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BMRB: 31141

8VU6

Wheat Germ Agglutinin (WGA) domain A

Authors

Titaux-Delgado, G.A., del Rio-Portilla, F., Garcia-Hernandez, E.

Assembly

Agglutinin isolectin 1

Entity

1. Agglutinin isolectin 1 (polymer, Thiol state: all disulfide bound), 46 monomers, 4762.264 Da Detail

AAAAQRCGEQ GSNMECPNNL CCSQYGYCGM GGDYCGKGCQ NGACWT

Formula weight

4762.264 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS22:SG
2	disulfide	sing	1:CYS16:SG	1:CYS28:SG
3	disulfide	sing	1:CYS21:SG	1:CYS35:SG
4	disulfide	sing	1:CYS39:SG	1:CYS44:SG

Source organism

Triticum aestivum

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chemcal Shifts

¹H: 237 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	3	ALA	H	H	8.404	0.020
2	1	3	ALA	HA	H	4.310	0.020
3	1	3	ALA	HB1	H	1.401	0.020
4	1	3	ALA	HB2	H	1.401	0.020
5	1	3	ALA	HB3	H	1.401	0.020
6	1	4	ALA	H	H	8.315	0.020
7	1	4	ALA	HA	H	4.386	0.020
8	1	4	ALA	HB1	H	1.514	0.020
9	1	4	ALA	HB2	H	1.514	0.020
10	1	4	ALA	HB3	H	1.514	0.020
11	1	5	GLN	H	H	8.532	0.020
12	1	5	GLN	HA	H	4.248	0.020
13	1	5	GLN	HB2	H	2.058	0.020
14	1	5	GLN	HB3	H	1.975	0.020
15	1	5	GLN	HG2	H	2.439	0.020
16	1	5	GLN	HG3	H	2.353	0.020
17	1	5	GLN	HE21	H	7.601	0.020
18	1	5	GLN	HE22	H	6.806	0.020
19	1	6	ARG	H	H	8.382	0.020
20	1	6	ARG	HA	H	4.924	0.020
21	1	6	ARG	HB2	H	1.676	0.020	2
22	1	6	ARG	HB3	H	1.676	0.020	2
23	1	6	ARG	HG2	H	1.506	0.020	2
24	1	6	ARG	HG3	H	1.506	0.020	2
25	1	6	ARG	HD2	H	3.067	0.020
26	1	6	ARG	HD3	H	2.693	0.020
27	1	6	ARG	HE	H	6.022	0.020
28	1	7	CYS	H	H	7.675	0.020
29	1	7	CYS	HA	H	4.812	0.020
30	1	7	CYS	HB2	H	3.051	0.020
31	1	7	CYS	HB3	H	2.732	0.020
32	1	8	GLY	H	H	8.760	0.020
33	1	8	GLY	HA2	H	3.560	0.020
34	1	8	GLY	HA3	H	3.658	0.020
35	1	9	GLU	H	H	9.462	0.020
36	1	9	GLU	HA	H	3.947	0.020
37	1	9	GLU	HB2	H	1.950	0.020	2
38	1	9	GLU	HB3	H	1.950	0.020	2
39	1	9	GLU	HG2	H	2.286	0.020
40	1	9	GLU	HG3	H	2.041	0.020
41	1	10	GLN	H	H	8.863	0.020
42	1	10	GLN	HA	H	4.178	0.020
43	1	10	GLN	HB2	H	2.109	0.020
44	1	10	GLN	HB3	H	2.020	0.020
45	1	10	GLN	HG2	H	2.641	0.020
46	1	10	GLN	HG3	H	2.430	0.020
47	1	10	GLN	HE21	H	7.477	0.020
48	1	10	GLN	HE22	H	6.636	0.020
49	1	11	GLY	H	H	7.536	0.020
50	1	11	GLY	HA2	H	4.481	0.020
51	1	11	GLY	HA3	H	2.818	0.020
52	1	12	SER	H	H	8.641	0.020
53	1	12	SER	HA	H	4.020	0.020
54	1	12	SER	HB2	H	3.828	0.020	2
55	1	12	SER	HB3	H	3.828	0.020	2
56	1	13	ASN	H	H	8.473	0.020
57	1	13	ASN	HA	H	3.885	0.020
58	1	13	ASN	HB2	H	2.971	0.020
59	1	13	ASN	HB3	H	2.839	0.020
60	1	13	ASN	HD21	H	7.530	0.020
61	1	13	ASN	HD22	H	6.883	0.020
62	1	14	MET	H	H	7.641	0.020
63	1	14	MET	HA	H	4.311	0.020
64	1	14	MET	HB2	H	2.159	0.020
65	1	14	MET	HB3	H	2.072	0.020
