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BMRB: 35008

Structure of nermertea worm Lineus viridis nemertide peptide toxin

Authors

Laborde, Q., Gunasekera, S.

Assembly

Nemertide

Entity

1. Nemertide (polymer, Thiol state: all disulfide bound), 33 monomers, 3599.068 Da Detail

GCNKAGAFCT KNNNCCPTKG RNRGECTWAF KCD

Formula weight

3599.068 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS2:SG	1:CYS16:SG
2	disulfide	sing	1:CYS9:SG	1:CYS15:SG
3	disulfide	sing	1:CYS9:SG	1:CYS26:SG
4	disulfide	sing	1:CYS15:SG	1:CYS26:SG
5	disulfide	sing	1:CYS15:SG	1:CYS32:SG

Source organism

Stryphnus fortis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 215, ¹³C: 33, ¹⁵N: 42 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	GLY	HA2	H	3.833	0.020	2
2	1	1	GLY	HA3	H	3.833	0.020	2
3	1	2	CYS	H	H	8.444	0.020	1
4	1	2	CYS	HA	H	4.741	0.020	1
5	1	2	CYS	HB2	H	3.055	0.020	2
6	1	2	CYS	HB3	H	2.879	0.020	2
7	1	3	ASN	H	H	8.999	0.020	1
8	1	3	ASN	HA	H	4.917	0.020	1
9	1	3	ASN	HB2	H	2.925	0.020	2
10	1	3	ASN	HB3	H	2.637	0.020	2
11	1	3	ASN	HD21	H	7.223	0.020	2
12	1	3	ASN	HD22	H	6.946	0.020	2
13	1	3	ASN	CA	C	52.163	0.400	1
14	1	3	ASN	N	N	120.034	0.400	1
15	1	3	ASN	ND2	N	110.570	0.400	1
16	1	4	LYS	H	H	8.397	0.020	1
17	1	4	LYS	HA	H	4.044	0.020	1
18	1	4	LYS	HB2	H	1.856	0.020	2
19	1	4	LYS	HB3	H	1.705	0.020	2
20	1	4	LYS	HG2	H	1.472	0.020	2
21	1	4	LYS	HG3	H	1.393	0.020	2
22	1	4	LYS	HD2	H	1.628	0.020	2
23	1	4	LYS	HD3	H	1.628	0.020	2
24	1	4	LYS	HE2	H	2.955	0.020	2
25	1	4	LYS	HE3	H	2.955	0.020	2
26	1	4	LYS	HZ1	H	7.471	0.020	1
27	1	4	LYS	HZ2	H	7.471	0.020	1
28	1	4	LYS	HZ3	H	7.471	0.020	1
29	1	4	LYS	CA	C	55.344	0.400	1
30	1	4	LYS	N	N	122.189	0.400	1
31	1	4	LYS	NZ	N	102.766	0.400	1
32	1	5	ALA	H	H	7.858	0.020	1
33	1	5	ALA	HA	H	3.661	0.020	1
34	1	5	ALA	HB1	H	1.216	0.020	1
35	1	5	ALA	HB2	H	1.216	0.020	1
36	1	5	ALA	HB3	H	1.216	0.020	1
37	1	5	ALA	CA	C	53.555	0.400	1
38	1	5	ALA	N	N	120.626	0.400	1
39	1	6	GLY	H	H	9.230	0.020	1
40	1	6	GLY	HA2	H	4.322	0.020	2
41	1	6	GLY	HA3	H	3.448	0.020	2
42	1	6	GLY	CA	C	44.963	0.400	1
43	1	6	GLY	N	N	111.330	0.400	1
44	1	7	ALA	H	H	7.864	0.020	1
45	1	7	ALA	HA	H	4.362	0.020	1
46	1	7	ALA	HB1	H	1.461	0.020	1
47	1	7	ALA	HB2	H	1.461	0.020	1
48	1	7	ALA	HB3	H	1.461	0.020	1
49	1	7	ALA	CA	C	51.296	0.400	1
50	1	7	ALA	N	N	123.115	0.400	1
51	1	8	PHE	H	H	8.185	0.020	1
52	1	8	PHE	HA	H	4.899	0.020	1
53	1	8	PHE	HB2	H	3.166	0.020	2
54	1	8	PHE	HB3	H	2.812	0.020	2
55	1	8	PHE	HD1	H	7.275	0.020	1
56	1	8	PHE	HD2	H	7.275	0.020	1
57	1	8	PHE	HE1	H	7.183	0.020	1
58	1	8	PHE	HE2	H	7.183	0.020	1
