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

General features for molecule PDB_00474 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00474 Molecule name [?]: CRYSTAL STRUCTURE OF ARCHAEAL TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(TYR) AND L-TYROSINE Source [?]: RCSB Protein Data Bank Source ID [?]: 1J1U Reference [?]: T.KOBAYASHI,O.NUREKI,R.ISHITANI,A.YAREMCHUK, M.TUKALO,S.CUSACK,K.SAKAMOTO,S.YOKOYAMA. STRUCTURAL BASIS FOR ORTHOGONAL TRNA SPECIFICITIES OF TYROSYL-TRNA SYNTHETASES FOR GENETIC CODE EXPANSION. NAT.STRUCT.BIOL. V. 10 425 2003 ASTM NSBIEW US ISSN 1072-8368 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: METHANOCOCCUS JANNASCHII Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 1.95 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 74 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 28 Number of paired bases [?]: 46

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 23 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5.75 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -5.5 Average estimated free energy [?]: -11.33 Minimum estimated free energy [?]: -18.1

Hairpin loop features Number of hairpin loops [?]: 3 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 7 Minimum number of free bases in hairpin loop [?]: 5

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: 4 Average number of free bases in multi-loops: 1.5 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 4 Average multi-loop absolute asymmetry: 2.33 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 2 Average multi-loop relative asymmetry: 0.42 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 [?]: 2 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 1

Pseudoknot features