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- PDB-5oat: PINK1 structure -

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Basic information

Entry
Database: PDB / ID: 5oat
TitlePINK1 structure
ComponentsSerine/threonine-protein kinase PINK1, mitochondrial-like Protein
KeywordsKinase / Kinase for phosphorylation
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / peptidyl-serine phosphorylation / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / non-specific serine/threonine protein kinase ...positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / peptidyl-serine phosphorylation / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ubiquitin protein ligase binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
AuthorsKumar, A. / Tamjar, J. / Woodroof, H.I. / Raimi, O.G. / Waddell, A.Y. / Peggie, M. / Muqit, M.M.K. / van Aalten, D.M.F.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101022/Z/13/Z United Kingdom
Wellcome Trust110061 United Kingdom
CitationJournal: Elife / Year: 2017
Title: Structure of PINK1 and mechanisms of Parkinson's disease associated mutations.
Authors: Kumar, A. / Tamjar, J. / Waddell, A.D. / Woodroof, H.I. / Raimi, O.G. / Shaw, A.M. / Peggie, M. / Muqit, M.M. / van Aalten, D.M.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_name_com / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
B: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
C: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
D: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
E: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
F: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,08112
Polymers278,9356
Non-polymers1466
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.915, 116.736, 179.344
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26C
17A
27C
18A
28C
19A
29C
110A
210C
111A
211D
112A
212D
113A
213D
114A
214D
115A
215D
116A
216E
117A
217E
118A
218E
119A
219E
120A
220E
121A
221F
122A
222F
123A
223F
124A
224F
125A
225F
126B
226C
127B
227D
128B
228E
129B
229F
130B
230C
131B
231D
132B
232E
133B
233F
134B
234C
135B
235D
136B
236E
137B
237F
138B
238C
139B
239D
140B
240E
141B
241F
142B
242C
143B
243D
144B
244E
145B
245F
146C
246D
147C
247E
148C
248F
149C
249D
150C
250E
151C
251F
152C
252D
153C
253E
154C
254F
155C
255D
156C
256E
157C
257F
158C
258D
159C
259E
160C
260F
161D
261E
162D
262F
163D
263E
164D
264F
165D
265E
166D
266F
167D
267E
168D
268F
169D
269E
170D
270F
171E
271F
172E
272F
173E
273F
174E
274F
175E
275F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA156 - 1817 - 32
21PROPROVALVALBB156 - 1817 - 32
12TYRTYRASPASPAA191 - 25942 - 110
22TYRTYRASPASPBB191 - 25942 - 110
13ASNASNPROPROAA287 - 493128 - 334
23ASNASNPROPROBB287 - 493128 - 334
14LYSLYSVALVALAA496 - 514337 - 355
24LYSLYSVALVALBB496 - 514337 - 355
15THRTHRASNASNAA536 - 565377 - 406
25THRTHRASNASNBB536 - 565377 - 406
16PROPROVALVALAA156 - 1817 - 32
26PROPROVALVALCC156 - 1817 - 32
17TYRTYRASPASPAA191 - 25942 - 110
27TYRTYRASPASPCC191 - 25942 - 110
18ASNASNPROPROAA287 - 493128 - 334
28ASNASNPROPROCC287 - 493128 - 334
