. THE BINDING MODE OF THE TRIGGER FACTOR ON THE RIBOSOME: IMPLICATIONS FOR PROTEIN FOLDING AND SRP INTERACTION. STRUCTURE V. 13 1685 2005 ASTM STRUE6 UK ISSN 0969-2126 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 3.35 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2802 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 1198 Number of paired bases [?]: 1604

Click on any header below for additional features.

Stem features Number of stems [?]: 138 Number of base pairs in stems [?]: 600 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.35 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.63 Minimum estimated free energy [?]: -20

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 19 Average number of free bases in hairpin loops [?]: 5.74 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 [?]: 20 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.78 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 45 Maximum number of free bases in internal loops: 13 Average number of free bases in internal loops: 2.84 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 10 Average internal loop absolute asymmetry: 1.33 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 5 Average internal loop relative asymmetry: 1.56 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 16 Average number of free bases in multi-loops: 3.33 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 3.09 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 16 Average multi-loop relative asymmetry: 1.47 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 [?]: 72 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 42 Total number of CC non-canonical base pairs: 2 Total number of CU non-canonical base pairs: 6 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 202 Maximum band length: 33 Average band length: 11.22 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.6 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.8 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 297 Average number of unpaired bases: 76.8 Minimum number of unpaired bases: 11 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: 4.4 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 7 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.4 Minimum number of bands to remove, per pseudoknot: 1

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