DNATCO v3.2: results

THREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME

Results of the assignment of 135 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
001	1hmh_A_C21_C30	AAA	AA00	79	0.28	AA00
002	1hmh_A_G21.L_A22.L	OPN	OP04	53	0.28	OP04
003	1hmh_A_A22.L_A23.L	AAA	AA08	69	0.30	AA08
004	1hmh_A_C22_C21	AAA	AA00	96	0.14	AA00
005	1hmh_A_A23_C22	AAA	AA00	58	0.24	AA00
006	1hmh_A_A23.L_A24.L	AAA	AA00	14	0.33	AA00
007	1hmh_A_A24.L_G114	AAA	AA08	35	0.69	AA08
008	1hmh_A_G24_A23	AAA	AA00	92	0.18	AA00
009	1hmh_A_C25_G24	AAA	AA00	54	0.31	AA00
010	1hmh_A_G26_C25	AAA	AA00	87	0.29	AA00
011	1hmh_A_G27_G26	AAA	AA00	85	0.23	AA00
012	1hmh_A_C30_U40	AAA	AA00	95	0.11	AA00
013	1hmh_A_U40_G50	OPN	OP04	66	0.13	OP04
014	1hmh_A_G50_A60	AAA	AA00	42	0.37	AA00
015	1hmh_A_A60_U70	NAN	NANT	0	0.52	OP01
016	1hmh_A_U70_G80	A-B	AB05	42	0.43	AB05
017	1hmh_A_G80_A90	OPN	OP10	50	0.20	OP10
018	1hmh_A_A90_G101	AAA	AA04	29	0.63	AA04
019	1hmh_A_G101_G102	AAA	AA00	88	0.22	AA00
020	1hmh_A_G102_C103	AAA	AA00	54	0.23	AA00
021	1hmh_A_C103_C104	AAA	AA00	53	0.26	AA00
022	1hmh_A_C104_G21.L	AAA	AA00	80	0.30	AA00
023	1hmh_A_C111_G120	AAA	AA00	20	0.52	AA00
024	1hmh_A_C112_C111	AAA	AA00	72	0.22	AA00
025	1hmh_A_G113_C112	AAA	AA00	88	0.21	AA00
026	1hmh_A_G114_G113	AAA	AA00	82	0.18	AA00
027	1hmh_A_G120_A130	AAu	AA12	74	0.38	AA12
028	1hmh_A_A130_A140	AAA	AA00	38	0.47	AA00
029	1hmh_A_A140_A151	AAA	AA00	87	0.09	AA00
030	1hmh_A_A151_C152	AAA	AA00	45	0.35	AA00
031	1hmh_A_C152_C153	AAA	AA00	87	0.13	AA00
032	1hmh_A_C153_G154	AAA	AA00	79	0.18	AA00
033	1hmh_A_G154_U155	AAA	AA00	85	0.17	AA00
034	1hmh_B_DG11_DG12	AAA	AA00	86	0.41	AA00
035	1hmh_B_DG12_DT13	AAA	AA00	61	0.37	AA00
036	1hmh_B_DT13_DC14	AAA	AA00	53	0.39	AA00
037	1hmh_B_DC14_DG15	AAA	AA00	39	0.44	AA00
038	1hmh_B_DG15_DC16	AAA	AA04	63	0.36	AA04
039	1hmh_B_DC16_DC17	AAA	AA00	22	0.43	AA00
040	1hmh_B_DT161_DC170	NAN	NANT	0	0.56	OP16
041	1hmh_B_DG162_DT161	A-B	AB01	43	0.33	AB01
042	1hmh_B_DG163_DG162	AAA	AA00	87	0.20	AA00
043	1hmh_B_DC164_DG163	AAA	AA00	83	0.15	AA00
044	1hmh_B_DA165_DC164	AAA	AA00	90	0.18	AA00
