Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU at the active site

Results of the assignment of 52 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
017k30_B_DG1_DT2BBwBB02260.34 BB02
027k30_B_DT2_DC3BBBBB00230.45 BB00
037k30_B_DC3_DG4NANNANT00.39 BB08
047k30_B_DG4_DT5BBBBB00220.27 BB00
057k30_B_DT5_DT6BBBBB00800.15 BB00
067k30_B_DT6_DC7miBBB15770.23 BB15
077k30_B_DC7_DG8BBBBB00320.31 BB00
087k30_B_DG8_DC9miBBB10740.31 BB10
097k30_B_DC9_DT10B12BB04720.21 BB04
107k30_B_DT10_DA11BBBBB00630.28 BB00
117k30_B_DA11_DC12BBBBB00570.26 BB00
127k30_B_DC12_DA13B-ABA08710.24 BA08
137k30_B_DA13_DG14NANNANT00.44 BB10
147k30_B_DG14_DG15NANNANT00.75 BB08
157k30_B_DG15_BRU16NANNANT00.37 BB00
167k30_B_BRU16_DC17B12BB04120.60 BB04
177k30_B_DC17_DG18B-ABA13340.53 BA13
187k30_B_DG18_DT19NANNANT00.54 AB02
197k30_B_DT19_DC20miBBB15320.35 BB15
207k30_B_DC20_DG21NANNANT00.44 BA13
217k30_B_DG21_DG22A-BAB03230.29 AB03
227k30_B_DG22_DT23BBBBB00600.25 BB00
237k30_B_DT23_DC24BBBBB00710.22 BB00
247k30_B_DC24_DT25miBBB10510.32 BB10
257k30_B_DT25_DG26B12BB04560.32 BB04
267k30_B_DG26_DC27miBBB13330.28 BB13
277k30_C_DG1_DC2BBBBB00210.31 BB00
287k30_C_DC2_DA3BB2BB07670.27 BB07
297k30_C_DA3_DG4BBBBB00680.23 BB00
307k30_C_DG4_DA5B12BB04790.19 BB04
317k30_C_DA5_DC6BBBBB00140.27 BB00
327k30_C_DC6_DC7BBBBB00600.20 BB00
337k30_C_DC7_DG8B12BB04770.31 BB04
347k30_C_DG8_DA9miBBB10560.29 BB10
357k30_C_DA9_DC10A-BAB02510.39 AB02
367k30_C_DC10_DG11B12BB04580.30 BB04
377k30_C_DG11_DA12B12BB04500.29 BB04
387k30_C_DA12_DC13NANNANT00.69 BA08
397k30_C_DC13_DU14NANNANT00.80 OP17
407k30_C_DU14_DT15NANNANT02.17 OP21
417k30_C_DT15_DG16BBBBB00570.32 BB00
427k30_C_DG16_DT17BBBBB00720.18 BB00
437k30_C_DT17_DA18NANNANT00.59 BB11
447k30_C_DA18_DG19NANNANT00.70 BB02
457k30_C_DG19_DC20BB2BB07140.31 BB07
467k30_C_DC20_DG21BBwBB11540.46 BB11
477k30_C_DG21_DA22A-BAB03370.35 AB03
487k30_C_DA22_DA23B12BB04780.12 BB04
497k30_C_DA23_DC24BBBBB00870.19 BB00
507k30_C_DC24_DG25BBBBB00360.35 BB00
517k30_C_DG25_DA26NANNANT00.62 BB11
527k30_C_DA26_DC27B-ABA10720.34 BA10

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