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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS

Results of the assignment of 35 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
012tpk_A_G1_C2NANNANT00.81AA11
022tpk_A_C2_U3NANNANT00.80AA04
032tpk_A_U3_G4AAAAA00970.10AA00
042tpk_A_G4_A5AAAAA00970.10AA00
052tpk_A_A5_C6AAAAA00950.12AA00
062tpk_A_C6_C7NANNANT00.53AA04
072tpk_A_C7_A8NANNANT02.04OP27
082tpk_A_A8_G9NANNANT01.67AA07
092tpk_A_G9_C10AAAAA00330.35AA00
102tpk_A_C10_U11AAAAA00970.11AA00
112tpk_A_U11_A12AAAAA00970.10AA00
122tpk_A_A12_U13AAAAA00970.11AA00
132tpk_A_U13_G14AAAAA00950.13AA00
142tpk_A_G14_A15AAwAA01480.30AA01
152tpk_A_A15_G16AAwAA11730.51AA11
162tpk_A_G16_G17AAAAA00370.33AA00
172tpk_A_G17_U18AAAAA00980.10AA00
182tpk_A_U18_C19AAAAA00970.12AA00
192tpk_A_C19_A20AAAAA00950.12AA00
202tpk_A_A20_U21NANNANT00.32AA05
212tpk_A_U21_A22NANNANT00.87OP24
222tpk_A_A22_C23NANNANT02.07OP08
232tpk_A_C23_A24NANNANT00.91BB13
242tpk_A_A24_U25AAwAA01130.39AA01
252tpk_A_U25_C26NANNANT00.69BB13
262tpk_A_C26_G27NANNANT01.00AA01
272tpk_A_G27_U28NANNANT00.60BA01
282tpk_A_U28_C29AAuAA12670.28AA12
292tpk_A_C29_A30AAAAA00970.10AA00
302tpk_A_A30_U31AAAAA00970.10AA00
312tpk_A_U31_A32AAAAA00960.11AA00
322tpk_A_A32_G33AAAAA00950.12AA00
332tpk_A_G33_C34AAwAA01820.19AA01
342tpk_A_C34_A35AAAAA00320.34AA00
352tpk_A_A35_C36AAAAA04210.71AA04

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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