045	1hmh_B_DC170_DG11	AAA	AA00	55	0.35	AA00
046	1hmh_C_C21_C30	AAA	AA00	34	0.43	AA00
047	1hmh_C_G21.L_A22.L	OPN	OP04	59	0.21	OP04
048	1hmh_C_A22.L_A23.L	AAA	AA08	65	0.29	AA08
049	1hmh_C_C22_C21	AAA	AA00	96	0.10	AA00
050	1hmh_C_A23_C22	AAA	AA00	54	0.17	AA00
051	1hmh_C_A23.L_A24.L	AAA	AA00	30	0.28	AA00
052	1hmh_C_A24.L_G114	AAA	AA08	13	0.88	AA08
053	1hmh_C_G24_A23	AAA	AA00	64	0.19	AA00
054	1hmh_C_C25_G24	AAA	AA00	97	0.18	AA00
055	1hmh_C_G26_C25	AAA	AA00	97	0.09	AA00
056	1hmh_C_G27_G26	AAA	AA00	87	0.09	AA00
057	1hmh_C_C30_U40	AAA	AA00	86	0.19	AA00
058	1hmh_C_U40_G50	OPN	OP04	71	0.10	OP04
059	1hmh_C_G50_A60	AAA	AA00	54	0.31	AA00
060	1hmh_C_A60_U70	OPN	OP01	70	0.46	OP01
061	1hmh_C_U70_G80	A-B	AB05	54	0.44	AB05
062	1hmh_C_G80_A90	OPN	OP10	25	0.27	OP10
063	1hmh_C_A90_G101	AAA	AA08	13	0.63	AA08
064	1hmh_C_G101_G102	AAA	AA00	68	0.25	AA00
065	1hmh_C_G102_C103	AAA	AA00	74	0.18	AA00
066	1hmh_C_C103_C104	AAA	AA00	89	0.17	AA00
067	1hmh_C_C104_G21.L	AAA	AA00	82	0.24	AA00
068	1hmh_C_C111_G120	AAA	AA00	32	0.43	AA00
069	1hmh_C_C112_C111	AAA	AA00	68	0.21	AA00
070	1hmh_C_G113_C112	AAw	AA10	88	0.12	AA10
071	1hmh_C_G114_G113	AAA	AA00	36	0.24	AA00
072	1hmh_C_G120_A130	AAu	AA12	78	0.39	AA12
073	1hmh_C_A130_A140	AAA	AA00	20	0.52	AA00
074	1hmh_C_A140_A151	AAA	AA00	72	0.11	AA00
075	1hmh_C_A151_C152	AAA	AA00	57	0.30	AA00
076	1hmh_C_C152_C153	AAA	AA00	62	0.16	AA00
077	1hmh_C_C153_G154	AAA	AA00	86	0.24	AA00
078	1hmh_C_G154_U155	AAA	AA00	86	0.27	AA00
079	1hmh_D_DG11_DG12	AAA	AA04	59	0.36	AA04
080	1hmh_D_DG12_DT13	AAA	AA00	64	0.29	AA00
081	1hmh_D_DT13_DC14	AAw	AA10	43	0.37	AA10
082	1hmh_D_DC14_DG15	AAA	AA00	70	0.18	AA00
083	1hmh_D_DG15_DC16	AAA	AA00	91	0.16	AA00
084	1hmh_D_DC16_DC17	AAA	AA00	11	0.33	AA00
085	1hmh_D_DT161_DC170	NAN	NANT	0	0.89	OP10
086	1hmh_D_DG162_DT161	A-B	AB01	59	0.33	AB01
087	1hmh_D_DG163_DG162	AAA	AA00	25	0.26	AA00
088	1hmh_D_DC164_DG163	AAA	AA00	74	0.20	AA00
089	1hmh_D_DA165_DC164	AAA	AA00	69	0.24	AA00
090	1hmh_D_DC170_DG11	AAA	AA08	28	0.30	AA08
091	1hmh_E_C21_C30	AAA	AA04	67	0.32	AA04
092	1hmh_E_G21.L_A22.L	OPN	OP04	55	0.32	OP04