59	1	8	PHE	HZ	H	7.032	0.020	1
60	1	8	PHE	CA	C	58.487	0.400	1
61	1	8	PHE	N	N	118.828	0.400	1
62	1	9	CYS	H	H	7.333	0.020	1
63	1	9	CYS	HA	H	4.399	0.020	1
64	1	9	CYS	HB2	H	3.000	0.020	2
65	1	9	CYS	HB3	H	3.000	0.020	2
66	1	9	CYS	CA	C	53.228	0.400	1
67	1	9	CYS	N	N	115.856	0.400	1
68	1	10	THR	H	H	8.001	0.020	1
69	1	10	THR	HA	H	4.334	0.020	1
70	1	10	THR	HB	H	4.173	0.020	1
71	1	10	THR	HG21	H	1.038	0.020	1
72	1	10	THR	HG22	H	1.038	0.020	1
73	1	10	THR	HG23	H	1.038	0.020	1
74	1	10	THR	CA	C	61.738	0.400	1
75	1	10	THR	CB	C	70.507	0.400	1
76	1	10	THR	N	N	103.575	0.400	1
77	1	11	LYS	H	H	7.624	0.020	1
78	1	11	LYS	HA	H	4.628	0.020	1
79	1	11	LYS	HB2	H	1.870	0.020	2
80	1	11	LYS	HB3	H	1.568	0.020	2
81	1	11	LYS	HG2	H	1.311	0.020	2
82	1	11	LYS	HG3	H	1.311	0.020	2
83	1	11	LYS	HD2	H	1.610	0.020	2
84	1	11	LYS	HD3	H	1.610	0.020	2
85	1	11	LYS	HE2	H	2.880	0.020	2
86	1	11	LYS	HE3	H	2.880	0.020	2
87	1	11	LYS	HZ1	H	7.429	0.020	1
88	1	11	LYS	HZ2	H	7.429	0.020	1
89	1	11	LYS	HZ3	H	7.429	0.020	1
90	1	11	LYS	N	N	120.445	0.400	1
91	1	11	LYS	NZ	N	102.767	0.400	1
92	1	12	ASN	H	H	8.938	0.020	1
93	1	12	ASN	HA	H	4.013	0.020	1
94	1	12	ASN	HB2	H	2.935	0.020	2
95	1	12	ASN	HB3	H	2.644	0.020	2
96	1	12	ASN	HD21	H	7.574	0.020	2
97	1	12	ASN	HD22	H	6.982	0.020	2
98	1	12	ASN	CA	C	56.825	0.400	1
99	1	12	ASN	N	N	127.641	0.400	1
100	1	12	ASN	ND2	N	112.647	0.400	1
101	1	13	ASN	H	H	8.239	0.020	1
102	1	13	ASN	HA	H	4.488	0.020	1
103	1	13	ASN	HB2	H	2.807	0.020	2
104	1	13	ASN	HB3	H	2.744	0.020	2
105	1	13	ASN	HD21	H	7.468	0.020	2
106	1	13	ASN	HD22	H	6.755	0.020	2
107	1	13	ASN	CA	C	54.303	0.400	1
108	1	13	ASN	N	N	112.586	0.400	1
109	1	13	ASN	ND2	N	111.175	0.400	1
110	1	14	ASN	H	H	7.793	0.020	1
111	1	14	ASN	HA	H	4.659	0.020	1
112	1	14	ASN	HB2	H	3.049	0.020	2
113	1	14	ASN	HB3	H	2.882	0.020	2
114	1	14	ASN	HD21	H	7.469	0.020	2
115	1	14	ASN	HD22	H	7.144	0.020	2
116	1	14	ASN	CA	C	54.337	0.400	1
117	1	14	ASN	N	N	115.005	0.400	1
118	1	14	ASN	ND2	N	110.073	0.400	1
119	1	15	CYS	H	H	7.905	0.020	1
120	1	15	CYS	HA	H	5.051	0.020	1
121	1	15	CYS	HB2	H	3.297	0.020	2
122	1	15	CYS	HB3	H	2.574	0.020	2
123	1	15	CYS	CA	C	53.636	0.400	1
124	1	15	CYS	N	N	118.191	0.400	1
125	1	16	CYS	H	H	9.662	0.020	1
126	1	16	CYS	HA	H	4.741	0.020	1
127	1	16	CYS	HB2	H	3.168	0.020	2
128	1	16	CYS	HB3	H	2.390	0.020	2
129	1	16	CYS	N	N	124.938	0.400	1
130	1	17	PRO	HA	H	4.108	0.020	1
131	1	17	PRO	HB2	H	1.780	0.020	2
132	1	17	PRO	HB3	H	1.780	0.020	2
133	1	17	PRO	HG2	H	2.005	0.020	2
134	1	17	PRO	HG3	H	1.624	0.020	2
135	1	17	PRO	HD2	H	3.798	0.020	2
136	1	17	PRO	HD3	H	3.555	0.020	2