66	1	14	MET	HG2	H	2.695	0.020
67	1	14	MET	HG3	H	2.570	0.020
68	1	15	GLU	H	H	8.613	0.020
69	1	15	GLU	HA	H	4.407	0.020
70	1	15	GLU	HB2	H	2.062	0.020
71	1	15	GLU	HB3	H	1.855	0.020
72	1	15	GLU	HG2	H	2.303	0.020
73	1	15	GLU	HG3	H	2.133	0.020
74	1	16	CYS	H	H	8.709	0.020
75	1	16	CYS	HA	H	4.707	0.020
76	1	16	CYS	HB2	H	2.544	0.020
77	1	16	CYS	HB3	H	2.809	0.020
78	1	17	PRO	HA	H	3.879	0.020
79	1	17	PRO	HB2	H	2.306	0.020
80	1	17	PRO	HB3	H	2.070	0.020
81	1	17	PRO	HG2	H	1.880	0.020
82	1	17	PRO	HG3	H	1.991	0.020
83	1	17	PRO	HD2	H	3.489	0.020	2
84	1	17	PRO	HD3	H	3.489	0.020	2
85	1	18	ASN	H	H	8.666	0.020
86	1	18	ASN	HA	H	4.280	0.020
87	1	18	ASN	HB2	H	2.870	0.020
88	1	18	ASN	HB3	H	2.681	0.020
89	1	19	ASN	H	H	8.540	0.020
90	1	19	ASN	HA	H	4.428	0.020
91	1	19	ASN	HB2	H	2.997	0.020
92	1	19	ASN	HB3	H	2.906	0.020
93	1	20	LEU	H	H	7.647	0.020
94	1	20	LEU	HA	H	4.483	0.020
95	1	20	LEU	HB2	H	1.671	0.020
96	1	20	LEU	HB3	H	1.749	0.020
97	1	20	LEU	HG	H	1.426	0.020
98	1	20	LEU	HD11	H	0.715	0.020
99	1	20	LEU	HD12	H	0.715	0.020
100	1	20	LEU	HD13	H	0.715	0.020
101	1	20	LEU	HD21	H	0.784	0.020
102	1	20	LEU	HD22	H	0.784	0.020
103	1	20	LEU	HD23	H	0.784	0.020
104	1	21	CYS	H	H	8.749	0.020
105	1	21	CYS	HA	H	4.566	0.020
106	1	21	CYS	HB2	H	2.672	0.020
107	1	21	CYS	HB3	H	3.692	0.020
108	1	22	CYS	H	H	8.437	0.020
109	1	22	CYS	HA	H	5.132	0.020
110	1	22	CYS	HB2	H	3.254	0.020
111	1	22	CYS	HB3	H	2.674	0.020
112	1	23	SER	H	H	9.734	0.020
113	1	23	SER	HA	H	4.854	0.020
114	1	23	SER	HB2	H	4.217	0.020	2
115	1	23	SER	HB3	H	4.217	0.020	2
116	1	24	GLN	H	H	9.251	0.020
117	1	24	GLN	HA	H	4.086	0.020
118	1	24	GLN	HB2	H	1.633	0.020
119	1	24	GLN	HB3	H	0.858	0.020
120	1	24	GLN	HG2	H	1.988	0.020
121	1	24	GLN	HG3	H	1.753	0.020
122	1	24	GLN	HE21	H	7.194	0.020
123	1	24	GLN	HE22	H	6.662	0.020
124	1	25	TYR	H	H	7.271	0.020
125	1	25	TYR	HA	H	4.598	0.020
126	1	25	TYR	HB2	H	3.604	0.020
127	1	25	TYR	HB3	H	2.713	0.020
128	1	25	TYR	HD1	H	7.142	0.020	3
129	1	25	TYR	HD2	H	7.142	0.020	3
130	1	25	TYR	HE1	H	6.813	0.020	3
131	1	25	TYR	HE2	H	6.813	0.020	3
132	1	26	GLY	H	H	8.247	0.020
133	1	26	GLY	HA2	H	3.730	0.020
134	1	26	GLY	HA3	H	3.845	0.020
135	1	27	TYR	H	H	7.362	0.020
136	1	27	TYR	HA	H	5.178	0.020
137	1	27	TYR	HB2	H	2.838	0.020
138	1	27	TYR	HB3	H	3.306	0.020
139	1	27	TYR	HD1	H	6.924	0.020	3
140	1	27	TYR	HD2	H	6.924	0.020	3
141	1	27	TYR	HE1	H	6.712	0.020	3
142	1	27	TYR	HE2	H	6.712	0.020	3
143	1	28	CYS	H	H	8.986	0.020
144	1	28	CYS	HA	H	5.704	0.020
145	1	28	CYS	HB2	H	2.968	0.020
146	1	28	CYS	HB3	H	2.788	0.020
147	1	29	GLY	H	H	9.095	0.020
148	1	29	GLY	HA2	H	3.561	0.020
149	1	29	GLY	HA3	H	1.951	0.020
150	1	30	MET	H	H	7.846	0.020
151	1	30	MET	HA	H	5.105	0.020
152	1	30	MET	HB2	H	2.117	0.020
