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- PDB-8p1f: X-ray structure of acetylcholine-binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 8p1f
TitleX-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001909.
ComponentsAcetylcholine-binding protein
KeywordsCHOLINE-BINDING PROTEIN / Fragment based drug design / Acetylcholine-binding protein / choline-binding proteins
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
: / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCederfelt, D. / Boronat, P. / Dobritzsch, D. / Hennig, S. / Fitzgerald, E.A. / de Esch, I.J.P. / Danielson, U.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675899European Union
CitationJournal: To Be Published
Title: Elucidating the regulation of ligand gated ion channels via biophysical studies of ligand-induced conformational dynamics of acetylcholine binding proteins
Authors: Fitzgerald, E.A. / Cederfelt, D. / Boronat, P. / Aarmo Lund, B. / de Esch, I.J.P. / Danielson, U.H.
History
DepositionMay 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
K: Acetylcholine-binding protein
L: Acetylcholine-binding protein
M: Acetylcholine-binding protein
N: Acetylcholine-binding protein
O: Acetylcholine-binding protein
P: Acetylcholine-binding protein
Q: Acetylcholine-binding protein
R: Acetylcholine-binding protein
S: Acetylcholine-binding protein
T: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)544,74336
Polymers541,20620
Non-polymers3,53716
Water12,665703
1
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9648
Polymers135,3025
Non-polymers6633
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
ΔGint-56 kcal/mol
Surface area43030 Å2
2
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,40610
Polymers135,3025
Non-polymers1,1045
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-47 kcal/mol
Surface area42860 Å2
3
K: Acetylcholine-binding protein
L: Acetylcholine-binding protein
M: Acetylcholine-binding protein
N: Acetylcholine-binding protein
O: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,40810
Polymers135,3025
Non-polymers1,1065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-49 kcal/mol
Surface area43320 Å2
4
P: Acetylcholine-binding protein
Q: Acetylcholine-binding protein
R: Acetylcholine-binding protein
S: Acetylcholine-binding protein
T: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9658
Polymers135,3025
Non-polymers6643
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-51 kcal/mol
Surface area42730 Å2
Unit cell
Length a, b, c (Å)116.710, 140.710, 147.170
Angle α, β, γ (deg.)90.00, 109.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216Q
117A
217R
118A
218S
119A
219T
120B
220C
121B
221D
122B
222E
123B
223F
124B
224G
125B
225H
126B
226I
127B
227J
128B
228K
129B
229L
130B
230M
131B
231N
132B
232O
133B
233P
134B
234Q
135B
235R
136B
236S
