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BMRB: 34706

7QZW

Hm-AMP8

Authors

Grafskaia, E.N., Pavlova, E.R., Latsis, I.A., Malakhova, M.V., Lavrenova, V.N., Ivchenkov, D.V., Bashkirov, P.V., Kot, E.F., Mineev, K.S., Arseniev, A.S., Klinov, D.V., Lazarev, V.N.

Assembly

Hm-AMP8

Entity

1. Hm-AMP8 (polymer), 24 monomers, 2673.250 Da Detail

RAVIYKIPYN AIASRWIIAP KKCX

Formula weight

2673.25 Da

Source organism

Hirudo medicinalis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chemcal Shifts

¹H: 184, ¹³C: 88, ¹⁵N: 23 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Ambig. code
1	1	1	ARG	HA	H	4.082	1
2	1	1	ARG	HB2	H	1.960	2
3	1	1	ARG	HB3	H	1.960	2
4	1	1	ARG	HG2	H	1.713	2
5	1	1	ARG	HG3	H	1.713	2
6	1	1	ARG	HD2	H	3.202	2
7	1	1	ARG	HD3	H	3.202	2
8	1	1	ARG	HE	H	7.441	1
9	1	1	ARG	CA	C	55.362	1
10	1	1	ARG	CB	C	30.976	1
11	1	1	ARG	CG	C	26.384	1
12	1	1	ARG	CD	C	43.305	1
13	1	1	ARG	NE	N	84.017	1
14	1	2	ALA	H	H	8.882	1
15	1	2	ALA	HA	H	4.466	1
16	1	2	ALA	HB1	H	1.441	1
17	1	2	ALA	HB2	H	1.441	1
18	1	2	ALA	HB3	H	1.441	1
19	1	2	ALA	CA	C	52.581	1
20	1	2	ALA	CB	C	19.511	1
21	1	2	ALA	N	N	126.882	1
22	1	3	VAL	H	H	8.453	1
23	1	3	VAL	HA	H	4.069	1
24	1	3	VAL	HB	H	2.088	1
25	1	3	VAL	HG11	H	0.973	1
26	1	3	VAL	HG12	H	0.973	1
27	1	3	VAL	HG13	H	0.973	1
28	1	3	VAL	HG21	H	0.890	1
29	1	3	VAL	HG22	H	0.890	1
30	1	3	VAL	HG23	H	0.890	1
31	1	3	VAL	CA	C	62.955	1
32	1	3	VAL	CB	C	32.672	1
33	1	3	VAL	CG1	C	21.033	1
34	1	3	VAL	CG2	C	21.339	1
35	1	3	VAL	N	N	119.770	1
36	1	4	ILE	H	H	8.044	1
37	1	4	ILE	HA	H	4.067	1
38	1	4	ILE	HB	H	1.858	1
39	1	4	ILE	HG12	H	1.333	2
40	1	4	ILE	HG13	H	1.142	2
41	1	4	ILE	HG21	H	0.827	1
42	1	4	ILE	HG22	H	0.827	1
43	1	4	ILE	HG23	H	0.827	1
44	1	4	ILE	HD11	H	0.836	1
45	1	4	ILE	HD12	H	0.836	1
46	1	4	ILE	HD13	H	0.836	1
47	1	4	ILE	CA	C	61.906	1
48	1	4	ILE	CB	C	38.510	1
49	1	4	ILE	CG1	C	27.446	1
50	1	4	ILE	CG2	C	17.815	1
51	1	4	ILE	CD1	C	13.378	1
52	1	4	ILE	N	N	121.069	1
53	1	5	TYR	H	H	7.660	1
54	1	5	TYR	HA	H	4.541	1
55	1	5	TYR	HB2	H	3.080	2
56	1	5	TYR	HB3	H	2.916	2
57	1	5	TYR	HD1	H	7.112	1
58	1	5	TYR	HD2	H	7.112	1
59	1	5	TYR	HE1	H	6.826	1
60	1	5	TYR	HE2	H	6.826	1
