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

General features for molecule PDB_00628 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00628 Molecule name [?]: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH Source [?]: RCSB Protein Data Bank Source ID [?]: 1OND Reference [?]: R.BERISIO,F.SCHLUENZEN,J.HARMS,A.BASHAN,T.AUERBACH, D.BARAM,A.YONATH. STRUCTURAL INSIGHT INTO THE ROLE OF THE RIBOSOMAL TUNNEL IN CELLULAR REGULATION. NAT.STRUCT.BIOL. V. 10 366 2003 ASTM NSBIEW US ISSN 1072-8368 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 3.40 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2765 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 1247 Number of paired bases [?]: 1518

Click on any header below for additional features.

Stem features Number of stems [?]: 138 Number of base pairs in stems [?]: 567 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.11 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.49 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 [?]: 5.54 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 22 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 [?]: 44 Maximum number of free bases in internal loops: 11 Average number of free bases in internal loops: 3.02 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 1.05 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.45 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 15 Average number of free bases in multi-loops: 3.74 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 3.14 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.12 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 [?]: 53 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 7 Total number of AG non-canonical base pairs: 32 Total number of CU non-canonical base pairs: 6 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 192 Maximum band length: 31 Average band length: 10.67 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: 22 Average number of in-bands: 4.8 Minimum number of in-bands: 0 Maximum number of unpaired bases: 321 Average number of unpaired bases: 83.2 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: 9 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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