19LYSLYSVALVALAA496 - 514337 - 355
29LYSLYSVALVALCC496 - 514337 - 355
110THRTHRASNASNAA536 - 565377 - 406
210THRTHRASNASNCC536 - 565377 - 406
111PROPROVALVALAA156 - 1817 - 32
211PROPROVALVALDD156 - 1817 - 32
112TYRTYRASPASPAA191 - 25942 - 110
212TYRTYRASPASPDD191 - 25942 - 110
113ASNASNPROPROAA287 - 493128 - 334
213ASNASNPROPRODD287 - 493128 - 334
114LYSLYSVALVALAA496 - 514337 - 355
214LYSLYSVALVALDD496 - 514337 - 355
115THRTHRASNASNAA536 - 565377 - 406
215THRTHRASNASNDD536 - 565377 - 406
116PROPROVALVALAA156 - 1817 - 32
216PROPROVALVALEE156 - 1817 - 32
117TYRTYRASPASPAA191 - 25942 - 110
217TYRTYRASPASPEE191 - 25942 - 110
118ASNASNPROPROAA287 - 493128 - 334
218ASNASNPROPROEE287 - 493128 - 334
119LYSLYSVALVALAA496 - 514337 - 355
219LYSLYSVALVALEE496 - 514337 - 355
120THRTHRASNASNAA536 - 565377 - 406
220THRTHRASNASNEE536 - 565377 - 406
121PROPROVALVALAA156 - 1817 - 32
221PROPROVALVALFF156 - 1817 - 32
122TYRTYRASPASPAA191 - 25942 - 110
222TYRTYRASPASPFF191 - 25942 - 110
123ASNASNPROPROAA287 - 493128 - 334
223ASNASNPROPROFF287 - 493128 - 334
124LYSLYSVALVALAA496 - 514337 - 355
224LYSLYSVALVALFF496 - 514337 - 355
125THRTHRASNASNAA536 - 565377 - 406
225THRTHRASNASNFF536 - 565377 - 406
126PROPROLYSLYSBB156 - 1827 - 33
226PROPROLYSLYSCC156 - 1827 - 33
127PROPROLYSLYSBB156 - 1827 - 33
227PROPROLYSLYSDD156 - 1827 - 33
128PROPROLYSLYSBB156 - 1827 - 33
228PROPROLYSLYSEE156 - 1827 - 33
129PROPROLYSLYSBB156 - 1827 - 33
229PROPROLYSLYSFF156 - 1827 - 33
130TYRTYRLEULEUBB191 - 26042 - 111
230TYRTYRLEULEUCC191 - 26042 - 111
131TYRTYRLEULEUBB191 - 26042 - 111
231TYRTYRLEULEUDD191 - 26042 - 111
132TYRTYRLEULEUBB191 - 26042 - 111
232TYRTYRLEULEUEE191 - 26042 - 111
133TYRTYRLEULEUBB191 - 26042 - 111
233TYRTYRLEULEUFF191 - 26042 - 111
134ASNASNGLYGLYBB287 - 494128 - 335
234ASNASNGLYGLYCC287 - 494128 - 335
135ASNASNGLYGLYBB287 - 494128 - 335
235ASNASNGLYGLYDD287 - 494128 - 335
136ASNASNGLYGLYBB287 - 494128 - 335
236ASNASNGLYGLYEE287 - 494128 - 335
137ASNASNGLYGLYBB287 - 494128 - 335
237ASNASNGLYGLYFF287 - 494128 - 335
138LYSLYSLEULEUBB496 - 515337 - 356
238LYSLYSLEULEUCC496 - 515337 - 356
139LYSLYSLEULEUBB496 - 515337 - 356
239LYSLYSLEULEUDD496 - 515337 - 356
140LYSLYSLEULEUBB496 - 515337 - 356
240LYSLYSLEULEUEE496 - 515337 - 356
141LYSLYSLEULEUBB496 - 515337 - 356
241LYSLYSLEULEUFF496 - 515337 - 356
142THRTHRLEULEUBB536 - 566377 - 407
242THRTHRLEULEUCC536 - 566377 - 407
143THRTHRLEULEUBB536 - 566377 - 407
243THRTHRLEULEUDD536 - 566377 - 407
144THRTHRLEULEUBB536 - 566377 - 407
244THRTHRLEULEUEE536 - 566377 - 407
145THRTHRLEULEUBB536 - 566377 - 407
245THRTHRLEULEUFF536 - 566377 - 407
146PROPROLYSLYSCC156 - 1827 - 33
246PROPROLYSLYSDD156 - 1827 - 33
147PROPROLYSLYSCC156 - 1827 - 33
247PROPROLYSLYSEE156 - 1827 - 33
148PROPROLYSLYSCC156 - 1827 - 33
248PROPROLYSLYSFF156 - 1827 - 33
149TYRTYRLEULEUCC191 - 26042 - 111
249TYRTYRLEULEUDD191 - 26042 - 111
150TYRTYRLEULEUCC191 - 26042 - 111
250TYRTYRLEULEUEE191 - 26042 - 111
151TYRTYRLEULEUCC191 - 26042 - 111
251TYRTYRLEULEUFF191 - 26042 - 111
152ASNASNGLYGLYCC287 - 494128 - 335
252ASNASNGLYGLYDD287 - 494128 - 335