61	1	5	TYR	CA	C	58.175	1
62	1	5	TYR	CB	C	38.795	1
63	1	5	TYR	CD1	C	132.860	1
64	1	5	TYR	CE1	C	118.374	1
65	1	5	TYR	N	N	119.823	1
66	1	6	LYS	H	H	7.946	1
67	1	6	LYS	HA	H	4.321	1
68	1	6	LYS	HB2	H	1.869	2
69	1	6	LYS	HB3	H	1.756	2
70	1	6	LYS	HG2	H	1.403	2
71	1	6	LYS	HG3	H	1.349	2
72	1	6	LYS	HD2	H	1.702	2
73	1	6	LYS	HD3	H	1.702	2
74	1	6	LYS	HE2	H	2.985	2
75	1	6	LYS	HE3	H	2.985	2
76	1	6	LYS	CA	C	56.215	1
77	1	6	LYS	CB	C	31.664	1
78	1	6	LYS	CG	C	25.042	1
79	1	6	LYS	CD	C	29.218	1
80	1	6	LYS	CE	C	42.157	1
81	1	6	LYS	N	N	120.194	1
82	1	7	ILE	H	H	8.023	1
83	1	7	ILE	HA	H	4.180	1
84	1	7	ILE	HB	H	1.882	1
85	1	7	ILE	HG12	H	1.708	2
86	1	7	ILE	HG13	H	1.178	2
87	1	7	ILE	HG21	H	0.762	1
88	1	7	ILE	HG22	H	0.762	1
89	1	7	ILE	HG23	H	0.762	1
90	1	7	ILE	HD11	H	0.932	1
91	1	7	ILE	HD12	H	0.932	1
92	1	7	ILE	HD13	H	0.932	1
93	1	7	ILE	CA	C	60.670	1
94	1	7	ILE	CB	C	38.682	1
95	1	7	ILE	CG1	C	28.218	1
96	1	7	ILE	CG2	C	17.046	1
97	1	7	ILE	CD1	C	13.098	1
98	1	7	ILE	N	N	121.536	1
99	1	8	PRO	HA	H	4.730	1
100	1	8	PRO	HB2	H	2.079	2
101	1	8	PRO	HB3	H	2.266	2
102	1	8	PRO	HG2	H	2.087	2
103	1	8	PRO	HD2	H	3.589	1
104	1	8	PRO	HD3	H	3.915	1
105	1	8	PRO	CB	C	29.585	1
106	1	8	PRO	CG	C	27.682	1
107	1	8	PRO	CD	C	50.597	1
108	1	9	TYR	H	H	8.103	1
109	1	9	TYR	HA	H	4.080	1
110	1	9	TYR	HB2	H	3.035	2
111	1	9	TYR	HB3	H	3.035	2
112	1	9	TYR	HD1	H	7.070	1
113	1	9	TYR	HD2	H	7.070	1
114	1	9	TYR	HE1	H	6.846	1
115	1	9	TYR	HE2	H	6.846	1
116	1	9	TYR	CA	C	61.505	1
117	1	9	TYR	CB	C	38.748	1
118	1	9	TYR	CD1	C	133.014	1
119	1	9	TYR	CE1	C	118.513	1
120	1	10	ASN	H	H	8.597	1
121	1	10	ASN	HA	H	4.397	1
122	1	10	ASN	HB2	H	2.835	2
123	1	10	ASN	HB3	H	2.799	2
124	1	10	ASN	HD21	H	7.719	2
125	1	10	ASN	HD22	H	6.936	2
126	1	10	ASN	CA	C	56.020	1
127	1	10	ASN	CB	C	38.004	1
128	1	10	ASN	N	N	117.087	1
129	1	10	ASN	ND2	N	112.340	1
130	1	11	ALA	H	H	7.993	1
131	1	11	ALA	HA	H	4.201	1
132	1	11	ALA	HB1	H	1.532	1
133	1	11	ALA	HB2	H	1.532	1
134	1	11	ALA	HB3	H	1.532	1
135	1	11	ALA	CA	C	54.549	1
136	1	11	ALA	CB	C	18.772	1
137	1	11	ALA	N	N	122.709	1
138	1	12	ILE	H	H	7.674	1
139	1	12	ILE	HA	H	3.874	1
140	1	12	ILE	HB	H	1.929	1
141	1	12	ILE	HG12	H	1.742	2
