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

General features for molecule PDB_01302 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01302 Molecule name [?]: T. TENGCONGENSIS GLMS RIBOZYME BOUND TO GLUCOSAMINE-6- PHOSPHATE AND A SUBSTRATE RNA WITH A 2'5'-PHO Source [?]: RCSB Protein Data Bank Source ID [?]: 3B4C Reference [?]: D.J.KLEIN,M.D.BEEN,A.R.FERRE-D'AMARE. ESSENTIAL ROLE OF AN ACTIVE-SITE GUANINE IN GLMS RIBOZYME CATALYSIS.. J.AM.CHEM.SOC. V. 129 14858 2007 ASTM JACSAT US ISSN 0002-7863 Type [?]: Other Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMOANAEROBACTER TENGCONGENSIS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 139 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 41 Number of paired bases [?]: 98

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 28 Maximum length of a stem [?]: 11 Average length of a stem [?]: 9.33 Minimum length of a stem [?]: 7 Maximum estimated free energy [?]: -11.8 Average estimated free energy [?]: -14.1 Minimum estimated free energy [?]: -18.4

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 2 Average number of free bases in hairpin loops [?]: 2 Minimum number of free bases in hairpin loop [?]: 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 [?]: 1 Maximum number of free bases in internal loops: 4 Average number of free bases in internal loops: 3 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 2 Minimum internal loop absolute asymmetry: 2 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 4 Total number of AA non-canonical base pairs: 1 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 2

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 21 Maximum band length: 8 Average band length: 5.25 Minimum band length: 3 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: 1 Average number of un-bands: 0.5 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 17 Average number of unpaired bases: 14.5 Minimum number of unpaired bases: 12 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 9 Maximum number of base pairs to remove, per pseudoknot: 6 Average number of base pairs to remove, per pseudoknot: 4.5 Minimum number of base pairs to remove, per pseudoknot: 3 Minimum number of bands to remove, per molecule: 2 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

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