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

©Jiří Černý & Bohdan Schneider

Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP)

Results of the assignment of 51 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
016tb7_A_G1_G2AAAAA00740.23AA00
026tb7_A_G2_C3AAAAA00820.18AA00
036tb7_A_C3_U4AAAAA03740.27AA03
046tb7_A_U4_U5AAAAA00730.24AA00
056tb7_A_U5_C6AAAAA04920.23AA04
066tb7_A_C6_A7A-BAB05790.27AB05
076tb7_A_A7_A8NANNANT00.62OP26
086tb7_A_A8_C9AAAAA08590.33AA08
096tb7_A_C9_A10NANNANT00.44IC06
106tb7_A_A10_A11NANNANT00.52OP13
116tb7_A_A11_C12NANNANT01.10OP30
126tb7_A_C12_C13AAAAA00460.44AA00
136tb7_A_C13_C14AAAAA00660.34AA00
146tb7_A_C14_C15AAAAA08720.30AA08
156tb7_A_C15_G16OPNOP29270.33OP29
166tb7_A_G16_U17AAAAA00250.33AA00
176tb7_A_U17_A18AAAAA00820.14AA00
186tb7_A_A18_G19AAAAA00780.22AA00
196tb7_A_G19_G20AAwAA01850.27AA01
206tb7_A_G20_U21AAAAA00430.30AA00
216tb7_A_U21_U22AAAAA00690.18AA00
226tb7_A_U22_G23AAAAA08820.22AA08
236tb7_A_G23_G24AAwAA10790.15AA10
246tb7_A_G24_G25AAAAA08450.28AA08
256tb7_A_G25_C26AAAAA00900.15AA00
266tb7_A_C26_C27AAAAA00810.20AA00
276tb7_A_C27_G28AAAAA00790.23AA00
286tb7_A_G28_A29OPNOP03820.09OP03
296tb7_A_A29_A30AAAAA08620.30AA08
306tb7_A_A30_A31AAAAA04670.26AA04
316tb7_A_A31_G32AAAAA0890.84AA08
326tb7_A_G32_G33AAAAA08700.27AA08
336tb7_A_G33_C34AAAAA08580.28AA08
346tb7_A_C34_A35NANNANT00.47AA03
356tb7_A_A35_G36NANNANT01.95OP09
366tb7_A_G36_C37NANNANT00.68OP14
376tb7_A_C37_G38NANNANT01.01OP20
386tb7_A_G38_A39NANNANT01.15OP31
396tb7_A_A39_A40AAAAA08900.24AA08
406tb7_A_A40_U41AAAAA00730.28AA00
416tb7_A_U41_C42AAAAA00670.23AA00
426tb7_A_C42_U43AAAAA03900.15AA03
436tb7_A_U43_A44AAAAA00810.16AA00
446tb7_A_A44_C45AAAAA08850.18AA08
456tb7_A_C45_U46AAAAA03650.31AA03
466tb7_A_U46_G47AAAAA08760.25AA08
476tb7_A_G47_G48AAwAA01650.33AA01
486tb7_A_G48_A49AAAAA08840.14AA08
496tb7_A_A49_G50AAAAA08770.15AA08
506tb7_A_G50_C51AAAAA08860.15AA08
516tb7_A_C51_C52AAAAA00820.20AA00

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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