BMRB: 34651

NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O

Authors

Santoro, A., Buonocore, M., Grimaldi, M., D'Ursi, A.

Assembly

Spike glycoprotein

Entity

1. Spike glycoprotein (polymer), 25 monomers, 2772.994 Da Detail

GVEGFNCYFP LQSYGFQPTN GVGYQ

Formula weight

2772.994 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chemcal Shifts

¹H: 140, ¹³C: 53 assignments Detail

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ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	GLY	HA2	H	3.831	0.016
2	1	1	GLY	HA3	H	3.831	0.016
3	1	1	GLY	CA	C	41.864	0.000
4	1	2	VAL	H	H	8.067	0.009
5	1	2	VAL	HA	H	4.032	0.013
6	1	2	VAL	HB	H	1.988	0.008
7	1	2	VAL	HG21	H	0.832	0.015
8	1	2	VAL	HG22	H	0.832	0.015
9	1	2	VAL	HG23	H	0.832	0.015
10	1	2	VAL	CA	C	61.295	0.000
11	1	2	VAL	CB	C	30.896	0.000
12	1	2	VAL	CG2	C	18.710	0.000
13	1	3	GLU	H	H	8.075	0.011
14	1	3	GLU	HA	H	4.317	0.009
15	1	3	GLU	HB2	H	2.014	0.009
16	1	3	GLU	HB3	H	1.889	0.008
17	1	3	GLU	HG2	H	2.362	0.004
18	1	3	GLU	HG3	H	2.362	0.004
19	1	3	GLU	CA	C	54.376	0.000
20	1	3	GLU	CB	C	27.324	0.018
21	1	3	GLU	CG	C	30.750	0.000
22	1	4	GLY	H	H	7.951	0.009
23	1	4	GLY	HA2	H	3.794	0.006
24	1	4	GLY	HA3	H	3.794	0.006
25	1	4	GLY	CA	C	43.639	0.000
26	1	5	PHE	H	H	7.636	0.009
27	1	5	PHE	HA	H	4.468	0.031
28	1	5	PHE	HB2	H	2.985	0.015
29	1	5	PHE	HB3	H	2.985	0.015
30	1	5	PHE	HD1	H	7.093	0.000
31	1	5	PHE	HD2	H	7.093	0.000
32	1	5	PHE	HE1	H	7.182	0.000
33	1	5	PHE	HE2	H	7.182	0.000
34	1	5	PHE	CA	C	54.978	0.000
35	1	5	PHE	CB	C	37.790	0.000
36	1	6	ASN	H	H	7.899	0.010
37	1	6	ASN	HA	H	4.498	0.009
38	1	6	ASN	HB2	H	2.619	0.004
39	1	6	ASN	HB3	H	2.619	0.004
40	1	6	ASN	CA	C	51.929	0.000
41	1	6	ASN	CB	C	37.028	0.000
42	1	7	CYS	H	H	7.642	0.005
43	1	7	CYS	HA	H	4.269	0.002
44	1	7	CYS	HB2	H	2.735	0.005
45	1	7	CYS	HB3	H	2.629	0.008
46	1	7	CYS	CA	C	56.954	0.000
47	1	7	CYS	CB	C	25.961	0.011
48	1	8	TYR	H	H	7.709	0.006
49	1	8	TYR	HA	H	4.483	0.005
50	1	8	TYR	HB2	H	2.957	0.006
51	1	8	TYR	HB3	H	2.805	0.011
52	1	8	TYR	HD1	H	6.722	0.007
53	1	8	TYR	HD2	H	6.722	0.007
54	1	8	TYR	HE1	H	6.970	0.003
55	1	8	TYR	HE2	H	6.970	0.003
56	1	8	TYR	CA	C	56.268	0.000
57	1	8	TYR	CB	C	37.120	0.014
58	1	9	PHE	H	H	8.026	0.003
59	1	9	PHE	HA	H	4.627	0.009
60	1	9	PHE	HB2	H	2.752	0.007
61	1	9	PHE	HB3	H	2.752	0.007