153	1	30	MET	HB3	H	1.932	0.020
154	1	30	MET	HG2	H	2.584	0.020
155	1	30	MET	HG3	H	2.485	0.020
156	1	31	GLY	H	H	8.114	0.020
157	1	31	GLY	HA2	H	4.072	0.020
158	1	31	GLY	HA3	H	4.711	0.020
159	1	32	GLY	H	H	9.259	0.020
160	1	32	GLY	HA2	H	3.063	0.020
161	1	32	GLY	HA3	H	4.059	0.020
162	1	33	ASP	H	H	8.938	0.020
163	1	33	ASP	HA	H	4.388	0.020
164	1	33	ASP	HB2	H	2.497	0.020
165	1	33	ASP	HB3	H	2.451	0.020
166	1	34	TYR	H	H	7.359	0.020
167	1	34	TYR	HA	H	3.902	0.020
168	1	34	TYR	HB2	H	2.768	0.020
169	1	34	TYR	HB3	H	2.302	0.020
170	1	34	TYR	HD1	H	7.156	0.020	3
171	1	34	TYR	HD2	H	7.156	0.020	3
172	1	34	TYR	HE1	H	6.694	0.020	3
173	1	34	TYR	HE2	H	6.694	0.020	3
174	1	35	CYS	H	H	8.019	0.020
175	1	35	CYS	HA	H	4.672	0.020
176	1	35	CYS	HB2	H	0.846	0.020
177	1	35	CYS	HB3	H	2.330	0.020
178	1	36	GLY	H	H	6.982	0.020
179	1	36	GLY	HA2	H	4.225	0.020
180	1	36	GLY	HA3	H	3.643	0.020
181	1	37	LYS	H	H	8.376	0.020
182	1	37	LYS	HA	H	3.978	0.020
183	1	37	LYS	HB2	H	1.791	0.020
184	1	37	LYS	HB3	H	1.697	0.020
185	1	37	LYS	HG2	H	1.389	0.020	2
186	1	37	LYS	HG3	H	1.389	0.020	2
187	1	37	LYS	HD2	H	1.470	0.020	2
188	1	37	LYS	HD3	H	1.470	0.020	2
189	1	37	LYS	HE2	H	2.995	0.020	2
190	1	37	LYS	HE3	H	2.995	0.020	2
191	1	38	GLY	H	H	8.995	0.020
192	1	38	GLY	HA2	H	4.016	0.020
193	1	38	GLY	HA3	H	3.512	0.020
194	1	39	CYS	H	H	7.736	0.020
195	1	39	CYS	HA	H	4.562	0.020
196	1	39	CYS	HB2	H	3.526	0.020
197	1	39	CYS	HB3	H	2.682	0.020
198	1	40	GLN	H	H	9.886	0.020
199	1	40	GLN	HA	H	4.415	0.020
200	1	40	GLN	HB2	H	1.486	0.020
201	1	40	GLN	HB3	H	2.181	0.020
202	1	40	GLN	HG2	H	2.355	0.020
203	1	40	GLN	HG3	H	2.291	0.020
204	1	40	GLN	HE21	H	8.069	0.020
205	1	40	GLN	HE22	H	8.286	0.020
206	1	41	ASN	H	H	7.531	0.020
207	1	41	ASN	HA	H	4.593	0.020
208	1	41	ASN	HB2	H	3.461	0.020
209	1	41	ASN	HB3	H	2.903	0.020
210	1	41	ASN	HD21	H	7.920	0.020
211	1	41	ASN	HD22	H	5.992	0.020
212	1	42	GLY	H	H	8.888	0.020
213	1	42	GLY	HA2	H	4.565	0.020
214	1	42	GLY	HA3	H	3.785	0.020
215	1	43	ALA	H	H	7.354	0.020
216	1	43	ALA	HA	H	4.603	0.020
217	1	43	ALA	HB1	H	1.340	0.020
218	1	43	ALA	HB2	H	1.340	0.020
219	1	43	ALA	HB3	H	1.340	0.020
220	1	44	CYS	H	H	8.039	0.020
221	1	44	CYS	HA	H	4.555	0.020
222	1	44	CYS	HB2	H	3.390	0.020
223	1	44	CYS	HB3	H	2.606	0.020
224	1	45	TRP	H	H	9.028	0.020
225	1	45	TRP	HA	H	4.999	0.020
226	1	45	TRP	HB2	H	3.287	0.020	2
227	1	45	TRP	HB3	H	3.287	0.020	2
228	1	45	TRP	HD1	H	7.166	0.020
229	1	45	TRP	HE1	H	10.004	0.020
230	1	45	TRP	HE3	H	7.622	0.020
231	1	45	TRP	HZ2	H	7.444	0.020
232	1	45	TRP	HZ3	H	7.165	0.020
233	1	46	THR	H	H	8.229	0.020
234	1	46	THR	HA	H	4.257	0.020
235	1	46	THR	HG21	H	1.199	0.020
236	1	46	THR	HG22	H	1.199	0.020
237	1	46	THR	HG23	H	1.199	0.020