142	1	12	ILE	HG13	H	1.153	2
143	1	12	ILE	HG21	H	0.953	1
144	1	12	ILE	HG22	H	0.953	1
145	1	12	ILE	HG23	H	0.953	1
146	1	12	ILE	HD11	H	0.847	1
147	1	12	ILE	HD12	H	0.847	1
148	1	12	ILE	HD13	H	0.847	1
149	1	12	ILE	CA	C	63.908	1
150	1	12	ILE	CB	C	38.516	1
151	1	12	ILE	CG1	C	28.748	1
152	1	12	ILE	CG2	C	17.899	1
153	1	12	ILE	CD1	C	13.631	1
154	1	12	ILE	N	N	116.519	1
155	1	13	ALA	H	H	8.316	1
156	1	13	ALA	HA	H	4.069	1
157	1	13	ALA	HB1	H	1.400	1
158	1	13	ALA	HB2	H	1.400	1
159	1	13	ALA	HB3	H	1.400	1
160	1	13	ALA	CA	C	54.756	1
161	1	13	ALA	CB	C	18.535	1
162	1	13	ALA	N	N	121.356	1
163	1	14	SER	H	H	7.992	1
164	1	14	SER	HA	H	4.271	1
165	1	14	SER	HB2	H	3.990	2
166	1	14	SER	HB3	H	3.990	2
167	1	14	SER	CA	C	60.788	1
168	1	14	SER	CB	C	63.420	1
169	1	14	SER	N	N	111.106	1
170	1	15	ARG	H	H	7.618	1
171	1	15	ARG	HA	H	4.218	1
172	1	15	ARG	HB2	H	1.674	2
173	1	15	ARG	HB3	H	1.674	2
174	1	15	ARG	HG2	H	1.510	2
175	1	15	ARG	HG3	H	1.372	2
176	1	15	ARG	HD2	H	3.067	2
177	1	15	ARG	HD3	H	2.938	2
178	1	15	ARG	HE	H	7.483	1
179	1	15	ARG	CA	C	57.115	1
180	1	15	ARG	CB	C	30.394	1
181	1	15	ARG	CG	C	27.496	1
182	1	15	ARG	CD	C	43.138	1
183	1	15	ARG	N	N	119.524	1
184	1	15	ARG	NE	N	84.551	1
185	1	16	TRP	H	H	7.901	1
186	1	16	TRP	HA	H	4.647	1
187	1	16	TRP	HB2	H	3.401	2
188	1	16	TRP	HB3	H	3.175	2
189	1	16	TRP	HD1	H	7.291	1
190	1	16	TRP	HE1	H	10.599	1
191	1	16	TRP	HE3	H	7.594	1
192	1	16	TRP	HZ2	H	7.461	1
193	1	16	TRP	HZ3	H	7.003	1
194	1	16	TRP	HH2	H	7.081	1
195	1	16	TRP	CA	C	58.723	1
196	1	16	TRP	CB	C	30.472	1
197	1	16	TRP	CD1	C	126.777	1
198	1	16	TRP	CE3	C	120.783	1
199	1	16	TRP	CZ2	C	114.406	1
200	1	16	TRP	CZ3	C	121.329	1
201	1	16	TRP	CH2	C	123.724	1
202	1	16	TRP	N	N	118.424	1
203	1	16	TRP	NE1	N	130.165	1
204	1	17	ILE	H	H	7.672	1
205	1	17	ILE	HA	H	4.163	1
206	1	17	ILE	HB	H	1.951	1
207	1	17	ILE	HG12	H	1.534	2
208	1	17	ILE	HG13	H	1.191	2
209	1	17	ILE	HG21	H	0.920	1
210	1	17	ILE	HG22	H	0.920	1
211	1	17	ILE	HG23	H	0.920	1
212	1	17	ILE	HD11	H	0.889	1
213	1	17	ILE	HD12	H	0.889	1
214	1	17	ILE	HD13	H	0.889	1
215	1	17	ILE	CA	C	61.661	1
216	1	17	ILE	CB	C	38.680	1
217	1	17	ILE	CG1	C	27.524	1