137B
237T
138C
238D
139C
239E
140C
240F
141C
241G
142C
242H
143C
243I
144C
244J
145C
245K
146C
246L
147C
247M
148C
248N
149C
249O
150C
250P
151C
251Q
152C
252R
153C
253S
154C
254T
155D
255E
156D
256F
157D
257G
158D
258H
159D
259I
160D
260J
161D
261K
162D
262L
163D
263M
164D
264N
165D
265O
166D
266P
167D
267Q
168D
268R
169D
269S
170D
270T
171E
271F
172E
272G
173E
273H
174E
274I
175E
275J
176E
276K
177E
277L
178E
278M
179E
279N
180E
280O
181E
281P
182E
282Q
183E
283R
184E
284S
185E
285T
186F
286G
187F
287H
188F
288I
189F
289J
190F
290K
191F
291L
192F
292M
193F
293N
194F
294O
195F
295P
196F
296Q
197F
297R
198F
298S
199F
299T
1100G
2100H
1101G
2101I
1102G
2102J
1103G
2103K
1104G
2104L
1105G
2105M
1106G
2106N
1107G
2107O
1108G
2108P
1109G
2109Q
1110G
2110R
1111G
2111S
1112G
2112T
1113H
2113I
1114H
2114J
1115H
2115K
1116H
2116L
1117H
2117M
1118H
2118N
1119H
2119O
1120H
2120P
1121H
2121Q
1122H
2122R
1123H
2123S
1124H
2124T
1125I
2125J
1126I
2126K
1127I
2127L
1128I
2128M
1129I
2129N
1130I
2130O
1131I
2131P
1132I
2132Q
1133I
2133R
1134I
2134S
1135I
2135T
1136J
2136K
1137J
2137L
1138J
2138M
1139J
2139N
1140J
2140O
1141J
2141P
1142J
2142Q
1143J
2143R
1144J
2144S
1145J
2145T
1146K
2146L
1147K
2147M
1148K
2148N
1149K
2149O
1150K
2150P
1151K
2151Q
1152K
2152R
1153K
2153S
1154K
2154T
1155L
2155M
1156L
2156N
1157L
2157O
1158L
2158P
1159L
2159Q
1160L
2160R
1161L
2161S
1162L
2162T
1163M
2163N
1164M
2164O
1165M
2165P
1166M
2166Q
1167M
2167R
1168M
2168S
1169M
2169T
1170N
2170O
1171N
2171P
1172N
2172Q
1173N
2173R
1174N
2174S
1175N
2175T
1176O
2176P
1177O
2177Q
1178O
2178R
1179O
2179S
1180O
2180T
1181P
2181Q
1182P
2182R
1183P
2183S
1184P
2184T
1185Q
2185R
1186Q
2186S
1187Q
2187T
1188R
2188S
1189R
2189T
1190S
2190T

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA20 - 22320 - 223
21LYSLYSBB20 - 22320 - 223
12LYSLYSAA20 - 22320 - 223
22LYSLYSCC20 - 22320 - 223
13LYSLYSAA20 - 22220 - 222
23LYSLYSDD20 - 22220 - 222
14LYSLYSAA20 - 22320 - 223
24LYSLYSEE20 - 22320 - 223
15LYSLYSAA20 - 22320 - 223
25LYSLYSFF20 - 22320 - 223
16LYSLYSAA20 - 22320 - 223
26LYSLYSGG20 - 22320 - 223
17LYSLYSAA20 - 22320 - 223
27LYSLYSHH20 - 22320 - 223
18LYSLYSAA20 - 22320 - 223
28LYSLYSII20 - 22320 - 223
19LYSLYSAA20 - 22320 - 223
29LYSLYSJJ20 - 22320 - 223
110LYSLYSAA20 - 22320 - 223
210LYSLYSKK20 - 22320 - 223
111LYSLYSAA20 - 22220 - 222
211LYSLYSLL20 - 22220 - 222
112LYSLYSAA20 - 22320 - 223
212LYSLYSMM20 - 22320 - 223
113LYSLYSAA20 - 22320 - 223
213LYSLYSNN20 - 22320 - 223
114LYSLYSAA20 - 22320 - 223
214LYSLYSOO20 - 22320 - 223
115LYSLYSAA20 - 22320 - 223
215LYSLYSPP20 - 22320 - 223
116LYSLYSAA20 - 22320 - 223
216LYSLYSQQ20 - 22320 - 223
117LYSLYSAA20 - 22320 - 223
217LYSLYSRR20 - 22320 - 223
118LYSLYSAA20 - 22320 - 223
218LYSLYSSS20 - 22320 - 223
119LYSLYSAA20 - 22220 - 222
219LYSLYSTT20 - 22220 - 222
