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

General features for molecule PDB_00713 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00713 Molecule name [?]: THE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA SER Source [?]: RCSB Protein Data Bank Source ID [?]: 1SER Reference [?]: V.BIOU,A.YAREMCHUK,M.TUKALO,S.CUSACK. THE 2.9 A CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(SER).. SCIENCE V. 263 1404 1994 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Other 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 2.90 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 64 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 22 Number of paired bases [?]: 42

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 16 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5.33 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -7.8 Average estimated free energy [?]: -11.93 Minimum estimated free energy [?]: -15.6

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 7 Average number of free bases in hairpin loops [?]: 3.5 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

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: 1 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 3 Average multi-loop absolute asymmetry: 1.67 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 3 Average multi-loop relative asymmetry: 0.56 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 4 Minimum number of branches in multi-loops: 4

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 0

Pseudoknot features Number of pseudoknots [?]: 1 Number of bands: 2 Number of base pairs in bands: 5 Maximum band length: 3 Average band length: 2.5 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: 0 Average number of un-bands: 0 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 9 Average number of unpaired bases: 9 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: 2 Maximum number of base pairs to remove, per pseudoknot: 2 Average number of base pairs to remove, per pseudoknot: 2 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 1 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