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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 Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein

Results of the assignment of 56 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
017d7v_A_G2_C3AAAAA00950.13AA00
027d7v_A_C3_G4AAAAA00890.14AA00
037d7v_A_G4_C5AAwAA01870.15AA01
047d7v_A_C5_A6A-BAB04920.17AB04
057d7v_A_A6_A7NANNANT00.64OP26
067d7v_A_A7_C8AAAAA08790.33AA08
077d7v_A_C8_A9NANNANT00.64AB04
087d7v_A_A9_U10NANNANT00.47OP13
097d7v_A_U10_C11NANNANT01.75OP10
107d7v_A_C11_C12AAAAA00730.27AA00
117d7v_A_C12_C13AAAAA08690.30AA08
127d7v_A_C13_C14NANNANT00.47AA10
137d7v_A_C14_G15OPNOP29170.38OP29
147d7v_A_G15_C16AAAAA00740.21AA00
157d7v_A_C16_C17AAAAA00440.18AA00
167d7v_A_C17_G18AAwAA01410.25AA01
177d7v_A_G18_G19AAAAA08890.16AA08
187d7v_A_G19_U20AAAAA00830.19AA00
197d7v_A_U20_U21AAAAA00780.12AA00
207d7v_A_U21_G22AAAAA08800.19AA08
217d7v_A_G22_G23AAAAA00770.18AA00
227d7v_A_G23_G24AAAAA00740.23AA00
237d7v_A_G24_C25AAAAA00790.07AA00
247d7v_A_C25_G26AAAAA00880.12AA00
257d7v_A_G26_C27AAAAA00860.16AA00
267d7v_A_C27_A28AAAAA00610.32AA00
277d7v_A_A28_U29AAAAA00850.20AA00
287d7v_A_U29_U30ICLIC02940.16IC02
297d7v_A_U30_G31ZZZZZ02130.59ZZ02
307d7v_A_G31_C32NANNANT00.98IC03
317d7v_A_C32_A33NANNANT00.73OP15
327d7v_A_A33_C34AAAAA08800.27AA08
337d7v_A_C34_U35NANNANT01.62OP31
347d7v_A_U35_C36NANNANT00.67IC03
357d7v_A_C36_C37AAAAA00670.29AA00
367d7v_A_C37_G38NANNANT01.63OP11
377d7v_A_G38_C39AAAAA08880.17AA08
387d7v_A_C39_G40AAAAA00890.12AA00
397d7v_A_G40_C41AAAAA00870.18AA00
407d7v_A_C41_A42AAAAA03530.20AA03
417d7v_A_A42_G43NANNANT02.71OP01
427d7v_A_G43_U44NANNANT00.60OP13
437d7v_A_U44_G45NANNANT00.83OP20
447d7v_A_G45_A46NANNANT01.91OP10
457d7v_A_A46_A47AAAAA00890.16AA00
467d7v_A_A47_C48AAwAA01900.13AA01
477d7v_A_C48_C49AAAAA00410.28AA00
487d7v_A_C49_G50AAuAA12400.43AA12
497d7v_A_G50_G51AAwAA06730.26AA06
507d7v_A_G51_C52AAAAA08900.18AA08
517d7v_A_C52_U53AAAAA00720.21AA00
527d7v_A_U53_G54AAAAA00770.21AA00
537d7v_A_G54_C55AAAAA00680.23AA00
547d7v_A_C55_G56AAAAA00960.09AA00
557d7v_A_G56_C57AAAAA00950.09AA00
567d7v_A_C57_C58AAwAA10280.52AA10

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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