120LYSLYSBB20 - 22220 - 222
220LYSLYSCC20 - 22220 - 222
121LYSLYSBB20 - 22220 - 222
221LYSLYSDD20 - 22220 - 222
122LYSLYSBB20 - 22220 - 222
222LYSLYSEE20 - 22220 - 222
123LYSLYSBB20 - 22320 - 223
223LYSLYSFF20 - 22320 - 223
124LYSLYSBB20 - 22320 - 223
224LYSLYSGG20 - 22320 - 223
125LYSLYSBB20 - 22220 - 222
225LYSLYSHH20 - 22220 - 222
126LYSLYSBB20 - 22320 - 223
226LYSLYSII20 - 22320 - 223
127LYSLYSBB20 - 22320 - 223
227LYSLYSJJ20 - 22320 - 223
128LYSLYSBB20 - 22320 - 223
228LYSLYSKK20 - 22320 - 223
129LYSLYSBB20 - 22320 - 223
229LYSLYSLL20 - 22320 - 223
130LYSLYSBB20 - 22320 - 223
230LYSLYSMM20 - 22320 - 223
131LYSLYSBB20 - 22320 - 223
231LYSLYSNN20 - 22320 - 223
132LYSLYSBB20 - 22320 - 223
232LYSLYSOO20 - 22320 - 223
133LYSLYSBB20 - 22320 - 223
233LYSLYSPP20 - 22320 - 223
134LYSLYSBB20 - 22320 - 223
234LYSLYSQQ20 - 22320 - 223
135LYSLYSBB20 - 22320 - 223
235LYSLYSRR20 - 22320 - 223
136LYSLYSBB20 - 22320 - 223
236LYSLYSSS20 - 22320 - 223
137LYSLYSBB20 - 22220 - 222
237LYSLYSTT20 - 22220 - 222
138LYSLYSCC20 - 22320 - 223
238LYSLYSDD20 - 22320 - 223
139GLYGLYCC20 - 22420 - 224
239GLYGLYEE20 - 22420 - 224
140GLYGLYCC20 - 22420 - 224
240GLYGLYFF20 - 22420 - 224
141LYSLYSCC20 - 22320 - 223
241LYSLYSGG20 - 22320 - 223
142GLYGLYCC20 - 22420 - 224
242GLYGLYHH20 - 22420 - 224
143GLYGLYCC20 - 22420 - 224
243GLYGLYII20 - 22420 - 224
144GLYGLYCC20 - 22420 - 224
244GLYGLYJJ20 - 22420 - 224
145LYSLYSCC20 - 22320 - 223
245LYSLYSKK20 - 22320 - 223
146GLYGLYCC20 - 22420 - 224
246GLYGLYLL20 - 22420 - 224
147LYSLYSCC20 - 22220 - 222
247LYSLYSMM20 - 22220 - 222
148LYSLYSCC20 - 22320 - 223
248LYSLYSNN20 - 22320 - 223
149LYSLYSCC20 - 22320 - 223
249LYSLYSOO20 - 22320 - 223
150LYSLYSCC20 - 22320 - 223
250LYSLYSPP20 - 22320 - 223
151LYSLYSCC20 - 22320 - 223
251LYSLYSQQ20 - 22320 - 223
152LYSLYSCC20 - 22220 - 222
252LYSLYSRR20 - 22220 - 222
153GLYGLYCC20 - 22420 - 224
253GLYGLYSS20 - 22420 - 224
154LYSLYSCC20 - 22320 - 223
254LYSLYSTT20 - 22320 - 223
155LYSLYSDD20 - 22320 - 223
255LYSLYSEE20 - 22320 - 223
156GLYGLYDD20 - 22420 - 224
256GLYGLYFF20 - 22420 - 224
157LYSLYSDD20 - 22320 - 223
257LYSLYSGG20 - 22320 - 223
158LYSLYSDD20 - 22320 - 223
258LYSLYSHH20 - 22320 - 223
159GLYGLYDD20 - 22420 - 224
259GLYGLYII20 - 22420 - 224
160ARGARGDD20 - 22520 - 225
260ARGARGJJ20 - 22520 - 225
161LYSLYSDD20 - 22220 - 222
261LYSLYSKK20 - 22220 - 222
162GLYGLYDD20 - 22420 - 224
262GLYGLYLL20 - 22420 - 224
163LYSLYSDD20 - 22220 - 222
263LYSLYSMM20 - 22220 - 222
164LYSLYSDD20 - 22220 - 222
264LYSLYSNN20 - 22220 - 222
165LYSLYSDD20 - 22220 - 222
265LYSLYSOO20 - 22220 - 222
166LYSLYSDD20 - 22320 - 223
266LYSLYSPP20 - 22320 - 223
167LYSLYSDD20 - 22320 - 223
267LYSLYSQQ20 - 22320 - 223
168LYSLYSDD20 - 22220 - 222
268LYSLYSRR20 - 22220 - 222
169ARGARGDD20 - 22520 - 225
269ARGARGSS20 - 22520 - 225
170ARGARGDD20 - 22520 - 225