093	1hmh_E_A22.L_A23.L	AAA	AA00	37	0.40	AA00
094	1hmh_E_C22_C21	AAA	AA00	65	0.33	AA00
095	1hmh_E_A23_C22	AAA	AA00	79	0.21	AA00
096	1hmh_E_A23.L_A24.L	AAA	AA00	50	0.27	AA00
097	1hmh_E_A24.L_G114	NAN	NANT	0	0.86	AA04
098	1hmh_E_G24_A23	AAA	AA00	83	0.13	AA00
099	1hmh_E_C25_G24	AAA	AA00	96	0.10	AA00
100	1hmh_E_G26_C25	AAA	AA00	93	0.20	AA00
101	1hmh_E_G27_G26	AAA	AA00	90	0.11	AA00
102	1hmh_E_C30_U40	AAA	AA00	80	0.12	AA00
103	1hmh_E_U40_G50	OPN	OP04	76	0.15	OP04
104	1hmh_E_G50_A60	AAA	AA08	46	0.28	AA08
105	1hmh_E_A60_U70	OPN	OP01	40	0.56	OP01
106	1hmh_E_U70_G80	A-B	AB05	22	0.44	AB05
107	1hmh_E_G80_A90	NAN	NANT	0	0.24	OP10
108	1hmh_E_A90_G101	AAA	AA08	13	0.56	AA08
109	1hmh_E_G101_G102	AAA	AA00	67	0.22	AA00
110	1hmh_E_G102_C103	AAA	AA00	77	0.17	AA00
111	1hmh_E_C103_C104	AAA	AA08	79	0.27	AA08
112	1hmh_E_C104_G21.L	AAA	AA00	83	0.27	AA00
113	1hmh_E_C111_G120	AAA	AA08	65	0.41	AA08
114	1hmh_E_C112_C111	AAA	AA00	64	0.25	AA00
115	1hmh_E_G113_C112	AAA	AA00	78	0.24	AA00
116	1hmh_E_G114_G113	AAA	AA00	76	0.32	AA00
117	1hmh_E_G120_A130	AAu	AA13	88	0.21	AA13
118	1hmh_E_A130_A140	AAA	AA00	21	0.51	AA00
119	1hmh_E_A140_A151	AAA	AA00	84	0.22	AA00
120	1hmh_E_A151_C152	AAA	AA00	77	0.29	AA00
121	1hmh_E_C152_C153	AAA	AA00	62	0.18	AA00
122	1hmh_E_C153_G154	AAA	AA00	82	0.23	AA00
123	1hmh_E_G154_U155	AAA	AA00	76	0.20	AA00
124	1hmh_F_DG11_DG12	AAA	AA00	67	0.38	AA00
125	1hmh_F_DG12_DT13	AAA	AA00	84	0.27	AA00
126	1hmh_F_DT13_DC14	AAA	AA00	72	0.29	AA00
127	1hmh_F_DC14_DG15	AAA	AA00	70	0.23	AA00
128	1hmh_F_DG15_DC16	AAA	AA00	88	0.18	AA00
129	1hmh_F_DC16_DC17	AAA	AA00	47	0.29	AA00
130	1hmh_F_DT161_DC170	NAN	NANT	0	0.67	OP10
131	1hmh_F_DG162_DT161	A-B	AB01	73	0.33	AB01
132	1hmh_F_DG163_DG162	AAA	AA00	30	0.43	AA00
133	1hmh_F_DC164_DG163	AAA	AA00	62	0.38	AA00
134	1hmh_F_DA165_DC164	AAw	AA10	17	0.46	AA10
135	1hmh_F_DC170_DG11	AAA	AA08	35	0.36	AA08

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

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B

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Z

N

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