218	1	17	ILE	CG2	C	17.761	1
219	1	17	ILE	CD1	C	13.161	1
220	1	17	ILE	N	N	117.931	1
221	1	18	ILE	H	H	7.880	1
222	1	18	ILE	HA	H	4.174	1
223	1	18	ILE	HB	H	1.885	1
224	1	18	ILE	HG12	H	1.467	2
225	1	18	ILE	HG13	H	1.178	2
226	1	18	ILE	HG21	H	0.909	1
227	1	18	ILE	HG22	H	0.909	1
228	1	18	ILE	HG23	H	0.909	1
229	1	18	ILE	HD11	H	0.857	1
230	1	18	ILE	HD12	H	0.857	1
231	1	18	ILE	HD13	H	0.857	1
232	1	18	ILE	CA	C	60.660	1
233	1	18	ILE	CB	C	38.697	1
234	1	18	ILE	CG1	C	27.303	1
235	1	18	ILE	CG2	C	17.712	1
236	1	18	ILE	CD1	C	13.005	1
237	1	18	ILE	N	N	121.882	1
238	1	19	ALA	H	H	8.269	1
239	1	19	ALA	HA	H	4.585	1
240	1	19	ALA	HB1	H	1.365	1
241	1	19	ALA	HB2	H	1.365	1
242	1	19	ALA	HB3	H	1.365	1
243	1	19	ALA	CA	C	50.602	1
244	1	19	ALA	CB	C	18.294	1
245	1	19	ALA	N	N	128.572	1
246	1	20	PRO	HA	H	4.428	1
247	1	20	PRO	HB2	H	2.304	2
248	1	20	PRO	HB3	H	1.906	2
249	1	20	PRO	HG2	H	2.023	2
250	1	20	PRO	HG3	H	2.023	2
251	1	20	PRO	HD2	H	3.804	2
252	1	20	PRO	HD3	H	3.650	2
253	1	20	PRO	CA	C	63.064	1
254	1	20	PRO	CB	C	32.108	1
255	1	20	PRO	CG	C	27.482	1
256	1	20	PRO	CD	C	50.472	1
257	1	21	LYS	H	H	8.359	1
258	1	21	LYS	HA	H	4.286	1
259	1	21	LYS	HB2	H	1.832	2
260	1	21	LYS	HB3	H	1.783	2
261	1	21	LYS	HG2	H	1.487	2
262	1	21	LYS	HG3	H	1.443	2
263	1	21	LYS	HD2	H	1.690	2
264	1	21	LYS	HD3	H	1.690	2
265	1	21	LYS	HE2	H	3.014	2
266	1	21	LYS	HE3	H	3.014	2
267	1	21	LYS	CA	C	56.368	1
268	1	21	LYS	CB	C	33.222	1
269	1	21	LYS	CG	C	24.780	1
270	1	21	LYS	CD	C	29.157	1
271	1	21	LYS	CE	C	42.178	1
272	1	21	LYS	N	N	121.128	1
273	1	22	LYS	H	H	8.395	1
274	1	22	LYS	HA	H	4.352	1
275	1	22	LYS	HB2	H	1.858	2
276	1	22	LYS	HB3	H	1.791	2
277	1	22	LYS	HG2	H	1.468	2
278	1	22	LYS	HG3	H	1.425	2
279	1	22	LYS	HD2	H	1.699	2
280	1	22	LYS	HD3	H	1.699	2
281	1	22	LYS	HE2	H	3.008	2
282	1	22	LYS	HE3	H	3.008	2
283	1	22	LYS	CA	C	56.391	1
284	1	22	LYS	CB	C	33.092	1
285	1	22	LYS	CG	C	24.735	1
286	1	22	LYS	CD	C	29.091	1
287	1	22	LYS	CE	C	42.174	1
288	1	22	LYS	N	N	122.534	1
289	1	23	CYS	H	H	8.351	1
290	1	23	CYS	HA	H	4.492	1
291	1	23	CYS	HB2	H	2.922	2
292	1	23	CYS	HB3	H	2.968	2
293	1	23	CYS	CA	C	58.281	1
294	1	23	CYS	CB	C	28.215	1
295	1	23	CYS	N	N	120.554	1