270ARGARGTT20 - 22520 - 225
171GLYGLYEE20 - 22420 - 224
271GLYGLYFF20 - 22420 - 224
172LYSLYSEE20 - 22320 - 223
272LYSLYSGG20 - 22320 - 223
173GLYGLYEE20 - 22420 - 224
273GLYGLYHH20 - 22420 - 224
174GLYGLYEE20 - 22420 - 224
274GLYGLYII20 - 22420 - 224
175GLYGLYEE20 - 22420 - 224
275GLYGLYJJ20 - 22420 - 224
176LYSLYSEE20 - 22320 - 223
276LYSLYSKK20 - 22320 - 223
177GLYGLYEE20 - 22420 - 224
277GLYGLYLL20 - 22420 - 224
178LYSLYSEE20 - 22220 - 222
278LYSLYSMM20 - 22220 - 222
179LYSLYSEE20 - 22320 - 223
279LYSLYSNN20 - 22320 - 223
180LYSLYSEE20 - 22320 - 223
280LYSLYSOO20 - 22320 - 223
181LYSLYSEE20 - 22320 - 223
281LYSLYSPP20 - 22320 - 223
182LYSLYSEE20 - 22320 - 223
282LYSLYSQQ20 - 22320 - 223
183LYSLYSEE20 - 22220 - 222
283LYSLYSRR20 - 22220 - 222
184GLYGLYEE20 - 22420 - 224
284GLYGLYSS20 - 22420 - 224
185LYSLYSEE20 - 22320 - 223
285LYSLYSTT20 - 22320 - 223
186LYSLYSFF20 - 22320 - 223
286LYSLYSGG20 - 22320 - 223
187GLYGLYFF20 - 22420 - 224
287GLYGLYHH20 - 22420 - 224
188GLYGLYFF20 - 22420 - 224
288GLYGLYII20 - 22420 - 224
189GLYGLYFF20 - 22420 - 224
289GLYGLYJJ20 - 22420 - 224
190LYSLYSFF20 - 22320 - 223
290LYSLYSKK20 - 22320 - 223
191GLYGLYFF20 - 22420 - 224
291GLYGLYLL20 - 22420 - 224
192LYSLYSFF20 - 22320 - 223
292LYSLYSMM20 - 22320 - 223
193LYSLYSFF20 - 22320 - 223
293LYSLYSNN20 - 22320 - 223
194LYSLYSFF20 - 22320 - 223
294LYSLYSOO20 - 22320 - 223
195LYSLYSFF20 - 22320 - 223
295LYSLYSPP20 - 22320 - 223
196LYSLYSFF20 - 22320 - 223
296LYSLYSQQ20 - 22320 - 223
197LYSLYSFF20 - 22320 - 223
297LYSLYSRR20 - 22320 - 223
198GLYGLYFF20 - 22420 - 224
298GLYGLYSS20 - 22420 - 224
199GLYGLYFF20 - 22420 - 224
299GLYGLYTT20 - 22420 - 224
1100LYSLYSGG20 - 22320 - 223
2100LYSLYSHH20 - 22320 - 223
1101LYSLYSGG20 - 22220 - 222
2101LYSLYSII20 - 22220 - 222
1102LYSLYSGG20 - 22320 - 223
2102LYSLYSJJ20 - 22320 - 223
1103LYSLYSGG20 - 22320 - 223
2103LYSLYSKK20 - 22320 - 223
1104LYSLYSGG20 - 22320 - 223
2104LYSLYSLL20 - 22320 - 223
1105LYSLYSGG20 - 22320 - 223
2105LYSLYSMM20 - 22320 - 223
1106LYSLYSGG20 - 22320 - 223
2106LYSLYSNN20 - 22320 - 223
1107LYSLYSGG20 - 22320 - 223
2107LYSLYSOO20 - 22320 - 223
1108LYSLYSGG20 - 22320 - 223
2108LYSLYSPP20 - 22320 - 223
1109LYSLYSGG20 - 22320 - 223
2109LYSLYSQQ20 - 22320 - 223
1110LYSLYSGG20 - 22320 - 223
2110LYSLYSRR20 - 22320 - 223
1111LYSLYSGG20 - 22220 - 222
2111LYSLYSSS20 - 22220 - 222
1112LYSLYSGG20 - 22320 - 223
2112LYSLYSTT20 - 22320 - 223
1113GLYGLYHH20 - 22420 - 224
2113GLYGLYII20 - 22420 - 224
1114GLYGLYHH20 - 22420 - 224
2114GLYGLYJJ20 - 22420 - 224
1115LYSLYSHH20 - 22320 - 223
2115LYSLYSKK20 - 22320 - 223
1116GLYGLYHH20 - 22420 - 224
2116GLYGLYLL20 - 22420 - 224
1117LYSLYSHH20 - 22220 - 222
2117LYSLYSMM20 - 22220 - 222
1118LYSLYSHH20 - 22320 - 223
2118LYSLYSNN20 - 22320 - 223
1119LYSLYSHH20 - 22320 - 223
2119LYSLYSOO20 - 22320 - 223
1120LYSLYSHH20 - 22320 - 223
