DNATCO v3.2: results

Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein

Results of the assignment of 56 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.

step number	Step name	CANA	NtC	confal	rmsd
01	7d7v_A_G2_C3	AAA	AA00	95	0.13	AA00
02	7d7v_A_C3_G4	AAA	AA00	89	0.14	AA00
03	7d7v_A_G4_C5	AAw	AA01	87	0.15	AA01
04	7d7v_A_C5_A6	A-B	AB04	92	0.17	AB04
05	7d7v_A_A6_A7	NAN	NANT	0	0.64	OP26
06	7d7v_A_A7_C8	AAA	AA08	79	0.33	AA08
07	7d7v_A_C8_A9	NAN	NANT	0	0.64	AB04
08	7d7v_A_A9_U10	NAN	NANT	0	0.47	OP13
09	7d7v_A_U10_C11	NAN	NANT	0	1.75	OP10
10	7d7v_A_C11_C12	AAA	AA00	73	0.27	AA00
11	7d7v_A_C12_C13	AAA	AA08	69	0.30	AA08
12	7d7v_A_C13_C14	NAN	NANT	0	0.47	AA10
13	7d7v_A_C14_G15	OPN	OP29	17	0.38	OP29
14	7d7v_A_G15_C16	AAA	AA00	74	0.21	AA00
15	7d7v_A_C16_C17	AAA	AA00	44	0.18	AA00
16	7d7v_A_C17_G18	AAw	AA01	41	0.25	AA01
17	7d7v_A_G18_G19	AAA	AA08	89	0.16	AA08
18	7d7v_A_G19_U20	AAA	AA00	83	0.19	AA00
19	7d7v_A_U20_U21	AAA	AA00	78	0.12	AA00
20	7d7v_A_U21_G22	AAA	AA08	80	0.19	AA08
21	7d7v_A_G22_G23	AAA	AA00	77	0.18	AA00
22	7d7v_A_G23_G24	AAA	AA00	74	0.23	AA00
23	7d7v_A_G24_C25	AAA	AA00	79	0.07	AA00
24	7d7v_A_C25_G26	AAA	AA00	88	0.12	AA00
25	7d7v_A_G26_C27	AAA	AA00	86	0.16	AA00
26	7d7v_A_C27_A28	AAA	AA00	61	0.32	AA00
27	7d7v_A_A28_U29	AAA	AA00	85	0.20	AA00
28	7d7v_A_U29_U30	ICL	IC02	94	0.16	IC02
29	7d7v_A_U30_G31	ZZZ	ZZ02	13	0.59	ZZ02
30	7d7v_A_G31_C32	NAN	NANT	0	0.98	IC03
31	7d7v_A_C32_A33	NAN	NANT	0	0.73	OP15
32	7d7v_A_A33_C34	AAA	AA08	80	0.27	AA08
33	7d7v_A_C34_U35	NAN	NANT	0	1.62	OP31
34	7d7v_A_U35_C36	NAN	NANT	0	0.67	IC03
35	7d7v_A_C36_C37	AAA	AA00	67	0.29	AA00
36	7d7v_A_C37_G38	NAN	NANT	0	1.63	OP11
37	7d7v_A_G38_C39	AAA	AA08	88	0.17	AA08
38	7d7v_A_C39_G40	AAA	AA00	89	0.12	AA00
39	7d7v_A_G40_C41	AAA	AA00	87	0.18	AA00
40	7d7v_A_C41_A42	AAA	AA03	53	0.20	AA03
41	7d7v_A_A42_G43	NAN	NANT	0	2.71	OP01
42	7d7v_A_G43_U44	NAN	NANT	0	0.60	OP13
43	7d7v_A_U44_G45	NAN	NANT	0	0.83	OP20
44	7d7v_A_G45_A46	NAN	NANT	0	1.91	OP10
45	7d7v_A_A46_A47	AAA	AA00	89	0.16	AA00
46	7d7v_A_A47_C48	AAw	AA01	90	0.13	AA01
47	7d7v_A_C48_C49	AAA	AA00	41	0.28	AA00
48	7d7v_A_C49_G50	AAu	AA12	40	0.43	AA12
49	7d7v_A_G50_G51	AAw	AA06	73	0.26	AA06
50	7d7v_A_G51_C52	AAA	AA08	90	0.18	AA08
51	7d7v_A_C52_U53	AAA	AA00	72	0.21	AA00
52	7d7v_A_U53_G54	AAA	AA00	77	0.21	AA00
53	7d7v_A_G54_C55	AAA	AA00	68	0.23	AA00
54	7d7v_A_C55_G56	AAA	AA00	96	0.09	AA00
55	7d7v_A_G56_C57	AAA	AA00	95	0.09	AA00
56	7d7v_A_C57_C58	AAw	AA10	28	0.52	AA10

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

step:
Table of conformers

δ1

ε1

ζ1

α2

β2

γ2

δ2

χ1

χ2

μ

NN

CC

step_torsions

ntC_average

Δ torsions

torsion scores

comments step confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

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

Show

Color by conformation group (pyramids)

Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

Color by NtC (balls)

A-B

B-A

B

IC

OPN

Z

N

Click the Summary/Torsions/Similar/... tabs for more details.
Center view on step or molecule.
Show reference and contacts	model altloc