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

General features for molecule PDB_01271 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01271 Molecule name [?]: CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA GGGU IN T Source [?]: RCSB Protein Data Bank Source ID [?]: 2UXB 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. RNA V. 13 817 2007 ASTM RNARFU US ISSN 1355-8382 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 3.1 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 1524 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 536 Number of paired bases [?]: 988

Click on any header below for additional features.

Stem features Number of stems [?]: 87 Number of base pairs in stems [?]: 431 Maximum length of a stem [?]: 15 Average length of a stem [?]: 4.95 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.19 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 29 Maximum number of free bases in hairpin loops [?]: 14 Average number of free bases in hairpin loops [?]: 4.59 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 [?]: 24 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.71 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 23 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.57 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 0.78 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.3 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: 2.62 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.18 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 [?]: 65 Total number of AA non-canonical base pairs: 7 Total number of AC non-canonical base pairs: 10 Total number of AG non-canonical base pairs: 39 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 5

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: 28.25 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: 10 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.5 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