2120LYSLYSPP20 - 22320 - 223
1121LYSLYSHH20 - 22320 - 223
2121LYSLYSQQ20 - 22320 - 223
1122LYSLYSHH20 - 22220 - 222
2122LYSLYSRR20 - 22220 - 222
1123GLYGLYHH20 - 22420 - 224
2123GLYGLYSS20 - 22420 - 224
1124LYSLYSHH20 - 22320 - 223
2124LYSLYSTT20 - 22320 - 223
1125GLYGLYII20 - 22420 - 224
2125GLYGLYJJ20 - 22420 - 224
1126LYSLYSII20 - 22320 - 223
2126LYSLYSKK20 - 22320 - 223
1127GLYGLYII20 - 22420 - 224
2127GLYGLYLL20 - 22420 - 224
1128LYSLYSII20 - 22320 - 223
2128LYSLYSMM20 - 22320 - 223
1129LYSLYSII20 - 22320 - 223
2129LYSLYSNN20 - 22320 - 223
1130LYSLYSII20 - 22320 - 223
2130LYSLYSOO20 - 22320 - 223
1131LYSLYSII20 - 22320 - 223
2131LYSLYSPP20 - 22320 - 223
1132LYSLYSII20 - 22220 - 222
2132LYSLYSQQ20 - 22220 - 222
1133LYSLYSII20 - 22320 - 223
2133LYSLYSRR20 - 22320 - 223
1134LYSLYSII20 - 22320 - 223
2134LYSLYSSS20 - 22320 - 223
1135GLYGLYII20 - 22420 - 224
2135GLYGLYTT20 - 22420 - 224
1136LYSLYSJJ20 - 22320 - 223
2136LYSLYSKK20 - 22320 - 223
1137GLYGLYJJ20 - 22420 - 224
2137GLYGLYLL20 - 22420 - 224
1138LYSLYSJJ20 - 22320 - 223
2138LYSLYSMM20 - 22320 - 223
1139LYSLYSJJ20 - 22320 - 223
2139LYSLYSNN20 - 22320 - 223
1140LYSLYSJJ20 - 22320 - 223
2140LYSLYSOO20 - 22320 - 223
1141LYSLYSJJ20 - 22320 - 223
2141LYSLYSPP20 - 22320 - 223
1142LYSLYSJJ20 - 22320 - 223
2142LYSLYSQQ20 - 22320 - 223
1143LYSLYSJJ20 - 22320 - 223
2143LYSLYSRR20 - 22320 - 223
1144ARGARGJJ20 - 22520 - 225
2144ARGARGSS20 - 22520 - 225
1145ARGARGJJ20 - 22520 - 225
2145ARGARGTT20 - 22520 - 225
1146LYSLYSKK20 - 22220 - 222
2146LYSLYSLL20 - 22220 - 222
1147LYSLYSKK20 - 22320 - 223
2147LYSLYSMM20 - 22320 - 223
1148LYSLYSKK20 - 22320 - 223
2148LYSLYSNN20 - 22320 - 223
1149LYSLYSKK20 - 22320 - 223
2149LYSLYSOO20 - 22320 - 223
1150LYSLYSKK20 - 22320 - 223
2150LYSLYSPP20 - 22320 - 223
1151LYSLYSKK20 - 22320 - 223
2151LYSLYSQQ20 - 22320 - 223
1152LYSLYSKK20 - 22320 - 223
2152LYSLYSRR20 - 22320 - 223
1153LYSLYSKK20 - 22320 - 223
2153LYSLYSSS20 - 22320 - 223
1154LYSLYSKK20 - 22220 - 222
2154LYSLYSTT20 - 22220 - 222
1155LYSLYSLL20 - 22320 - 223
2155LYSLYSMM20 - 22320 - 223
1156LYSLYSLL20 - 22220 - 222
2156LYSLYSNN20 - 22220 - 222
1157LYSLYSLL20 - 22220 - 222
2157LYSLYSOO20 - 22220 - 222
1158LYSLYSLL20 - 22320 - 223
2158LYSLYSPP20 - 22320 - 223
1159LYSLYSLL20 - 22320 - 223
2159LYSLYSQQ20 - 22320 - 223
1160LYSLYSLL20 - 22320 - 223
2160LYSLYSRR20 - 22320 - 223
1161GLYGLYLL20 - 22420 - 224
2161GLYGLYSS20 - 22420 - 224
1162GLYGLYLL20 - 22420 - 224
2162GLYGLYTT20 - 22420 - 224
1163LYSLYSMM20 - 22320 - 223
2163LYSLYSNN20 - 22320 - 223
1164LYSLYSMM20 - 22320 - 223
2164LYSLYSOO20 - 22320 - 223
1165LYSLYSMM20 - 22320 - 223
2165LYSLYSPP20 - 22320 - 223
1166LYSLYSMM20 - 22320 - 223
2166LYSLYSQQ20 - 22320 - 223
1167LYSLYSMM20 - 22320 - 223
2167LYSLYSRR20 - 22320 - 223
1168LYSLYSMM20 - 22320 - 223
2168LYSLYSSS20 - 22320 - 223
