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

General features for molecule PDB_00440 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00440 Molecule name [?]: CRYSTAL STRUCTURE OF INITIATION FACTOR IF1 BOUND TO THE 30S RIBOSOMAL SUBUNIT Source [?]: RCSB Protein Data Bank Source ID [?]: 1HR0 Reference [?]: A.P.CARTER,W.M.CLEMONS JR.,D.E.BRODERSEN, R.J.MORGAN-WARREN,T.HARTSCH,B.T.WIMBERLY, V.RAMAKRISHNAN. CRYSTAL STRUCTURE OF AN INITIATION FACTOR BOUND TO THE 30S RIBOSOMAL SUBUNIT.. SCIENCE V. 291 498 2001 ASTM SCIEAS US ISSN 0036-8075 Type [?]: 16S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: ESCHERICHIA COLI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 1513 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00408, PDB_00436, PDB_00437, PDB_00438, PDB_00478, PDB_00589 Number of domains [?]: 4 Number of unpaired bases [?]: 483 Number of paired bases [?]: 1030

Click on any header below for additional features.

Stem features Number of stems [?]: 84 Number of base pairs in stems [?]: 452 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.39 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.84 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.21 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 [?]: 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 [?]: 19 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.29 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.63 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: 2.89 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.32 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.15 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 [?]: 70 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 9 Total number of AG non-canonical base pairs: 40 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 4 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