Release date

2022-02-22

Citation

The study of the interaction of cationic peptides from a medical leech with blood components as a first step to the systemic use of antimicrobial peptides for therapy of infectious diseases
Grafskaia, E.N., Pavlova, E.R., Latsis, I.A., Malakhova, M.V., Lavrenova, V.N., Ivchenkov, D.V., Bashkirov, P.V., Kot, E.F., Mineev, K.S., Arseniev, A.S., Klinov, D.V., Lazarev, V.N.

Related entities 1. Hm-AMP8, : 1 : 2 entities Detail

Experiments performed 5 experiments Detail

1 NOESY

Instrument

Bruker AVANCE III - 600 MHz cryogenic triple-resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.0 (±0.1) K, pH 4.8 (±0.1), Details 0.9 mM prok_02022 peptide, 91.3 mM [U-2H] dodecyl phosphocholine, 20 mM [U-2H] sodium acetate buffer, 0.01 % w/v sodium azide, 2 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	prok_02022 peptide	natural abundance	0.9 mM
2	dodecyl phosphocholine	[U-2H]	91.3 mM
3	sodium acetate buffer	[U-2H]	20 mM
4	sodium azide	natural abundance	0.01 % w/v
5	TCEP	natural abundance	2 mM

2 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 700 MHz room-temperature triple resonance probe

Sample

#	Name	Isotope labeling	Concentration
1	prok_02022 peptide	natural abundance	0.9 mM
2	dodecyl phosphocholine	[U-2H]	91.3 mM
3	sodium acetate buffer	[U-2H]	20 mM
4	sodium azide	natural abundance	0.01 % w/v
5	TCEP	natural abundance	2 mM

3 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 600 MHz cryogenic triple-resonance probe

Sample

#	Name	Isotope labeling	Concentration
1	prok_02022 peptide	natural abundance	0.9 mM
2	dodecyl phosphocholine	[U-2H]	91.3 mM
3	sodium acetate buffer	[U-2H]	20 mM
4	sodium azide	natural abundance	0.01 % w/v
5	TCEP	natural abundance	2 mM

4 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 600 MHz cryogenic triple-resonance probe

Sample

#	Name	Isotope labeling	Concentration
1	prok_02022 peptide	natural abundance	0.9 mM
2	dodecyl phosphocholine	[U-2H]	91.3 mM
3	sodium acetate buffer	[U-2H]	20 mM
4	sodium azide	natural abundance	0.01 % w/v
5	TCEP	natural abundance	2 mM

5 2D 1H-13C-HSQC-TOCSY

Instrument

Bruker AVANCE III - 600 MHz cryogenic triple-resonance probe

Sample

#	Name	Isotope labeling	Concentration
1	prok_02022 peptide	natural abundance	0.9 mM
2	dodecyl phosphocholine	[U-2H]	91.3 mM
3	sodium acetate buffer	[U-2H]	20 mM
4	sodium azide	natural abundance	0.01 % w/v
5	TCEP	natural abundance	2 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34706_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr34706_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	295		95.8 (chain: 1, length: 24)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 24, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 184
  - ¹³C chemical shifts: 88
  - ¹⁵N chemical shifts: 23
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	156	152	97.4
¹³C chemical shifts	116	88	75.9
¹⁵N chemical shifts	26	23	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	43	97.7
¹³C chemical shifts	46	22	47.8
¹⁵N chemical shifts	22	19	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	109	97.3
¹³C chemical shifts	70	66	94.3
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	13	9	69.2
¹⁵N chemical shifts	1	1	100.0

Keywords ANTIMICROBIAL, ANTIMICROBIAL PROTEIN, LEECH, PROTEIN

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BMRB: 34706

Related entities 1. Hm-AMP8, : 1 : 2 entities Detail

Experiments performed 5 experiments Detail

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Chemical shift validation 3 contents Detail