1169LYSLYSMM20 - 22220 - 222
2169LYSLYSTT20 - 22220 - 222
1170LYSLYSNN20 - 22320 - 223
2170LYSLYSOO20 - 22320 - 223
1171LYSLYSNN20 - 22320 - 223
2171LYSLYSPP20 - 22320 - 223
1172LYSLYSNN20 - 22320 - 223
2172LYSLYSQQ20 - 22320 - 223
1173LYSLYSNN20 - 22320 - 223
2173LYSLYSRR20 - 22320 - 223
1174LYSLYSNN20 - 22320 - 223
2174LYSLYSSS20 - 22320 - 223
1175LYSLYSNN20 - 22220 - 222
2175LYSLYSTT20 - 22220 - 222
1176LYSLYSOO20 - 22320 - 223
2176LYSLYSPP20 - 22320 - 223
1177LYSLYSOO20 - 22320 - 223
2177LYSLYSQQ20 - 22320 - 223
1178LYSLYSOO20 - 22320 - 223
2178LYSLYSRR20 - 22320 - 223
1179LYSLYSOO20 - 22320 - 223
2179LYSLYSSS20 - 22320 - 223
1180LYSLYSOO20 - 22220 - 222
2180LYSLYSTT20 - 22220 - 222
1181LYSLYSPP20 - 22320 - 223
2181LYSLYSQQ20 - 22320 - 223
1182LYSLYSPP20 - 22320 - 223
2182LYSLYSRR20 - 22320 - 223
1183LYSLYSPP20 - 22320 - 223
2183LYSLYSSS20 - 22320 - 223
1184LYSLYSPP20 - 22320 - 223
2184LYSLYSTT20 - 22320 - 223
1185LYSLYSQQ20 - 22320 - 223
2185LYSLYSRR20 - 22320 - 223
1186LYSLYSQQ20 - 22220 - 222
2186LYSLYSSS20 - 22220 - 222
1187LYSLYSQQ20 - 22320 - 223
2187LYSLYSTT20 - 22320 - 223
1188LYSLYSRR20 - 22320 - 223
2188LYSLYSSS20 - 22320 - 223
1189LYSLYSRR20 - 22220 - 222
2189LYSLYSTT20 - 22220 - 222
1190ARGARGSS20 - 22520 - 225
2190ARGARGTT20 - 22520 - 225

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190

-
Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 27060.320 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P58154
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-WCW / 4-azanyl-1-phenyl-piperidine-4-carboxylic acid


Mass: 220.268 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→49.37 Å / Num. obs: 259396 / % possible obs: 99.68 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rrim(I) all: 0.079871 / Net I/σ(I): 15.49
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 25710 / CC1/2: 0.507 / Rrim(I) all: 1.578

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.238 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25479 12970 5 %RANDOM
Rwork0.2251 ---
obs0.22657 246406 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å21.03 Å2
2---0.81 Å20 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32303 0 230 703 33236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01333503
X-RAY DIFFRACTIONr_bond_other_d0.0010.01730103
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.65245770
X-RAY DIFFRACTIONr_angle_other_deg1.2381.58269959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54354045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.78121.8941880
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.741155515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.83215276
X-RAY DIFFRACTIONr_chiral_restr0.060.24568
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0237271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027111
