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

General features for molecule PDB_00985 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00985 Molecule name [?]: CRYSTAL STRUCTURE OF THE TRNA DOMAIN OF TMRNA FROM THERMUS THERMOPHILUS HB8 Source [?]: RCSB Protein Data Bank Source ID [?]: 2CZJ Reference [?]: Y.BESSHO,R.SHIBATA,S.SEKINE,K.MURAYAMA,M.SHIROUZU, S.YOKOYAMA. CRYSTAL STRUCTURE OF THE TRNA DOMAIN OF TMRNA FROM THERMUS THERMOPHILUS HB8. TO BE PUBLISHED 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 3.01 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 248 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 120 Number of paired bases [?]: 128

Click on any header below for additional features.

Stem features Number of stems [?]: 14 Number of base pairs in stems [?]: 64 Maximum length of a stem [?]: 7 Average length of a stem [?]: 4.57 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.5 Average estimated free energy [?]: -7.13 Minimum estimated free energy [?]: -14.5

Hairpin loop features Number of hairpin loops [?]: 8 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 5.5 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 2

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 Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 1 Average number of free bases in internal loops: 1 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 0 Average internal loop absolute asymmetry: 0 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 4 Maximum number of free bases in multi-loops: 13 Average number of free bases in multi-loops: 6 Minimum number of free bases in multi-loop: 2 Maximum multi-loop absolute asymmetry: 11 Average multi-loop absolute asymmetry: 6.33 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 6.5 Average multi-loop relative asymmetry: 2.01 Minimum multi-loop relative asymmetry: 0.15 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 [?]: 4 Total number of AG non-canonical base pairs: 4

Pseudoknot features