Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot

Results of the assignment of 64 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
017mlx_R_G1_G2AAAAA00480.34 AA00
027mlx_R_G2_C3AAAAA00830.20 AA00
037mlx_R_C3_G4AAAAA00900.13 AA00
047mlx_R_G4_G5AAAAA00900.16 AA00
057mlx_R_G5_U6AAAAA00830.13 AA00
067mlx_R_U6_G7AAAAA00820.09 AA00
077mlx_R_G7_U8AAAAA00820.14 AA00
087mlx_R_U8_A9AAAAA00940.12 AA00
097mlx_R_A9_A10AAAAA00790.12 AA00
107mlx_R_A10_G11AAAAA00850.10 AA00
117mlx_R_G11_U12AAAAA00700.29 AA00
127mlx_R_U12_G13NANNANT00.39 IC07
137mlx_R_G13_C14OPNOP11710.44 OP11
147mlx_R_C14_A15OPNOP04790.16 OP04
157mlx_R_A15_G16AAAAA00540.30 AA00
167mlx_R_G16_C17AAAAA00700.13 AA00
177mlx_R_C17_C18AAAAA00890.16 AA00
187mlx_R_C18_C19AAAAA00800.14 AA00
197mlx_R_C19_G20AAAAA00650.30 AA00
207mlx_R_G20_U21AAAAA00590.28 AA00
217mlx_R_U21_C22AAAAA00620.36 AA00
227mlx_R_C22_U23AAAAA00920.11 AA00
237mlx_R_U23_U24AAAAA00650.13 AA00
247mlx_R_U24_A25AAAAA00920.10 AA00
257mlx_R_A25_C26AAAAA00770.10 AA00
267mlx_R_C26_A27AAAAA00900.12 AA00
277mlx_R_A27_C28AAAAA08900.25 AA08
287mlx_R_C28_C29AAAAA00950.12 AA00
297mlx_R_C29_G30NANNANT00.35 AA10
307mlx_R_G30_U31AAAAA08860.21 AA08
317mlx_R_U31_G32NANNANT01.18 AA11
327mlx_R_G32_C33AAAAA00830.21 AA00
337mlx_R_C33_G34AAwAA01840.20 AA01
347mlx_R_G34_G35AAAAA08640.23 AA08
357mlx_R_G35_C36AAAAA08770.20 AA08
367mlx_R_C36_A37AAwAA01600.26 AA01
377mlx_R_A37_C38AAAAA08110.55 AA08
387mlx_R_C38_A39AAAAA00910.13 AA00
397mlx_R_A39_G40AAAAA00850.09 AA00
407mlx_R_G40_A41NANNANT00.60 OP05
417mlx_R_A41_A42NANNANT00.73 OP20
427mlx_R_A42_A43NANNANT00.63 OP13
437mlx_R_A43_C44OPNOP12740.28 OP12
447mlx_R_C44_A45AAAAA00560.35 AA00
457mlx_R_A45_C46AAAAA00760.26 AA00
467mlx_R_C46_U47AAAAA00920.16 AA00
477mlx_R_U47_G48AAAAA00900.12 AA00
487mlx_R_G48_A49NANNANT00.33 AA06
497mlx_R_A49_U50AAAAA08830.22 AA08
507mlx_R_U50_G51NANNANT00.42 AA06
517mlx_R_G51_U52AAwAA05290.52 AA05
527mlx_R_U52_C53AAAAA08450.26 AA08
537mlx_R_C53_G54NANNANT00.50 AA06
547mlx_R_G54_U55AAwAA01570.20 AA01
557mlx_R_U55_A56A-BAB05240.37 AB05
567mlx_R_A56_U57NANNANT01.42 IC01
577mlx_R_U57_A58NANNANT01.77 OP20
587mlx_R_A58_C59NANNANT00.91 OP13
597mlx_R_C59_A60NANNANT00.81 IC02
607mlx_R_A60_G61NANNANT00.82 BA17
617mlx_R_G61_G62AAAAA04730.25 AA04
627mlx_R_G62_G63AAAAA00690.19 AA00
637mlx_R_G63_C64AAAAA00870.20 AA00
647mlx_R_C64_G65NANNANT00.77 BB2S

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