137	1	17	PRO	CA	C	63.213	0.400	1
138	1	17	PRO	CD	C	50.530	0.400	1
139	1	18	THR	H	H	8.657	0.020	1
140	1	18	THR	HA	H	4.481	0.020	1
141	1	18	THR	HB	H	4.251	0.020	1
142	1	18	THR	HG1	H	4.475	0.020	1
143	1	18	THR	HG21	H	1.138	0.020	1
144	1	18	THR	HG22	H	1.138	0.020	1
145	1	18	THR	HG23	H	1.138	0.020	1
146	1	18	THR	CA	C	60.202	0.400	1
147	1	18	THR	CB	C	72.154	0.400	1
148	1	18	THR	N	N	118.514	0.400	1
149	1	19	LYS	H	H	8.678	0.020	1
150	1	19	LYS	HA	H	3.852	0.020	1
151	1	19	LYS	HB2	H	1.810	0.020	2
152	1	19	LYS	HB3	H	1.755	0.020	2
153	1	19	LYS	HG2	H	1.376	0.020	2
154	1	19	LYS	HG3	H	1.285	0.020	2
155	1	19	LYS	HD2	H	1.622	0.020	2
156	1	19	LYS	HD3	H	1.510	0.020	2
157	1	19	LYS	HE2	H	2.888	0.020	2
158	1	19	LYS	HE3	H	2.888	0.020	2
159	1	19	LYS	HZ1	H	7.426	0.020	1
160	1	19	LYS	HZ2	H	7.426	0.020	1
161	1	19	LYS	HZ3	H	7.426	0.020	1
162	1	19	LYS	CA	C	57.604	0.400	1
163	1	19	LYS	N	N	116.588	0.400	1
164	1	19	LYS	NZ	N	102.331	0.400	1
165	1	20	GLY	H	H	8.560	0.020	1
166	1	20	GLY	HA2	H	4.024	0.020	2
167	1	20	GLY	HA3	H	3.595	0.020	2
168	1	20	GLY	CA	C	45.269	0.400	1
169	1	20	GLY	N	N	107.697	0.400	1
170	1	21	ARG	H	H	7.763	0.020	1
171	1	21	ARG	HA	H	4.373	0.020	1
172	1	21	ARG	HB2	H	1.972	0.020	2
173	1	21	ARG	HB3	H	1.920	0.020	2
174	1	21	ARG	HG2	H	1.616	0.020	2
175	1	21	ARG	HG3	H	1.616	0.020	2
176	1	21	ARG	HD2	H	3.235	0.020	2
177	1	21	ARG	HD3	H	3.041	0.020	2
178	1	21	ARG	HE	H	6.962	0.020	1
179	1	21	ARG	HH21	H	6.655	0.020	2
180	1	21	ARG	HH22	H	6.629	0.020	2
181	1	21	ARG	CA	C	55.807	0.400	1
182	1	21	ARG	N	N	120.171	0.400	1
183	1	21	ARG	NE	N	120.404	0.400	1
184	1	21	ARG	NH2	N	106.613	0.400	1
185	1	22	ASN	H	H	8.454	0.020	1
186	1	22	ASN	HA	H	4.649	0.020	1
187	1	22	ASN	HB2	H	2.856	0.020	2
188	1	22	ASN	HB3	H	2.760	0.020	2
189	1	22	ASN	HD21	H	7.484	0.020	2
190	1	22	ASN	HD22	H	6.787	0.020	2
191	1	22	ASN	CA	C	52.921	0.400	1
192	1	22	ASN	N	N	116.058	0.400	1
193	1	22	ASN	ND2	N	111.536	0.400	1
194	1	23	ARG	H	H	7.378	0.020	1
195	1	23	ARG	HA	H	4.573	0.020	1
196	1	23	ARG	HB2	H	1.856	0.020	2
197	1	23	ARG	HB3	H	1.656	0.020	2
198	1	23	ARG	HG2	H	1.542	0.020	2
199	1	23	ARG	HG3	H	1.542	0.020	2
200	1	23	ARG	HD2	H	3.128	0.020	2
201	1	23	ARG	HD3	H	3.128	0.020	2
202	1	23	ARG	HE	H	7.114	0.020	1
203	1	23	ARG	CA	C	54.069	0.400	1
204	1	23	ARG	N	N	120.447	0.400	1
205	1	23	ARG	NE	N	120.180	0.400	1
206	1	24	GLY	H	H	8.784	0.020	1
207	1	24	GLY	HA2	H	3.756	0.020	2
208	1	24	GLY	HA3	H	3.519	0.020	2
209	1	24	GLY	CA	C	45.207	0.400	1
210	1	24	GLY	N	N	110.171	0.400	1
211	1	25	GLU	H	H	8.487	0.020	1
212	1	25	GLU	HA	H	4.282	0.020	1
213	1	25	GLU	HB2	H	1.849	0.020	2