153ASNASNGLYGLYCC287 - 494128 - 335
253ASNASNGLYGLYEE287 - 494128 - 335
154ASNASNGLYGLYCC287 - 494128 - 335
254ASNASNGLYGLYFF287 - 494128 - 335
155LYSLYSLEULEUCC496 - 515337 - 356
255LYSLYSLEULEUDD496 - 515337 - 356
156LYSLYSLEULEUCC496 - 515337 - 356
256LYSLYSLEULEUEE496 - 515337 - 356
157LYSLYSLEULEUCC496 - 515337 - 356
257LYSLYSLEULEUFF496 - 515337 - 356
158THRTHRLEULEUCC536 - 566377 - 407
258THRTHRLEULEUDD536 - 566377 - 407
159THRTHRLEULEUCC536 - 566377 - 407
259THRTHRLEULEUEE536 - 566377 - 407
160THRTHRLEULEUCC536 - 566377 - 407
260THRTHRLEULEUFF536 - 566377 - 407
161PROPROLYSLYSDD156 - 1827 - 33
261PROPROLYSLYSEE156 - 1827 - 33
162PROPROLYSLYSDD156 - 1827 - 33
262PROPROLYSLYSFF156 - 1827 - 33
163TYRTYRLEULEUDD191 - 26042 - 111
263TYRTYRLEULEUEE191 - 26042 - 111
164TYRTYRLEULEUDD191 - 26042 - 111
264TYRTYRLEULEUFF191 - 26042 - 111
165ASNASNGLYGLYDD287 - 494128 - 335
265ASNASNGLYGLYEE287 - 494128 - 335
166ASNASNGLYGLYDD287 - 494128 - 335
266ASNASNGLYGLYFF287 - 494128 - 335
167LYSLYSLEULEUDD496 - 515337 - 356
267LYSLYSLEULEUEE496 - 515337 - 356
168LYSLYSLEULEUDD496 - 515337 - 356
268LYSLYSLEULEUFF496 - 515337 - 356
169THRTHRLEULEUDD536 - 566377 - 407
269THRTHRLEULEUEE536 - 566377 - 407
170THRTHRLEULEUDD536 - 566377 - 407
270THRTHRLEULEUFF536 - 566377 - 407
171PROPROLYSLYSEE156 - 1827 - 33
271PROPROLYSLYSFF156 - 1827 - 33
172TYRTYRLEULEUEE191 - 26042 - 111
272TYRTYRLEULEUFF191 - 26042 - 111
173ASNASNGLYGLYEE287 - 494128 - 335
273ASNASNGLYGLYFF287 - 494128 - 335
174LYSLYSLEULEUEE496 - 515337 - 356
274LYSLYSLEULEUFF496 - 515337 - 356
175THRTHRLEULEUEE536 - 566377 - 407
275THRTHRLEULEUFF536 - 566377 - 407

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

NCS oper:
IDCodeMatrixVector
1given(0.995592, 0.09251, -0.015417), (0.057675, -0.474306, 0.878469), (0.073955, -0.875486, -0.477551)28.41683, -60.01979, 165.45854
2given(0.996265, 0.086091, -0.006731), (0.045689, -0.459364, 0.887072), (0.073277, -0.884066, -0.461582)27.62628, -59.92745, 164.14888
3given(0.997254, 0.066407, -0.032767), (0.060443, -0.474342, 0.878263), (0.04278, -0.877832, -0.477054)30.4757, -60.04947, 168.4165
4given(0.998168, 0.059098, -0.012977), (0.039368, -0.471466, 0.881005), (0.045948, -0.879902, -0.472929)28.08702, -58.50647, 167.54953
5given(0.998308, 0.05155, -0.026905), (0.048427, -0.480911, 0.875431), (0.032189, -0.875253, -0.482593)29.57728, -58.84623, 169.88838
6given(0.995059, -0.041746, 0.090085), (0.065305, -0.408253, -0.91053), (0.074788, 0.911914, -0.403509)48.3651, 124.6976, 118.84543
7given(0.995485, -0.055918, 0.076705), (0.046852, -0.413336, -0.909373), (0.082556, 0.90886, -0.408849)49.99892, 125.85579, 118.97699
8given(0.995372, -0.023763, 0.093108), (0.07634, -0.392926, -0.916396), (0.058361, 0.919263, -0.389294)47.55735, 124.16548, 118.21523
9given(0.996272, -0.026752, 0.082021), (0.065821, -0.37891, -0.92309), (0.055773, 0.925047, -0.375736)48.40938, 124.75771, 117.13657
10given(0.996536, -0.023965, 0.07963), (0.064482, -0.381982, -0.921917), (0.052511, 0.923859, -0.379114)48.40635, 124.84362, 117.61876
