Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Structure of a c-di-GMP riboswitch from V. cholerae

Results of the assignment of 90 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Your browser does not support the HTML5 canvas tag.
Your browser does not support the HTML5 canvas tag.
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
013irw_R_GTP8_G9NANNANT00.61 AA04
023irw_R_G9_U10AAAAA00820.21 AA00
033irw_R_U10_C11AAAAA08930.19 AA08
043irw_R_C11_A12AAwAA06910.18 AA06
053irw_R_A12_C13AAAAA08240.38 AA08
063irw_R_C13_G14NANNANT00.39 AB04
073irw_R_G14_C15NANNANT00.64 OP25
083irw_R_C15_A16NANNANT00.72 AA11
093irw_R_A16_C17AAAAA00210.47 AA00
103irw_R_C17_A18AAAAA03480.34 AA03
113irw_R_A18_G19AAAAA04310.37 AA04
123irw_R_G19_G20NANNANT00.25 AA10
133irw_R_G20_G21AAAAA04910.25 AA04
143irw_R_G21_C22AAAAA08870.18 AA08
153irw_R_C22_A23A-BAB01140.57 AB01
163irw_R_A23_A24NANNANT00.49 OP10
173irw_R_A24_A25AAAAA00570.34 AA00
183irw_R_A25_C26AAAAA00200.48 AA00
193irw_R_C26_C27AAAAA00920.15 AA00
203irw_R_C27_A28AAAAA00570.15 AA00
213irw_R_A28_U29AAAAA00700.16 AA00
223irw_R_U29_U30AAAAA00140.32 AA00
233irw_R_U30_C31NANNANT00.38 AA10
243irw_R_C31_G32AAAAA03820.24 AA03
253irw_R_G32_A33OPNOP03640.26 OP03
263irw_R_A33_A34AAAAA08780.22 AA08
273irw_R_A34_A35AAAAA04840.17 AA04
283irw_R_A35_G36NANNANT00.90 AA08
293irw_R_G36_A37AAAAA08790.24 AA08
303irw_R_A37_G38AAAAA00470.20 AA00
313irw_R_G38_U39AAAAA08580.22 AA08
323irw_R_U39_G40AAAAA04860.23 AA04
333irw_R_G40_G41AAAAA08770.27 AA08
343irw_R_G41_G42AAAAA04650.49 AA04
353irw_R_G42_A43NANNANT00.66 AA10
363irw_R_A43_C44NANNANT01.46 OPS1
373irw_R_C44_G45AAwAA05760.23 AA05
383irw_R_G45_C46AAAAA04900.26 AA04
393irw_R_C46_A47ICLIC03800.20 IC03
403irw_R_A47_A48NANNANT02.10 OP19
413irw_R_A48_A49NANNANT01.05 OP13
423irw_R_A49_G50NANNANT01.01 OP27
433irw_R_G50_C51AAAAA08810.27 AA08
443irw_R_C51_C52AAAAA00830.18 AA00
453irw_R_C52_U53ICLIC04620.33 IC04
463irw_R_U53_C54OPNOP26170.47 OP26
473irw_R_C54_C55AAAAA00350.29 AA00
483irw_R_C55_G56AAAAA04640.32 AA04
493irw_R_G56_G57AAwAA10770.18 AA10
503irw_R_G57_C58AAAAA08840.20 AA08
513irw_R_C58_C59AAAAA00900.21 AA00
523irw_R_C59_U60AAAAA04840.24 AA04
533irw_R_U60_A61AAAAA00340.50 AA00
543irw_R_A61_A62NANNANT00.86 OP02
553irw_R_A62_A63AAAAA04550.41 AA04
563irw_R_A63_C64AAAAA03450.31 AA03
573irw_R_C64_C65NANNANT00.34 AA00
583irw_R_C65_A660AAAAA04580.23 AA04
593irw_R_G75_G76AAAAA03750.28 AA03
603irw_R_G76_U77NANNANT00.50 AA04
613irw_R_U77_A78AAAAA00620.30 AA00
623irw_R_A78_G79AAAAA04800.16 AA04
633irw_R_G79_G80AAAAA08780.21 AA08
643irw_R_G80_U81AAAAA08870.16 AA08
653irw_R_U81_A82ICLIC01600.53 IC01
663irw_R_A82_G83NANNANT00.39 OP21
673irw_R_G83_C84NANNANT00.59 OP21
683irw_R_C84_G85AAwAA10210.30 AA10
693irw_R_G85_G86AAAAA08100.32 AA08
703irw_R_G86_G87AAAAA03630.32 AA03
713irw_R_G87_G88AAAAA04430.40 AA04
723irw_R_G88_U89AAAAA04630.31 AA04
733irw_R_U89_U90AAAAA04820.30 AA04
743irw_R_U90_A91AAAAA00590.18 AA00
753irw_R_A91_C92AAuAA12490.29 AA12
763irw_R_C92_C93AAAAA04660.33 AA04
773irw_R_C93_G94NANNANT00.61 AA11
783irw_R_G94_A95NANNANT00.93 IC07
793irw_R_A95_U96NANNANT02.15 OP15
803irw_R_U96_G97AAAAA03670.26 AA03
813irw_R_A660_U661AAAAA03480.27 AA03
823irw_R_U661_U662NANNANT00.63 IC03
833irw_R_U662_G663NANNANT01.59 AB02
843irw_R_G663_C664NANNANT00.92 IC03
853irw_R_C664_A665NANNANT00.58 OP15
863irw_R_A665_C666AAAAA00760.21 AA00
873irw_R_C666_U667NANNANT01.12 OP30
883irw_R_U667_C668AAAAA08940.21 AA08
893irw_R_C668_C669AAAAA04490.29 AA04
903irw_R_C669_G75NANNANT00.82 OP29

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.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

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).

Browse conformers

Return up to random steps in PDB structures ( include large structures )

Show




Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N