Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of xanthine riboswitch with xanthine

Results of the assignment of 88 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
017elr_A_G2_A3AAAAA08840.24 AA08
027elr_A_A3_G4AAAAA00840.10 AA00
037elr_A_G4_U5AAAAA08890.22 AA08
047elr_A_U5_A6A-BAB05790.27 AB05
057elr_A_A6_G7OPNOP15650.46 OP15
067elr_A_G7_A8AAwAA01700.24 AA01
077elr_A_A8_A9NANNANT00.73 AA11
087elr_A_A9_G10AAAAA08720.39 AA08
097elr_A_G10_C11NANNANT00.38 AA01
107elr_A_C11_G12A-BAB05450.23 AB05
117elr_A_G12_U13OPNOP15760.38 OP15
127elr_A_U13_U14AAAAA00550.28 AA00
137elr_A_U14_C15AAAAA00890.17 AA00
147elr_A_C15_A16AAAAA00710.23 AA00
157elr_A_A16_G17AAAAA00630.34 AA00
167elr_A_G17_C18AAAAA08950.10 AA08
177elr_A_C18_G19AAAAA08860.16 AA08
187elr_A_G19_G20AAAAA00690.13 AA00
197elr_A_G20_C21AAAAA00780.13 AA00
207elr_A_C21_C22AAAAA00700.10 AA00
217elr_A_C22_G23AAAAA00820.28 AA00
227elr_A_G23_A24NANNANT00.47 OP04
237elr_A_A24_A25AAAAA08740.30 AA08
247elr_A_A25_A26AAAAA00700.28 AA00
257elr_A_A26_G27NANNANT00.99 AA08
267elr_A_G27_G28AAAAA08690.30 AA08
277elr_A_G28_C29AAAAA00800.10 AA00
287elr_A_C29_C30AAAAA00870.23 AA00
297elr_A_C30_G31AAwAA10250.33 AA10
307elr_A_G31_C32AAAAA08980.10 AA08
317elr_A_C32_C33AAAAA08820.30 AA08
327elr_A_C33_C34NANNANT01.32 AA10
337elr_A_C34_G35NANNANT01.25 IC01
347elr_A_G35_G36NANNANT01.92 OP12
357elr_A_G36_A37AAAAA00640.24 AA00
367elr_A_A37_A38AAAAA00750.19 AA00
377elr_A_A38_A39AAAAA08740.30 AA08
387elr_A_A39_U40AAAAA08700.18 AA08
397elr_A_U40_U41AAAAA08900.14 AA08
407elr_A_U41_G42AAAAA00830.16 AA00
417elr_A_G42_C43AAAAA00970.10 AA00
427elr_A_C43_U44AAAAA00860.17 AA00
437elr_A_U44_C45AAAAA00910.15 AA00
447elr_A_C45_C46A-BAB05670.30 AB05
457elr_B_G2_A3AAAAA00690.24 AA00
467elr_B_A3_G4AAAAA08730.28 AA08
477elr_B_G4_U5AAAAA08950.25 AA08
487elr_B_U5_A6A-BAB05520.37 AB05
497elr_B_A6_G7OPNOP15270.42 OP15
507elr_B_G7_A8AAAAA00600.30 AA00
517elr_B_A8_A9NANNANT00.77 AA11
527elr_B_A9_G10AAAAA08790.35 AA08
537elr_B_G10_C11AAAAA08840.31 AA08
547elr_B_C11_G12A-BAB05370.18 AB05
557elr_B_G12_U13OPNOP15150.51 OP15
567elr_B_U13_U14AAAAA00570.27 AA00
577elr_B_U14_C15AAAAA00870.26 AA00
587elr_B_C15_A16AAwAA01620.23 AA01
597elr_B_A16_G17AAAAA08380.48 AA08
607elr_B_G17_C18AAAAA03680.24 AA03
617elr_B_C18_G19NANNANT01.23 OP24
627elr_B_G19_G20AAAAA08850.20 AA08
637elr_B_G20_C21AAAAA00610.08 AA00
647elr_B_C21_C22AAAAA08880.15 AA08
657elr_B_C22_G23AAAAA00760.26 AA00
667elr_B_G23_A24OPNOP04420.40 OP04
677elr_B_A24_A25AAAAA08740.37 AA08
687elr_B_A25_A26AAAAA00790.25 AA00
697elr_B_A26_G27AAwAA05260.31 AA05
707elr_B_G27_G28NANNANT00.57 AB02
717elr_B_G28_C29AAwAA11390.39 AA11
727elr_B_C29_C30AAAAA08480.39 AA08
737elr_B_C30_G31NANNANT01.19 OP24
747elr_B_G31_C32AAAAA08940.11 AA08
757elr_B_C32_C33AAAAA08700.26 AA08
767elr_B_C33_C34NANNANT00.87 AA10
777elr_B_C34_G35NANNANT00.81 OPS1
787elr_B_G35_G36NANNANT01.66 OP26
797elr_B_G36_A37AAAAA00560.25 AA00
807elr_B_A37_A38AAwAA01740.20 AA01
817elr_B_A38_A39AAAAA08630.37 AA08
827elr_B_A39_U40AAAAA00600.33 AA00
837elr_B_U40_U41AAAAA00890.20 AA00
847elr_B_U41_G42AAAAA00570.25 AA00
857elr_B_G42_C43AAAAA08840.20 AA08
867elr_B_C43_U44NANNANT00.53 AA06
877elr_B_U44_C45NANNANT00.67 AB02
887elr_B_C45_C46NANNANT00.48 AA01

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