11given(-0.995972, 0.089101, 0.010067), (-0.050081, -0.459624, -0.886701), (-0.074379, -0.883633, 0.462234)174.47696, 187.43269, 54.10045
12given(-0.997249, 0.073334, 0.010814), (-0.042504, -0.446178, -0.893934), (-0.060731, -0.891935, 0.448067)174.71968, 188.08467, 55.93037
13given(-0.99699, 0.074338, 0.022005), (-0.052919, -0.445122, -0.893905), (-0.056656, -0.892379, 0.447716)172.88831, 188.80759, 55.7837
14given(-0.996777, 0.079974, 0.006285), (-0.041564, -0.447851, -0.893141), (-0.068614, -0.890524, 0.449732)175.39119, 187.75586, 56.36553
15given(-0.997679, 0.065827, 0.017405), (-0.045161, -0.448421, -0.892681), (-0.050958, -0.891395, 0.450353)173.5856, 187.98726, 55.06374
16given(-0.999645, -0.025935, 0.006043), (-0.026431, 0.993983, -0.106297), (-0.00325, -0.106419, -0.994316)149.77829, 15.0525, 271.73584
17given(-0.999691, -0.024802, 0.001372), (-0.024825, 0.995651, -0.089788), (0.000861, -0.089794, -0.99596)150.4454, 12.36825, 271.53592
18given(-0.999649, -0.026271, -0.003469), (-0.025835, 0.995327, -0.093043), (0.005897, -0.092921, -0.995656)151.24353, 12.9845, 271.42752
19given(-0.999688, -0.024935, -0.001401), (-0.024666, 0.994586, -0.100951), (0.003911, -0.100885, -0.99489)150.80978, 14.26114, 271.75012
20given(-0.999666, -0.025719, -0.00248), (-0.025378, 0.995364, -0.092771), (0.004855, -0.092677, -0.995684)151.07394, 12.96904, 271.44266
21given(-0.992625, -0.057312, -0.106818), (-0.076459, -0.387792, 0.91857), (-0.094069, 0.919963, 0.380551)225.15512, -110.10123, 23.23346
22given(-0.993449, -0.07232, -0.088477), (-0.052677, -0.397256, 0.916195), (-0.101407, 0.914854, 0.390844)222.5544, -111.49461, 22.26297
23given(-0.993664, -0.04295, -0.103858), (-0.080624, -0.371402, 0.924965), (-0.0783, 0.927478, 0.365586)224.33752, -111.36979, 24.19684
24given(-0.994768, -0.045668, -0.091387), (-0.069681, -0.35086, 0.933832), (-0.07471, 0.935314, 0.345842)222.01207, -114.93782, 27.5215
25given(-0.994804, -0.043695, -0.091955), (-0.070237, -0.359294, 0.930578), (-0.073701, 0.932201, 0.354358)222.08292, -113.90993, 25.75983
26given(0.99997, 0.002496, 0.007361), (-0.004321, -0.60872, 0.793373), (0.006461, -0.793381, -0.608691)27.0581, -44.94761, 184.22339
27given(-0.99997, -0.003129, -0.007112), (-0.003249, 0.999851, 0.016968), (0.007058, 0.016991, -0.999831)151.48251, -6.38999, 268.29153
28given(-0.996996, 0.023495, -0.073805), (-0.077187, -0.380534, 0.92154), (-0.006433, 0.924468, 0.381205)133.04396, -117.43245, 13.35614
29given(-0.999618, -0.011219, -0.025276), (0.026723, -0.626978, -0.778578), (-0.007113, -0.778956, 0.627038)182.4671, 166.45876, 20.87132
30given(0.999958, -0.007867, 0.004808), (-0.008644, -0.618478, 0.785755), (-0.003208, -0.785763, -0.618519)27.4739, -43.48745, 185.50475
31given(-0.999917, -0.012541, 0.003014), (-0.012493, 0.999803, 0.015416), (-0.003207, 0.015377, -0.999877)149.90355, -5.5959, 268.98248
32given(-0.997033, 0.014166, -0.075656), (-0.075353, -0.380092, 0.921874), (-0.015697, 0.92484, 0.380032)133.52431, -117.58001, 13.74195