62	1	9	PHE	CB	C	37.044	0.000
63	1	10	PRO	HA	H	4.196	0.007
64	1	10	PRO	HB2	H	2.162	0.016
65	1	10	PRO	HB3	H	1.749	0.015
66	1	10	PRO	HG2	H	1.816	0.006
67	1	10	PRO	HG3	H	1.816	0.006
68	1	10	PRO	HD2	H	3.577	0.001
69	1	10	PRO	HD3	H	3.188	0.002
70	1	10	PRO	CA	C	63.150	0.000
71	1	10	PRO	CB	C	29.779	0.106
72	1	10	PRO	CG	C	25.523	0.000
73	1	10	PRO	CD	C	48.912	0.000
74	1	11	LEU	H	H	6.787	0.010
75	1	11	LEU	HA	H	4.130	0.010
76	1	11	LEU	HB2	H	1.522	0.011
77	1	11	LEU	HB3	H	1.522	0.011
78	1	11	LEU	HD11	H	0.828	0.006
79	1	11	LEU	HD12	H	0.828	0.006
80	1	11	LEU	HD13	H	0.828	0.006
81	1	11	LEU	HD21	H	0.750	0.008
82	1	11	LEU	HD22	H	0.750	0.008
83	1	11	LEU	HD23	H	0.750	0.008
84	1	11	LEU	CA	C	54.847	0.000
85	1	11	LEU	CB	C	40.239	0.000
86	1	11	LEU	CD1	C	22.265	0.000
87	1	11	LEU	CD2	C	20.802	0.000
88	1	12	GLN	H	H	7.950	0.006
89	1	12	GLN	HA	H	4.130	0.009
90	1	12	GLN	HB2	H	2.019	0.005
91	1	12	GLN	HB3	H	2.019	0.005
92	1	12	GLN	HG2	H	2.276	0.006
93	1	12	GLN	HG3	H	2.276	0.006
94	1	12	GLN	CA	C	55.632	0.000
95	1	12	GLN	CB	C	27.221	0.000
96	1	12	GLN	CG	C	32.250	0.000
97	1	13	SER	H	H	7.797	0.007
98	1	13	SER	HA	H	4.230	0.011
99	1	13	SER	HB2	H	3.765	0.004
100	1	13	SER	HB3	H	3.653	0.008
101	1	13	SER	CA	C	57.619	0.000
102	1	13	SER	CB	C	62.120	0.012
103	1	14	TYR	H	H	7.634	0.010
104	1	14	TYR	HA	H	4.414	0.007
105	1	14	TYR	HB2	H	2.920	0.007
106	1	14	TYR	HB3	H	2.920	0.007
107	1	14	TYR	HD1	H	6.723	0.000
108	1	14	TYR	HD2	H	6.723	0.000
109	1	14	TYR	HE1	H	6.970	0.000
110	1	14	TYR	HE2	H	6.970	0.000
111	1	14	TYR	CB	C	37.207	0.000
112	1	15	GLY	H	H	7.775	0.013
113	1	15	GLY	HA2	H	3.728	0.007
114	1	15	GLY	HA3	H	3.728	0.007
115	1	15	GLY	CA	C	41.676	0.000
116	1	16	PHE	H	H	7.514	0.040
117	1	16	PHE	HA	H	4.497	0.013
118	1	16	PHE	HB2	H	2.969	0.016
119	1	16	PHE	HB3	H	2.969	0.016
120	1	16	PHE	HD1	H	7.099	0.000
121	1	16	PHE	HD2	H	7.099	0.000
122	1	16	PHE	HE1	H	7.181	0.000
123	1	16	PHE	HE2	H	7.181	0.000
124	1	16	PHE	CA	C	56.367	0.000
125	1	16	PHE	CB	C	37.625	0.000
126	1	17	GLN	H	H	7.618	0.039
127	1	17	GLN	HA	H	4.519	0.001
128	1	17	GLN	HB2	H	1.973	0.004
129	1	17	GLN	HB3	H	1.834	0.007
130	1	17	GLN	HG2	H	2.229	0.009
131	1	17	GLN	HG3	H	2.229	0.009
132	1	17	GLN	CB	C	27.805	0.003
133	1	17	GLN	CG	C	31.735	0.000
134	1	18	PRO	HA	H	4.262	0.008
