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

General features for molecule PDB_00535 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00535 Molecule name [?]: CRYSTAL STRUCTURE OF T3C MUTANT S15 RIBOSOMAL PROTEIN IN COMPLEX WITH 16S RRNA Source [?]: RCSB Protein Data Bank Source ID [?]: 1KUQ Reference [?]: S.V.REVTOVICH,A.D.NIKULIN,S.V.NIKONOV. ROLE OF N-TERMINAL HELIX IN INTERACTION OF RIBOSOMAL PROTEIN S15 WITH 16S RRNA.. BIOCHEMISTRY MOSC. V. 69 1319 2004 US ISSN 0006-2979 Type [?]: Other 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 2.84 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 57 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00343, PDB_00394 Number of domains [?]: 1 Number of unpaired bases [?]: 17 Number of paired bases [?]: 40

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 20 Maximum length of a stem [?]: 7 Average length of a stem [?]: 4 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -4.6 Average estimated free energy [?]: -6.58 Minimum estimated free energy [?]: -9.1

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 4 Average number of free bases in hairpin loops [?]: 4 Minimum number of free bases in hairpin loop [?]: 4 Total number of UUCG hairpin motifs per molecule [?]: 2

Bulge loop features Number of bulge loops [?]: 2 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 3 Average number of free bases in multi-loops: 2.33 Minimum number of free bases in multi-loop: 1 Maximum multi-loop absolute asymmetry: 2 Average multi-loop absolute asymmetry: 1.33 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 3 Average multi-loop relative asymmetry: 1.44 Minimum multi-loop relative asymmetry: 0.33 Maximum number of branches in multi-loops: 3 Average number of branches in multi-loops: 3 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of AG non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1

Pseudoknot features

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