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

General features for molecule PDB_01272 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01272 Molecule name [?]: CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA UCGU IN T Source [?]: RCSB Protein Data Bank Source ID [?]: 2UXC Reference [?]: C.M.DUNHAM,M.SELMER,S.S.PHELPS,A.C.KELLEY,T.SUZUKI, S.JOSEPH,V.RAMAKRISHNAN. STRUCTURES OF TRNAS WITH AN EXPANDED ANTICODON LOOP IN THE DECODING CENTER OF THE 30S RIBOSOMAL SUBUNIT. TO BE PUBLISHED 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 2.90 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 1525 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 521 Number of paired bases [?]: 1004

Click on any header below for additional features.

Stem features Number of stems [?]: 83 Number of base pairs in stems [?]: 439 Maximum length of a stem [?]: 24 Average length of a stem [?]: 5.3 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.62 Minimum estimated free energy [?]: -41.6

Hairpin loop features Number of hairpin loops [?]: 29 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.24 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 25 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 [?]: 17 Maximum number of free bases in internal loops: 11 Average number of free bases in internal loops: 3.24 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1.06 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.65 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.14 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.2 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.12 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.18 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 66 Total number of AA non-canonical base pairs: 8 Total number of AC non-canonical base pairs: 8 Total number of AG non-canonical base pairs: 39 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