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

General features for molecule PDB_00408 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00408 Molecule name [?]: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTICS STREPTOM Source [?]: RCSB Protein Data Bank Source ID [?]: 1FJG Reference [?]: A.P.CARTER,W.M.CLEMONS JR.,D.E.BRODERSEN, R.J.MORGAN-WARREN,B.T.WIMBERLY,V.RAMAKRISHNAN. FUNCTIONAL INSIGHTS FROM THE STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT AND ITS INTERACTIONS WITH ANTIBIOTICS. NATURE V. 407 340 2000 ASTM NATUAS UK ISSN 0028-0836 Type [?]: 16S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 1513 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00436, PDB_00437, PDB_00438, PDB_00440, PDB_00478, PDB_00589 Number of domains [?]: 4 Number of unpaired bases [?]: 481 Number of paired bases [?]: 1032

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Stem features Number of stems [?]: 80 Number of base pairs in stems [?]: 453 Maximum length of a stem [?]: 24 Average length of a stem [?]: 5.67 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -9.18 Minimum estimated free energy [?]: -41.6

Hairpin loop features Number of hairpin loops [?]: 27 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.15 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 [?]: 26 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 16 Maximum number of free bases in internal loops: 19 Average number of free bases in internal loops: 3 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 16 Average internal loop absolute asymmetry: 2.13 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 6 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 10 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.97 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.42 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.13 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.2 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 74 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 43 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 63 Maximum band length: 32 Average band length: 7.88 Minimum band length: 2 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 62 Average number of unpaired bases: 28.5 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.75 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1