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Conformers: ABBIImiBZICOPNSYNN
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Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)

Results of the assignment of 70 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 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
017tzu_A_G9_C10AAAAA00900.11 AA00
027tzu_A_C10_G11AAAAA00880.11 AA00
037tzu_A_G11_A12AAAAA00360.20 AA00
047tzu_A_A12_C13AAAAA04640.24 AA04
057tzu_A_C13_U14AAAAA00830.19 AA00
067tzu_A_U14_C15AAAAA00660.25 AA00
077tzu_A_C15_G16AAAAA00470.30 AA00
087tzu_A_G16_G17AAAAA00730.19 AA00
097tzu_A_G17_G18AAAAA00690.25 AA00
107tzu_A_G18_G19AAAAA00670.29 AA00
117tzu_A_G19_U20AAwAA01410.32 AA01
127tzu_A_U20_G21NANNANT02.42 OP18
137tzu_A_G21_C22AAAAA08750.18 AA08
147tzu_A_C22_C23AAAAA00720.24 AA00
157tzu_A_C23_C24A-BAB05670.35 AB05
167tzu_A_C24_U25NANNANT00.65 OP15
177tzu_A_C30_G31AAAAA00110.56 AA00
187tzu_A_G31_U32NANNANT00.49 AA10
197tzu_A_U32_G33NANNANT00.75 AA05
207tzu_A_G33_A34NANNANT01.33 ZZS1
217tzu_A_A34_A35AAAAA04210.66 AA04
227tzu_A_A35_G36AAAAA08550.49 AA08
237tzu_A_G36_G37AAAAA00520.17 AA00
247tzu_A_G37_C38AAAAA00160.37 AA00
257tzu_A_C38_U39AAAAA00850.16 AA00
267tzu_A_U39_G40AAAAA08720.33 AA08
277tzu_A_G40_A41NANNANT00.26 OP04
287tzu_A_A41_G42AAAAA08680.40 AA08
297tzu_A_G42_A43ICLIC01720.28 IC01
307tzu_A_A43_A44NANNANT01.11 OP22
317tzu_A_A44_A45NANNANT00.61 ZZ02
327tzu_A_A47_C48AAAAA08880.14 AA08
337tzu_A_C48_C49AAAAA08880.09 AA08
347tzu_A_C49_C50AAAAA00830.21 AA00
357tzu_A_C50_G51AAAAA00650.18 AA00
367tzu_A_G51_U52OPNOP28600.19 OP28
377tzu_A_U52_A53NANNANT00.62 ZZ1S
387tzu_A_A56_C57AAAAA08440.50 AA08
397tzu_A_C57_C58AAAAA00620.23 AA00
407tzu_A_C58_U59AAAAA00680.23 AA00
417tzu_A_U59_G60AAAAA08770.38 AA08
427tzu_A_G60_A61NANNANT00.48 ZZ01
437tzu_A_C63_U64AAAAA08270.35 AA08
447tzu_A_U64_G65AAAAA08500.35 AA08
457tzu_A_G65_G66AAAAA00700.21 AA00
467tzu_A_G66_A67AAwAA11620.23 AA11
477tzu_A_A67_U68AAAAA08110.40 AA08
487tzu_A_U68_A69OPNOP03530.35 OP03
497tzu_A_A69_A70AAAAA00530.30 AA00
507tzu_A_A70_U71AAAAA00810.17 AA00
517tzu_A_U71_G72NANNANT01.23 OP17
527tzu_A_G72_C73NANNANT01.89 OP29
537tzu_A_C73_C74AAuAA12540.46 AA12
547tzu_A_C74_A75AAAAA00690.26 AA00
557tzu_A_A75_G76AAwAA01250.37 AA01
567tzu_A_G76_C77AAAAA08760.34 AA08
577tzu_A_C77_G78NANNANT00.40 ZZ01
587tzu_A_G78_U79NANNANT00.98 OP21
597tzu_A_U79_A80NANNANT01.00 OP13
607tzu_A_A80_G81AAAAA08400.40 AA08
617tzu_A_G81_G82AAAAA00850.16 AA00
627tzu_A_G82_G83AAAAA04450.43 AA04
637tzu_A_G83_A84AAuAA07340.34 AA07
647tzu_A_A84_A85NANNANT00.54 IC07
657tzu_A_A85_G86B-ABA16880.11 BA16
667tzu_A_G86_U87AAAAA00850.12 AA00
677tzu_A_U87_C88AAAAA00840.20 AA00
687tzu_A_C88_G89AAAAA08850.17 AA08
697tzu_A_G89_C90AAAAA00840.16 AA00
707tzu_A_C90_A91NANNANT01.30 OP01

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).

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