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7215.86716207
X-RAY DIFFRACTIONr_mcbond_other4.725.86716206
X-RAY DIFFRACTIONr_mcangle_it6.7588.78220210
X-RAY DIFFRACTIONr_mcangle_other6.7588.78220211
X-RAY DIFFRACTIONr_scbond_it5.4576.50117296
X-RAY DIFFRACTIONr_scbond_other5.4576.50217297
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0519.51325550
X-RAY DIFFRACTIONr_long_range_B_refined10.83566.26234690
X-RAY DIFFRACTIONr_long_range_B_other10.84266.24134603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61720.1
12B61720.1
21A62160.09
22C62160.09
31A61490.1
32D61490.1
41A61880.1
42E61880.1
51A60600.1
52F60600.1
61A60890.11
62G60890.11
71A61840.09
72H61840.09
81A61260.1
82I61260.1
91A59550.1
92J59550.1
101A61910.09
102K61910.09
111A61440.1
112L61440.1
121A61960.09
122M61960.09
131A61560.1
132N61560.1
141A62130.09
142O62130.09
151A61730.08
152P61730.08
161A61580.1
162Q61580.1
171A62180.09
172R62180.09
181A60850.1
182S60850.1
191A61410.09
192T61410.09
201B61790.09
202C61790.09
211B61410.1
212D61410.1
221B61350.1
222E61350.1
231B60800.1
232F60800.1
241B61410.09
242G61410.09
251B61560.09
252H61560.09
261B61410.1
262I61410.1
271B59700.09
272J59700.09
281B61160.1
282K61160.1
291B61880.09
292L61880.09
301B61420.09
302M61420.09
311B61220.1
312N61220.1
321B61310.09
322O61310.09
331B60990.1
332P60990.1
341B61740.09
342Q61740.09
351B62170.08
352R62170.08
361B61110.1
362S61110.1
371B61110.1
372T61110.1
381C62040.08
382D62040.08
391C61720.1
392E61720.1
401C61700.1
402F61700.1
411C61520.1
412G61520.1
421C63360.08
422H63360.08
431C62350.09
432I62350.09
441C60250.09
442J60250.09
451C62200.09
452K62200.09
461C62150.08
462L62150.08
471C61990.09
472M61990.09
481C62090.09
482N62090.09
491C61790.09
492O61790.09
501C61230.09
502P61230.09
511C61870.1
512Q61870.1
521C62770.08
522R62770.08
531C62490.09
532S62490.09
541C61790.09
542T61790.09
551D61600.09
552E61600.09
561D60380.1
562F60380.1
571D60820.1
572G60820.1
581D61620.09
582H61620.09
591D62130.08
592I62130.08
601D60080.1
602J60080.1
611D60870.09
612K60870.09
621D61820.09
622L61820.09
631D61330.09
632M61330.09
641D61480.08
642N61480.08
651D61490.08
652O61490.08
661D60540.1
662P60540.1
671D61970.08
672Q61970.08
681D61540.08
682R61540.08
691D62080.08
692S62080.08
701D62010.09
702T62010.09
711E60570.1
712F60570.1
721E61520.09
722G61520.09
731E61630.09
732H61630.09
741E62250.09
742I62250.09
751E60440.09
752J60440.09
761E61170.1
762K61170.1
771E61650.09
772L61650.09
781E60990.1
782M60990.1
791E61340.1
792N61340.1
801E61970.08
802O61970.08
811E61070.1
812P61070.1
821E61850.09
822Q61850.09
831E61980.09
832R61980.09
841E61630.1
842S61630.1
851E62480.08
852T62480.08
861F60690.11
862G60690.11
871F61240.1
872H61240.1
881F61100.1
882I61100.1
891F59270.11
892J59270.11
901F60600.1
902K60600.1
911F60340.11
912L60340.11
921F61050.1