Release date

2024-02-29

Citation

Decoding the mechanism governing the structural stability of wheat germ agglutinin and its isolated domains: A combined calorimetric, NMR, and MD simulation study
Medrano-Cerano, J.L., Cofas-Vargas, L.F., Leyva, E., Rauda-Ceja, J.A., Calderon-Vargas, M., Cano-Sanchez, P., Titaux-Delgado, G., Melchor-Meneses, C.M., Hernandez-Arana, A., Del Rio-Portilla, F., Garcia-Hernandez, E.
Protein Sci. (2024), 33, e5020-e5020, PubMed , DOI:

Related entities 1. Agglutinin isolectin 1, : 1 : 16 : 185 entities Detail

Experiments performed 3 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	WGA_domA	natural abundance		1 mM
2	Phosphate buffer	natural abundance		30 mM

#	Name	Isotope labeling	Type	Concentration
1	WGA_domA	natural abundance		1 mM
2	Phosphate buffer	natural abundance		30 mM

#	Name	Isotope labeling	Type	Concentration
1	WGA_domA	natural abundance		1 mM
2	Phosphate buffer	natural abundance		30 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr31141_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	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:CYS:SG	1:22:CYS:SG	unknown	unknown	n/a
1:16:CYS:SG	1:28:CYS:SG	unknown	unknown	n/a
1:21:CYS:SG	1:35:CYS:SG	unknown	unknown	n/a
1:39:CYS:SG	1:44:CYS:SG	unknown	unknown	n/a

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

None

Non-standard residues

None

Content subtype: bmr31141_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	237		95.7 (chain: 1, length: 46)
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: 46, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 237
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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	239	225	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	96	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	139	129	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	6	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4

Keywords Lectin, Multidomain protein, SUGAR BINDING PROTEIN, Structural stability

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Found 1 Document (0.626 seconds)

BMRB: 31141

Related entities 1. Agglutinin isolectin 1, : 1 : 16 : 185 entities Detail

Experiments performed 3 experiments Detail

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Chemical shift validation 3 contents Detail