33given(-0.999582, -0.022987, -0.017531), (0.028121, -0.632483, -0.774064), (0.006705, -0.774233, 0.632865)181.42259, 165.93102, 18.45298
34given(0.999752, -0.008134, 0.020734), (-0.021292, -0.62217, 0.782593), (0.006535, -0.78284, -0.622189)26.02759, -42.17961, 185.18187
35given(-0.999875, 0.009021, -0.012982), (0.008596, 0.999437, 0.03243), (0.013268, 0.032314, -0.99939)152.25293, -9.70679, 267.62399
36given(-0.998213, 0.030004, -0.05167), (-0.059305, -0.392233, 0.917952), (0.007275, 0.919377, 0.393311)129.25537, -117.05778, 11.05207
37given(-0.999161, -0.025617, -0.031966), (0.040955, -0.640875, -0.766552), (-0.00085, -0.767218, 0.641386)184.04681, 163.81908, 17.36568
38given(0.999607, 0.000953, 0.02801), (-0.020988, -0.636861, 0.770693), (0.018573, -0.770978, -0.636591)25.19455, -40.86082, 185.04382
39given(-0.999735, 0.021283, -0.008808), (0.021049, 0.999442, 0.025919), (0.009355, 0.025727, -0.999625)151.70627, -9.59274, 267.59088
40given(-0.998682, 0.009225, -0.050495), (-0.050197, -0.381177, 0.923138), (-0.010731, 0.924456, 0.381137)130.10268, -118.82602, 13.29095
41given(-0.999154, -0.016379, -0.037721), (0.03914, -0.660194, -0.750074), (-0.012617, -0.750916, 0.660277)184.73534, 161.35313, 13.964
42given(0.999644, -0.013598, 0.022941), (-0.026399, -0.62636, 0.779087), (0.003775, -0.779416, -0.626496)26.02232, -41.55217, 185.56796
43given(-0.999802, 0.016044, -0.011757), (0.015614, 0.999237, 0.035804), (0.012323, 0.035613, -0.99929)152.08643, -10.79545, 267.59683
44given(-0.99907, 0.019807, -0.038304), (-0.043026, -0.398624, 0.916105), (0.002876, 0.916901, 0.399105)127.92292, -117.21579, 10.60359
45given(-0.998903, -0.03098, -0.035107), (0.046812, -0.645429, -0.762384), (0.000959, -0.763192, 0.646172)184.82863, 162.56711, 16.15036
46given(-0.99988, -0.007334, -0.013632), (-0.00611, -0.622135, 0.782886), (-0.014222, 0.782876, 0.622015)124.79475, -89.85591, -19.66874
47given(-0.996673, 0.031125, -0.075328), (0.049601, -0.501756, -0.863586), (-0.064675, -0.864449, 0.498542)105.19261, 179.95061, 47.27906
48given(-0.999749, -0.013555, -0.017845), (-0.013132, 0.999635, -0.023621), (0.018159, -0.023381, -0.999562)153.43358, 1.30455, 268.30087
49given(-0.999756, -0.021224, 0.006097), (0.018115, -0.630341, 0.776107), (-0.012629, 0.776028, 0.630572)121.82757, -89.9918, -21.27138
50given(-0.996289, 0.014485, -0.084846), (0.066786, -0.491738, -0.868178), (-0.054297, -0.870623, 0.488945)107.23815, 179.95503, 48.53013
51given(-0.999804, -0.015032, -0.012873), (-0.014794, 0.999721, -0.0184), (0.013146, -0.018206, -0.999748)152.66826, 0.5305, 268.61618
52given(-0.999723, -0.012049, -0.020205), (-0.007606, -0.647191, 0.76229), (-0.022261, 0.762233, 0.64692)126.042, -85.76876, -23.26443
53given(-0.996655, 0.044362, -0.068631), (0.039318, -0.475926, -0.878606), (-0.071639, -0.878366, 0.47259)103.65802, 182.0636, 51.8843
54given(-0.99979, -0.016975, -0.011446), (-0.016685, 0.99955, -0.024919), (0.011864, -0.024723, -0.999624)152.49724, 1.92168, 268.90277
55given(-0.99961, 0.000786, -0.027915), (-0.021577, -0.656323, 0.754172), (-0.017728, 0.75448, 0.656084)127.3391, -83.4341, -24.90791