135	1	18	PRO	HB2	H	2.150	0.010
136	1	18	PRO	HB3	H	1.893	0.007
137	1	18	PRO	HG2	H	1.850	0.026
138	1	18	PRO	HG3	H	1.850	0.026
139	1	18	PRO	HD2	H	3.519	0.023
140	1	18	PRO	HD3	H	3.464	0.008
141	1	18	PRO	CA	C	62.286	0.000
142	1	18	PRO	CB	C	29.805	0.017
143	1	18	PRO	CG	C	25.362	0.000
144	1	18	PRO	CD	C	48.782	0.024
145	1	19	THR	H	H	7.451	0.003
146	1	19	THR	HA	H	4.204	0.002
147	1	19	THR	HB	H	4.254	0.008
148	1	19	THR	HG21	H	1.087	0.004
149	1	19	THR	HG22	H	1.087	0.004
150	1	19	THR	HG23	H	1.087	0.004
151	1	19	THR	CA	C	60.060	0.000
152	1	19	THR	CG2	C	19.212	0.000
153	1	20	ASN	H	H	7.951	0.006
154	1	20	ASN	HA	H	4.619	0.008
155	1	20	ASN	HB2	H	2.724	0.008
156	1	20	ASN	HB3	H	2.724	0.008
157	1	20	ASN	CA	C	51.908	0.000
158	1	20	ASN	CB	C	37.088	0.000
159	1	21	GLY	H	H	8.025	0.003
160	1	21	GLY	HA2	H	3.883	0.011
161	1	21	GLY	HA3	H	3.883	0.011
162	1	21	GLY	CA	C	43.691	0.000
163	1	22	VAL	H	H	7.530	0.004
164	1	22	VAL	HA	H	3.963	0.003
165	1	22	VAL	HB	H	1.995	0.010
166	1	22	VAL	HG21	H	0.833	0.008
167	1	22	VAL	HG22	H	0.833	0.008
168	1	22	VAL	HG23	H	0.833	0.008
169	1	22	VAL	CA	C	61.452	0.000
170	1	22	VAL	CB	C	30.997	0.000
171	1	22	VAL	CG2	C	18.441	0.000
172	1	23	GLY	H	H	7.943	0.008
173	1	23	GLY	HA2	H	3.856	0.047
174	1	23	GLY	HA3	H	3.680	0.008
175	1	23	GLY	CA	C	43.512	0.028
176	1	24	TYR	H	H	7.512	0.010
177	1	24	TYR	HA	H	4.443	0.009
178	1	24	TYR	HB2	H	2.892	0.030
179	1	24	TYR	HB3	H	2.892	0.030
180	1	24	TYR	HD1	H	6.725	0.000
181	1	24	TYR	HD2	H	6.725	0.000
182	1	24	TYR	HE1	H	6.969	0.000
183	1	24	TYR	HE2	H	6.969	0.000
184	1	24	TYR	CB	C	37.161	0.000
185	1	25	GLN	H	H	7.771	0.008
186	1	25	GLN	HA	H	4.268	0.009
187	1	25	GLN	HB2	H	2.028	0.014
188	1	25	GLN	HB3	H	1.874	0.009
189	1	25	GLN	HG2	H	2.205	0.009
190	1	25	GLN	HG3	H	2.205	0.009
191	1	25	GLN	CA	C	53.230	0.000
192	1	25	GLN	CB	C	27.590	0.028
193	1	25	GLN	CG	C	31.978	0.000

Release date

2022-07-17

Citation

Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site
Buonocore, M., Santoro, A., Grimaldi, M., Covelli, V., Firoznezhad, M., Rodriquez, M., Santin, M., D'Ursi, A.M.
Heliyon (2022), 8, e11568-e11568, PubMed 36406731 , DOI 10.1016/j.heliyon.2022.e11568 , Abstract

Related entities 1. Spike glycoprotein, : 1 : 99 : 4 entities Detail

Experiments performed 3 experiments Detail