Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state

Results of the assignment of 48 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
017kef_R_A1_U2AAAAA00610.22 AA00
027kef_R_U2_C3AAAAA00890.12 AA00
037kef_R_C3_G4AAAAA00540.29 AA00
047kef_R_G4_A5AAAAA0880.57 AA08
057kef_R_A5_G6AAAAA0060.55 AA00
067kef_R_G6_A7AAAAA00810.15 AA00
077kef_R_A7_G8AAAAA04840.34 AA04
087kef_R_G8_G9AAAAA00830.20 AA00
097kef_R_G9_A10NANNANT00.60 AA04
107kef_T_DC1_DT2B-ABA08680.42 BA08
117kef_T_DT2_DA3NANNANT00.80 AB05
127kef_T_DA3_DC4NANNANT00.69 BB02
137kef_T_DC4_DC5BBBBB00160.40 BB00
147kef_T_DC5_DG6NANNANT00.49 BB07
157kef_T_DG6_DA7miBBB10600.25 BB10
167kef_T_DA7_DT8NANNANT00.69 BA10
177kef_T_DT8_DA9NANNANT00.39 BB16
187kef_T_DA9_DA10B-ABA09610.38 BA09
197kef_T_DA10_DG11A-BAB01120.42 AB01
207kef_T_DG11_DC12BBBBB01320.32 BB01
217kef_T_DC12_DA13NANNANT00.84 BB00
227kef_T_DA13_DG14B-ABA08130.57 BA08
237kef_T_DG14_DA15NANNANT00.42 AB02
247kef_T_DA15_DC16NANNANT00.64 BB10
257kef_T_DC16_DG17B-ABA09450.36 BA09
267kef_T_DT19_DC20AAwAA06650.28 AA06
277kef_T_DC20_DC21AAAAA08750.29 AA08
287kef_T_DC21_DT22NANNANT00.75 AB02
297kef_T_DT22_DC23AAwAA0190.35 AA01
307kef_T_DC23_DT24NANNANT00.44 AB03
317kef_T_DT24_DC25BBBBB01410.39 BB01
327kef_T_DC25_DG26BBBBB00210.38 BB00
337kef_T_DG26_DA27NANNANT00.58 BB10
347kef_T_DA27_DT28NANNANT00.87 AB02
357kef_N_DT3_DC4AAAAA04180.35 AA04
367kef_N_DC4_DT5NANNANT00.70 AB02
377kef_N_DT5_DG6BBwBB03350.42 BB03
387kef_N_DG6_DC7BBwBB03490.45 BB03
397kef_N_DC7_DT8BBwBB03540.35 BB03
407kef_N_DT8_DT9NANNANT00.36 BB17
417kef_N_DT9_DA10NANNANT00.57 BB07
427kef_N_DA10_DT11NANNANT00.35 BB10
437kef_N_DT11_DC12B12BB04190.47 BB04
447kef_N_DC12_DG13B12BB04540.41 BB04
457kef_N_DG13_DG14NANNANT00.45 BB15
467kef_N_DG14_DT15BBBBB00360.38 BB00
477kef_N_DT15_DA16B12BB04200.42 BB04
487kef_N_DA16_DG17BBBBB01370.47 BB01

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