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

General features for molecule PDB_00608 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00608 Molecule name [?]: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH Source [?]: RCSB Protein Data Bank Source ID [?]: 1NJP Reference [?]: A.BASHAN,I.AGMON,R.ZARIVATCH,F.SCHLUENZEN, J.M.HARMS,R.BERISIO,H.BARTELS,F.FRANCESCHI, T.AUERBACH,H.A.HANSEN,E.KOSSOY,M.KESSLER,A.YONATH. STRUCTURAL BASIS OF THE RIBOSOMAL MACHINERY FOR PEPTIDE BOND FORMATION, TRANSLOCATION, AND NASCENT CHAIN PROGRESSION. MOL. CELL V. 11 91 2003 ASTM MOCEFL US ISSN 1097-2765 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 [?]: 2 Length [?]: 2791 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00605 Number of domains [?]: 2 Number of unpaired bases [?]: 1269 Number of paired bases [?]: 1522

Click on any header below for additional features.

Stem features Number of stems [?]: 139 Number of base pairs in stems [?]: 564 Maximum length of a stem [?]: 10 Average length of a stem [?]: 4.06 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.54 Minimum estimated free energy [?]: -20.1

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

Bulge loop features Number of bulge loops [?]: 17 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.76 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 50 Maximum number of free bases in internal loops: 11 Average number of free bases in internal loops: 2.82 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.4 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 24 Average number of free bases in multi-loops: 4.27 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 21 Average multi-loop absolute asymmetry: 4.02 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.48 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 6 Average number of branches in multi-loops: 3.73 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 48 Total number of AA non-canonical base pairs: 5 Total number of AC non-canonical base pairs: 4 Total number of AG non-canonical base pairs: 32 Total number of CC non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 3 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 18 Number of base pairs in bands: 197 Maximum band length: 36 Average band length: 10.94 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: 1.6 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 5.2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 307 Average number of unpaired bases: 80 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 20 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 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