214	1	25	GLU	HB3	H	1.628	0.020	2
215	1	25	GLU	HG2	H	2.078	0.020	2
216	1	25	GLU	HG3	H	1.986	0.020	2
217	1	25	GLU	CA	C	55.041	0.400	1
218	1	25	GLU	N	N	116.164	0.400	1
219	1	26	CYS	H	H	8.960	0.020	1
220	1	26	CYS	HA	H	4.906	0.020	1
221	1	26	CYS	HB2	H	2.572	0.020	2
222	1	26	CYS	HB3	H	2.494	0.020	2
223	1	26	CYS	CA	C	54.103	0.400	1
224	1	26	CYS	N	N	121.772	0.400	1
225	1	27	THR	H	H	8.540	0.020	1
226	1	27	THR	HA	H	4.373	0.020	1
227	1	27	THR	HB	H	4.333	0.020	1
228	1	27	THR	HG21	H	1.207	0.020	1
229	1	27	THR	HG22	H	1.207	0.020	1
230	1	27	THR	HG23	H	1.207	0.020	1
231	1	27	THR	CB	C	72.288	0.400	1
232	1	27	THR	N	N	121.279	0.400	1
233	1	28	TRP	H	H	8.166	0.020	1
234	1	28	TRP	HA	H	4.074	0.020	1
235	1	28	TRP	HB2	H	3.321	0.020	2
236	1	28	TRP	HB3	H	3.143	0.020	2
237	1	28	TRP	HD1	H	7.299	0.020	1
238	1	28	TRP	HE1	H	10.099	0.020	1
239	1	28	TRP	HE3	H	7.423	0.020	1
240	1	28	TRP	HZ2	H	7.418	0.020	1
241	1	28	TRP	HZ3	H	7.293	0.020	1
242	1	28	TRP	HH2	H	7.106	0.020	1
243	1	28	TRP	CA	C	57.765	0.400	1
244	1	28	TRP	N	N	119.404	0.400	1
245	1	28	TRP	NE1	N	129.449	0.400	1
246	1	29	ALA	H	H	6.640	0.020	1
247	1	29	ALA	HA	H	3.855	0.020	1
248	1	29	ALA	HB1	H	0.481	0.020	1
249	1	29	ALA	HB2	H	0.481	0.020	1
250	1	29	ALA	HB3	H	0.481	0.020	1
251	1	29	ALA	CA	C	50.799	0.400	1
252	1	29	ALA	N	N	121.474	0.400	1
253	1	30	PHE	H	H	7.791	0.020	1
254	1	30	PHE	HA	H	3.840	0.020	1
255	1	30	PHE	HB2	H	3.602	0.020	2
256	1	30	PHE	HB3	H	3.189	0.020	2
257	1	30	PHE	HD1	H	7.223	0.020	1
258	1	30	PHE	HD2	H	7.223	0.020	1
259	1	30	PHE	HE1	H	7.328	0.020	1
260	1	30	PHE	HE2	H	7.328	0.020	1
261	1	30	PHE	CA	C	59.200	0.400	1
262	1	30	PHE	CB	C	34.076	0.400	1
263	1	30	PHE	N	N	115.479	0.400	1
264	1	31	LYS	H	H	6.477	0.020	1
265	1	31	LYS	HA	H	5.105	0.020	1
266	1	31	LYS	HB2	H	1.281	0.020	2
267	1	31	LYS	HB3	H	1.207	0.020	2
268	1	31	LYS	HG2	H	1.187	0.020	2
269	1	31	LYS	HG3	H	1.046	0.020	2
270	1	31	LYS	HD2	H	1.520	0.020	2
271	1	31	LYS	HD3	H	1.611	0.020	2
272	1	31	LYS	HE2	H	2.830	0.020	2
273	1	31	LYS	HE3	H	2.830	0.020	2
274	1	31	LYS	HZ1	H	7.415	0.020	1
275	1	31	LYS	HZ2	H	7.415	0.020	1
276	1	31	LYS	HZ3	H	7.415	0.020	1
277	1	31	LYS	CA	C	53.724	0.400	1
278	1	31	LYS	N	N	113.363	0.400	1
279	1	32	CYS	H	H	8.849	0.020	1
280	1	32	CYS	HA	H	5.127	0.020	1
281	1	32	CYS	HB2	H	3.155	0.020	2
282	1	32	CYS	HB3	H	2.871	0.020	2
283	1	32	CYS	CA	C	53.933	0.400	1
284	1	32	CYS	N	N	121.400	0.400	1
285	1	33	ASP	H	H	9.062	0.020	1
286	1	33	ASP	HA	H	4.458	0.020	1
287	1	33	ASP	HB2	H	2.476	0.020	2
288	1	33	ASP	HB3	H	2.476	0.020	2
289	1	33	ASP	CA	C	55.190	0.400	1
290	1	33	ASP	N	N	131.701	0.400	1