922M61050.1
931F60540.1
932N60540.1
941F60000.1
942O60000.1
951F59920.1
952P59920.1
961F60730.11
962Q60730.11
971F60840.1
972R60840.1
981F60730.11
982S60730.11
991F60550.1
992T60550.1
1001G61700.1
1002H61700.1
1011G63040.08
1012I63040.08
1021G61290.09
1022J61290.09
1031G61220.1
1032K61220.1
1041G61370.09
1042L61370.09
1051G61060.09
1052M61060.09
1061G61280.1
1062N61280.1
1071G61280.09
1072O61280.09
1081G61000.1
1082P61000.1
1091G61830.1
1092Q61830.1
1101G61940.09
1102R61940.09
1111G62430.09
1112S62430.09
1121G61640.09
1122T61640.09
1131H62650.08
1132I62650.08
1141H60400.09
1142J60400.09
1151H62210.09
1152K62210.09
1161H62140.09
1162L62140.09
1171H61460.09
1172M61460.09
1181H61980.09
1182N61980.09
1191H61830.08
1192O61830.08
1201H61340.09
1202P61340.09
1211H61550.1
1212Q61550.1
1221H62240.08
1222R62240.08
1231H62350.09
1232S62350.09
1241H62070.08
1242T62070.08
1251I62520.09
1252J62520.09
1261I62290.09
1262K62290.09
1271I62630.09
1272L62630.09
1281I62020.09
1282M62020.09
1291I63000.08
1292N63000.08
1301I62550.08
1302O62550.08
1311I61640.1
1312P61640.1
1321I63000.09
1322Q63000.09
1331I63050.07
1332R63050.07
1341I64520.07
1342S64520.07
1351I63240.08
1352T63240.08
1361J60290.1
1362K60290.1
1371J60510.09
1372L60510.09
1381J59950.1
1382M59950.1
1391J60220.1
1392N60220.1
1401J60560.08
1402O60560.08
1411J59710.09
1412P59710.09
1421J60910.11
1422Q60910.11
1431J60730.09
1432R60730.09
1441J62270.09
1442S62270.09
1451J61440.09
1452T61440.09
1461K61880.1
1462L61880.1
1471K61990.09
1472M61990.09
1481K62130.1
1482N62130.1
1491K62060.09
1492O62060.09
1501K61870.09
1502P61870.09
1511K61770.1
1512Q61770.1
1521K62230.1
1522R62230.1
1531K61830.1
1532S61830.1
1541K61590.09
1542T61590.09
1551L61260.1
1552M61260.1
1561L61430.09
1562N61430.09
1571L61630.09
1572O61630.09
1581L60960.1
1582P60960.1
1591L61730.08
1592Q61730.08
1601L61780.09
1602R61780.09
1611L61650.09
1612S61650.09
1621L61980.09
1622T61980.09
1631M61670.09
1632N61670.09
1641M61500.09
1642O61500.09
1651M61290.1
1652P61290.1
1661M61930.09
1662Q61930.09
1671M62090.09
1672R62090.09
1681M61210.1
1682S61210.1
1691M60850.09
1692T60850.09
1701N62340.08
1702O62340.08
1711N61720.1
1712P61720.1
1721N62120.09
1722Q62120.09
1731N62200.09
1732R62200.09
1741N62210.09
1742S62210.09
1751N61900.08
1752T61900.08
1761O61630.08
1762P61630.08
1771O61900.09
1772Q61900.09
1781O62190.09
1782R62190.09
1791O61980.08
1792S61980.08
1801O61920.08
1802T61920.08
1811P60730.11
1812Q60730.11
1821P61740.09
1822R61740.09
1831P60880.11
1832S60880.11
1841P61140.09
1842T61140.09
1851Q62030.1
1852R62030.1
1861Q61960.1
1862S61960.1
1871Q61510.1
1872T61510.1
1881R62160.09
1882S62160.09
1891R61760.09
1892T61760.09
1901S62390.1
1902T62390.1
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 950 -
Rwork0.354 18044 -
obs--99.28 %

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