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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
Homeobox transcription factor CDX1 bound to methylated DNA

Results of the assignment of 66 detected steps in 1 model(s), can be also downloaded as csv 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
015lux_A_DT1_DT2A-BAB03660.33AB03
025lux_A_DT2_DG3BB2BB07440.43BB07
035lux_A_DG3_DT4BBBBB00720.26BB00
045lux_A_DT4_DG5miBBB10610.25BB10
055lux_A_DG5_DT6BBBBB00890.21BB00
065lux_A_DT6_DT7BBBBB00730.22BB00
075lux_A_DT7_DT8BBBBB00580.28BB00
085lux_A_DT8_DT9BB1BB11410.42BB11
095lux_A_DT9_DA10BBBBB01420.43BB01
105lux_A_DA10_5CM11B-ABA05390.37BA05
115lux_A_5CM11_DG12A-BAB01810.27AB01
125lux_A_DG12_DA13NANNANT00.46BB02
135lux_A_DA13_DC14BBBBB00700.33BB00
145lux_A_DC14_DC15BBBBB00790.19BB00
155lux_A_DC15_DT16BBBBB00750.17BB00
165lux_A_DT16_DC17NANNANT00.45BB10
175lux_B_DT1_DT2A-BAB01380.31AB01
185lux_B_DT2_DG3B12BB04310.21BB04
195lux_B_DG3_DT4BBBBB00630.27BB00
205lux_B_DT4_DG5B12BB04340.23BB04
215lux_B_DG5_DT6BBBBB00810.22BB00
225lux_B_DT6_DT7BBBBB00690.23BB00
235lux_B_DT7_DT8BBBBB01430.24BB01
245lux_B_DT8_DT9NANNANT00.43BB11
255lux_B_DT9_DA10BBBBB01490.42BB01
265lux_B_DA10_5CM11B-ABA05450.36BA05
275lux_B_5CM11_DG12A-BAB01520.30AB01
285lux_B_DG12_DA13BB1BB02290.40BB02
295lux_B_DA13_DC14BBBBB00730.34BB00
305lux_B_DC14_DC15BBBBB00820.18BB00
315lux_B_DC15_DT16BBBBB00810.20BB00
325lux_B_DT16_DC17B-ABA01390.28BA01
335lux_B_DC17_DC18NANNANT00.65BA10
345lux_F_DG20_DA21NANNANT00.38BA08
355lux_F_DA21_DG22AA1AA06240.46AA06
365lux_F_DG22_DG23AAAAA04760.34AA04
375lux_F_DG23_DT24NANNANT00.55AB04
385lux_F_DT24_5CM25BBBBB00310.45BB00
395lux_F_5CM25_DG26B12BB04570.18BB04
405lux_F_DG26_DT27BBBBB00390.30BB00
415lux_F_DT27_DA28BBBBB00400.36BB00
425lux_F_DA28_DA29B-ABA05670.36BA05
435lux_F_DA29_DA30miBBB14560.45BB14
445lux_F_DA30_DA31BBBBB00470.17BB00
455lux_F_DA31_DC32B-ABA05670.17BA05
465lux_F_DC32_DA33A-BAB03910.28AB03
475lux_F_DA33_DC34NANNANT00.44BB10
485lux_F_DC34_DA35NANNANT00.34BB07
495lux_F_DA35_DA36BBBBB00100.36BB00
505lux_E_DG19_DG20NANNANT01.02BB08
515lux_E_DG20_DA21NANNANT00.40BA08
525lux_E_DA21_DG22NANNANT00.62BA10
535lux_E_DG22_DG23AAAAA04670.35AA04
545lux_E_DG23_DT24NANNANT00.54AB04
555lux_E_DT24_5CM25BBBBB00350.45BB00
565lux_E_5CM25_DG26B12BB04730.19BB04
575lux_E_DG26_DT27BBBBB01360.23BB01
585lux_E_DT27_DA28miBBB15540.38BB15
595lux_E_DA28_DA29B-ABA05760.32BA05
605lux_E_DA29_DA30miBBB14780.45BB14
615lux_E_DA30_DA31BBBBB00660.16BB00
625lux_E_DA31_DC32BBBBB01840.14BB01
635lux_E_DC32_DA33BBBBB00270.34BB00
645lux_E_DA33_DC34NANNANT00.43BB10
655lux_E_DC34_DA35BB2BB07270.32BB07
665lux_E_DA35_DA36NANNANT00.41BB14

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
step:
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
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

Drag the plot for panning, scroll to zoom, click a point to show superposition in JSmol.

Download

Results (as csv)
Restraints (default edits file)
Best NtC fitted to input structure.

Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the 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).

Show



Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N