Release date

2025-08-21

Citation

Structure of nermertea worm Lineus viridis nemertide peptide toxin
Laborde, Q., Gunasekera, S.

Related entities 1. Nemertide, : 4 entities Detail

Experiments performed 5 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	Nermertide peptide	natural abundance		1 (±0.2) mM

#	Name	Isotope labeling	Type	Concentration
2	Nermertide peptide	natural abundance		1 (±0.2) mM

#	Name	Isotope labeling	Type	Concentration
3	Nermertide peptide	natural abundance		1 (±0.2) mM

#	Name	Isotope labeling	Type	Concentration
4	Nermertide peptide	natural abundance		1 (±0.2) mM

#	Name	Isotope labeling	Type	Concentration
5	Nermertide peptide	natural abundance		1 (±0.2) mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr35008_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:2:CYS:SG	1:16:CYS:SG	unknown	unknown	n/a
1:9:CYS:SG	1:15:CYS:SG	unknown, CA 53.228 ppm	unknown, CA 53.636 ppm	n/a
1:9:CYS:SG	1:26:CYS:SG	unknown, CA 53.228 ppm	unknown, CA 54.103 ppm	n/a
1:15:CYS:SG	1:26:CYS:SG	unknown, CA 53.636 ppm	unknown, CA 54.103 ppm	n/a
1:15:CYS:SG	1:32:CYS:SG	unknown, CA 53.636 ppm	unknown, CA 53.933 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr35008_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	290		100.0 (chain: 1, length: 33)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 33, Sequence coverage: 100.0%

--------10--------20--------30---
GCNKAGAFCTKNNNCCPTKGRNRGECTWAFKCD
|||||||||||||||||||||||||||||||||
GCNKAGAFCTKNNNCCPTKGRNRGECTWAFKCD

Total number of assignments
- ¹H chemical shifts: 215
- ¹³C chemical shifts: 33
- ¹⁵N chemical shifts: 42

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	LYS	HZ1	7.471
4	LYS	HZ2	7.471
4	LYS	HZ3	7.471
4	LYS	NZ	102.766
11	LYS	HZ1	7.429
11	LYS	HZ2	7.429
11	LYS	HZ3	7.429
11	LYS	NZ	102.767
18	THR	HG1	4.475
19	LYS	HZ1	7.426
19	LYS	HZ2	7.426
19	LYS	HZ3	7.426
19	LYS	NZ	102.331
21	ARG	HH21	6.655
21	ARG	HH22	6.629
21	ARG	NE	120.404
21	ARG	NH2	106.613
23	ARG	NE	120.18
31	LYS	HZ1	7.415
31	LYS	HZ2	7.415
31	LYS	HZ3	7.415

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	190	188	98.9
¹³C chemical shifts	132	33	25.0
¹⁵N chemical shifts	38	36	94.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	68	98.6
¹³C chemical shifts	66	28	42.4
¹⁵N chemical shifts	32	30	93.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	120	99.2
¹³C chemical shifts	66	5	7.6
¹⁵N chemical shifts	6	6	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	15	93.8
¹³C chemical shifts	15	0	0.0
¹⁵N chemical shifts	1	1	100.0

Redox state of CYS
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: 1

Keywords nemertide, toxin

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BMRB: 35008

Related entities 1. Nemertide, : 4 entities Detail

Experiments performed 5 experiments Detail

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Chemical shift validation 3 contents Detail