56given(-0.997431, 0.034408, -0.062825), (0.039329, -0.469985, -0.881798), (-0.059868, -0.882003, 0.467425)103.3193, 182.16878, 52.18711
57given(-0.999818, -0.016453, -0.009691), (-0.016141, 0.999376, -0.031407), (0.010201, -0.031245, -0.99946)152.05418, 3.26884, 269.2225
58given(-0.999812, -0.010226, -0.016464), (-0.005772, -0.653856, 0.756597), (-0.018502, 0.75655, 0.653674)125.51589, -84.91496, -24.53562
59given(-0.997568, 0.033785, -0.060968), (0.038292, -0.465237, -0.884358), (-0.058243, -0.884541, 0.462811)103.20113, 182.377, 53.00321
60given(-0.99978, -0.016811, -0.012524), (-0.016485, 0.999535, -0.025633), (0.012949, -0.025421, -0.999593)152.72072, 2.03527, 268.80969
61given(0.997171, -0.015741, 0.073495), (-0.074164, -0.364837, 0.928113), (0.012205, -0.930938, -0.364972)17.00023, -115.30032, 253.13855
62given(0.999451, 0.007764, 0.032224), (0.029725, -0.6401, -0.767716), (0.014666, 0.768252, -0.639979)-33.29072, 168.5208, 250.09482
63given(0.997942, -0.012368, 0.062923), (-0.06308, -0.36597, 0.928486), (0.011545, -0.930544, -0.365997)18.59344, -115.68173, 253.4321
64given(0.999126, 0.033368, 0.025165), (0.040749, -0.643978, -0.763958), (-0.009286, 0.764316, -0.644775)-32.85495, 167.24565, 253.23853
65given(0.997675, -0.021173, 0.064773), (-0.068042, -0.362033, 0.929679), (0.003766, -0.931925, -0.362632)18.66776, -115.78884, 253.23259
66given(0.999376, 0.009919, 0.033886), (0.031889, -0.665539, -0.745681), (0.015156, 0.746297, -0.665441)-33.61906, 165.62808, 255.31978
67given(0.997257, -0.008611, 0.073511), (-0.071736, -0.356977, 0.931355), (0.018222, -0.934074, -0.356616)16.91619, -116.17356, 251.56296
68given(0.999595, -0.004566, 0.028086), (0.017505, -0.679497, -0.733469), (0.022433, 0.733664, -0.679142)-31.79103, 165.03023, 257.67209
69given(0.998236, -0.014726, 0.057509), (-0.058911, -0.365348, 0.929005), (0.00733, -0.930754, -0.365572)19.33146, -115.87961, 253.28467
70given(0.999448, 0.011506, 0.03117), (0.030801, -0.672613, -0.739353), (0.012458, 0.739905, -0.672596)-33.13006, 164.799, 257.09015
71given(0.994596, 0.064601, 0.081271), (-0.040235, -0.481789, 0.875363), (0.095705, -0.873903, -0.476586)-71.23752, -99.9222, 260.8317
72given(0.994392, 0.082733, 0.065883), (-0.018655, -0.475966, 0.879266), (0.104102, -0.875564, -0.471753)-69.19513, -102.72418, 259.52744
73given(0.994941, 0.05799, 0.08204), (-0.046831, -0.454751, 0.889387), (0.088883, -0.888729, -0.449734)-71.3057, -102.7207, 257.48282
74given(0.996005, 0.05758, 0.068253), (-0.035804, -0.442696, 0.895957), (0.081805, -0.894821, -0.438866)-68.63625, -105.67027, 256.13992
75given(0.995963, 0.056529, 0.069733), (-0.037563, -0.443099, 0.895685), (0.081531, -0.894689, -0.439186)-68.87456, -105.31569, 256.34393

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Components

#1: Protein
Serine/threonine-protein kinase PINK1, mitochondrial-like Protein / PINK1


Mass: 46489.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Ser is phosphorylated / Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC013202 / Production host: Escherichia coli (E. coli) / References: UniProt: D6WMX4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 100 mM HEPES pH 7.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.78→178.84 Å / Num. obs: 87762 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13
Reflection shellResolution: 2.78→2.83 Å / Rmerge(I) obs: 1.224

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.78→178.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.476 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 4195 4.8 %RANDOM
Rwork0.20466 ---
obs0.20661 83545 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.641 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.72 Å2
2---2 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.78→178.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16722 0 6 30 16758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01917118
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216304
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.97623364
X-RAY DIFFRACTIONr_angle_other_deg1.164337427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28652124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62824.348690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.645152700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2321572
X-RAY DIFFRACTIONr_chiral_restr0.1050.22712
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02119128
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023792
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_it6.5077.7268604
X-RAY DIFFRACTIONr_mcbond_other6.5037.7258603
X-RAY DIFFRACTIONr_mcangle_it9.78211.56510692
X-RAY DIFFRACTIONr_mcangle_other9.78211.56610693
X-RAY DIFFRACTIONr_scbond_it7.3538.2958514
X-RAY DIFFRACTIONr_scbond_other7.3528.2958515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.12212.26212673
X-RAY DIFFRACTIONr_long_range_B_refined14.48361.90918639
X-RAY DIFFRACTIONr_long_range_B_other14.48361.91218640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A273TIGHT POSITIONAL0.10.25
1A215TIGHT POSITIONAL0.090.25
1A665TIGHT POSITIONAL0.10.25
1A1833TIGHT POSITIONAL0.10.25
1A175TIGHT POSITIONAL0.080.25
1A273TIGHT POSITIONAL0.10.25
1A215TIGHT POSITIONAL0.080.25
1A665TIGHT POSITIONAL0.090.25
1A1833TIGHT POSITIONAL0.090.25
1A175TIGHT POSITIONAL0.070.25
1A215TIGHT THERMAL5.982.5
2A273TIGHT POSITIONAL0.090.25
2A215TIGHT POSITIONAL0.090.25
2A665TIGHT POSITIONAL0.140.25
2A1833TIGHT POSITIONAL0.110.25
2A175TIGHT POSITIONAL0.080.25
2A273TIGHT POSITIONAL0.10.25
2A220TIGHT POSITIONAL0.060.11
2A220TIGHT POSITIONAL0.040.11
2A220TIGHT POSITIONAL0.060.11
2A220TIGHT POSITIONAL0.070.11
2A665TIGHT THERMAL6.222.5
3A687TIGHT POSITIONAL0.080.11
3A687TIGHT POSITIONAL0.070.11
3A687TIGHT POSITIONAL0.070.11
3A687TIGHT POSITIONAL0.080.11
3A1854TIGHT POSITIONAL0.070.11
3A1854TIGHT POSITIONAL0.060.11
3A1854TIGHT POSITIONAL0.080.11
3A1854TIGHT POSITIONAL0.070.11
3A191TIGHT POSITIONAL0.050.11
3A191TIGHT POSITIONAL0.050.11
3A1833TIGHT THERMAL5.942.5
4A191TIGHT POSITIONAL0.040.11
4A191TIGHT POSITIONAL0.050.11
4A290TIGHT POSITIONAL0.050.11
4A290TIGHT POSITIONAL0.050.11
4A290TIGHT POSITIONAL0.050.11
4A290TIGHT POSITIONAL0.050.11
4A220TIGHT POSITIONAL0.070.11
4A220TIGHT POSITIONAL0.050.11
4A220TIGHT POSITIONAL0.040.11
4A687TIGHT POSITIONAL0.090.11
4A175TIGHT THERMAL7.372.5
5A687TIGHT POSITIONAL0.080.11
5A687TIGHT POSITIONAL0.050.11
5A1854TIGHT POSITIONAL0.070.11
5A1854TIGHT POSITIONAL0.070.11
5A1854TIGHT POSITIONAL0.050.11
5A191TIGHT POSITIONAL0.050.11
5A191TIGHT POSITIONAL0.050.11
5A191TIGHT POSITIONAL0.040.11
5A290TIGHT POSITIONAL0.050.11
5A290TIGHT POSITIONAL0.050.11
5A273TIGHT THERMAL7.372.5
6A290TIGHT POSITIONAL0.050.11
6A220TIGHT POSITIONAL0.060.11
6A220TIGHT POSITIONAL0.080.11
6A687TIGHT POSITIONAL0.060.11
6A687TIGHT POSITIONAL0.10.11
6A1854TIGHT POSITIONAL0.070.11
6A1854TIGHT POSITIONAL0.070.11
6A191TIGHT POSITIONAL0.060.11
6A191TIGHT POSITIONAL0.050.11
6A290TIGHT POSITIONAL0.050.11
6A215TIGHT THERMAL9.812.5
7A290TIGHT POSITIONAL0.050.11
7A220TIGHT POSITIONAL0.050.11
7A687TIGHT POSITIONAL0.080.11
7A1854TIGHT POSITIONAL0.070.11
7A191TIGHT POSITIONAL0.050.11
7A290TIGHT POSITIONAL0.050.11
7A665TIGHT THERMAL6.122.5
8A1833TIGHT THERMAL6.532.5
9A175TIGHT THERMAL5.252.5
10A273TIGHT THERMAL5.472.5
11A215TIGHT THERMAL6.732.5
12A665TIGHT THERMAL5.932.5
13A1833TIGHT THERMAL4.752.5
14A175TIGHT THERMAL6.992.5
15A273TIGHT THERMAL6.732.5
16A215TIGHT THERMAL5.662.5
17A665TIGHT THERMAL4.842.5
18A1833TIGHT THERMAL5.642.5
19A175TIGHT THERMAL6.032.5
20A273TIGHT THERMAL7.992.5
21A215TIGHT THERMAL7.582.5
22A665TIGHT THERMAL6.142.5
23A1833TIGHT THERMAL6.262.5
24A175TIGHT THERMAL5.772.5
25A273TIGHT THERMAL4.92.5
26B220TIGHT THERMAL8.991.12
27B220TIGHT THERMAL4.81.12
28B220TIGHT THERMAL6.651.12
29B220TIGHT THERMAL7.461.12
30B687TIGHT THERMAL6.591.12
31B687TIGHT THERMAL6.261.12
32B687TIGHT THERMAL5.491.12
33B687TIGHT THERMAL6.31.12
34B1854TIGHT THERMAL6.671.12
35B1854TIGHT THERMAL4.411.12
36B1854TIGHT THERMAL7.421.12
37B1854TIGHT THERMAL4.871.12
38B191TIGHT THERMAL5.941.12
39B191TIGHT THERMAL3.891.12
40B191TIGHT THERMAL8.961.12
41B191TIGHT THERMAL5.031.12
42B290TIGHT THERMAL7.361.12
43B290TIGHT THERMAL5.071.12
44B290TIGHT THERMAL11.271.12
45B290TIGHT THERMAL6.261.12
46C220TIGHT THERMAL8.911.12
47C220TIGHT THERMAL8.41.12
48C220TIGHT THERMAL5.631.12
49C687TIGHT THERMAL6.821.12
50C687TIGHT THERMAL5.481.12
51C687TIGHT THERMAL4.441.12
52C1854TIGHT THERMAL6.71.12
53C1854TIGHT THERMAL5.871.12
54C1854TIGHT THERMAL4.771.12
55C191TIGHT THERMAL6.161.12
56C191TIGHT THERMAL5.931.12
57C191TIGHT THERMAL4.761.12
58C290TIGHT THERMAL6.531.12
59C290TIGHT THERMAL7.31.12
60C290TIGHT THERMAL4.761.12
61D220TIGHT THERMAL6.341.12
62D220TIGHT THERMAL7.711.12
63D687TIGHT THERMAL6.331.12
64D687TIGHT THERMAL7.221.12
65D1854TIGHT THERMAL6.61.12
66D1854TIGHT THERMAL5.811.12
67D191TIGHT THERMAL8.561.12
68D191TIGHT THERMAL5.631.12
69D290TIGHT THERMAL10.161.12
70D290TIGHT THERMAL4.971.12
71E220TIGHT THERMAL6.411.12
72E687TIGHT THERMAL6.291.12
73E1854TIGHT THERMAL6.941.12
74E191TIGHT THERMAL7.661.12
75E290TIGHT THERMAL7.931.12
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 339 -
Rwork0.332 6080 -
obs--99.52 %

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