1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sakata, E.
Yamaguchi, Y.
Kurimoto, E.
Kikuchi, J.
Yokoyama, S.
Kawahara, H.
Yokosawa, H.
Hattori, N.
Mizuno, Y.
Tanaka, K.
Kato, K.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
S
C
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
N
N
181
S
C
N
182
N
C
N
183
N
O
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
N
N
211
N
O
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
N
N
228
S
C
N
229
N
C
N
230
N
O
N
231
N
C
N
232
N
C
N
233
N
S
N
234
N
C
N
235
N
O
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
Y
252
N
C
Y
253
N
C
Y
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
N
258
N
O
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
O
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
O
N
293
N
O
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
R
C
N
306
N
O
N
307
N
C
N
308
N
O
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
N
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
N
N
346
S
C
N
347
N
C
N
348
N
O
N
349
N
C
N
350
N
C
N
351
N
C
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
doub
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
doub
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
Y
246
N
doub
Y
247
N
sing
Y
248
N
sing
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
doub
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
Y
315
N
doub
Y
316
N
sing
Y
317
N
sing
N
318
N
sing
Y
319
N
doub
Y
320
N
sing
Y
321
N
sing
N
322
N
sing
Y
323
N
sing
Y
324
N
doub
N
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
UK
EMBO REP.
1469-221X
4
301
306
10.1038/sj.embor.embor764
12634850
Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
2003
10.2210/pdb1iyf/pdb
pdb_00001iyf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
9247.536
parkin
6.3.2.19
ubiquitin-like domain
1
man
polymer
no
no
GPLGSMIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWR
K
GPLGSMIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWR
K
A
my_001000012.1
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)Codonplus
PLASMID
pGEX6P3
RIKEN Structural Genomics/Proteomics Initiative
RSGI
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2003-03-25
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
5500 is chemical shift
Y
PDBJ
Y
PDBJ
2002-08-13
REL
The structure was determined using triple-resonance NMR spectroscopy.
structures with the lowest energy
50
10
3D_13C-separated_NOESY
3D_15N-separated_NOESY
2D_1H-coupled_1H-15N_HSQC
0.3
6.0
1
atm
303
K
0.3
6.0
1
atm
310
K
The structures are based on a total of 720 restraints, 489 are NOE-derived distance constraints, 82 dihedral angle restraints, 129 residual dipolar coupling constraints, 20 distance restraints for hydrogen bonds.
distance geometry, simulated annealing
1
lowest energy
0.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer
90% H2O/10% D2O
0.1mM parkin ubiquitin-like domain U-15N, 13C; 50mM potassium phosphate buffer
90% H2O, 10% D2O, 5%-DMPC/DHPC; 90% H2O, 10% D2O, 5%-DMPC/DHPC/CTAB
collection
XwinNMR
2.6
data analysis
XwinNMR
2.6
processing
XwinNMR
2.6
Brunger
structure solution
CNS
1.1
Brunger
refinement
CNS
1.1
800
Bruker
DRX
n
1
-4
A
n
2
-3
A
n
3
-2
A
n
4
-1
A
n
5
0
A
MET
1
n
6
MET
1
A
ILE
2
n
7
ILE
2
A
VAL
3
n
8
VAL
3
A
PHE
4
n
9
PHE
4
A
VAL
5
n
10
VAL
5
A
ARG
6
n
11
ARG
6
A
PHE
7
n
12
PHE
7
A
ASN
8
n
13
ASN
8
A
SER
9
n
14
SER
9
A
SER
10
n
15
SER
10
A
HIS
11
n
16
HIS
11
A
GLY
12
n
17
GLY
12
A
PHE
13
n
18
PHE
13
A
PRO
14
n
19
PRO
14
A
VAL
15
n
20
VAL
15
A
GLU
16
n
21
GLU
16
A
VAL
17
n
22
VAL
17
A
ASP
18
n
23
ASP
18
A
SER
19
n
24
SER
19
A
ASP
20
n
25
ASP
20
A
THR
21
n
26
THR
21
A
SER
22
n
27
SER
22
A
ILE
23
n
28
ILE
23
A
PHE
24
n
29
PHE
24
A
GLN
25
n
30
GLN
25
A
LEU
26
n
31
LEU
26
A
LYS
27
n
32
LYS
27
A
GLU
28
n
33
GLU
28
A
VAL
29
n
34
VAL
29
A
VAL
30
n
35
VAL
30
A
ALA
31
n
36
ALA
31
A
LYS
32
n
37
LYS
32
A
ARG
33
n
38
ARG
33
A
GLN
34
n
39
GLN
34
A
GLY
35
n
40
GLY
35
A
VAL
36
n
41
VAL
36
A
PRO
37
n
42
PRO
37
A
ALA
38
n
43
ALA
38
A
ASP
39
n
44
ASP
39
A
GLN
40
n
45
GLN
40
A
LEU
41
n
46
LEU
41
A
ARG
42
n
47
ARG
42
A
VAL
43
n
48
VAL
43
A
ILE
44
n
49
ILE
44
A
PHE
45
n
50
PHE
45
A
ALA
46
n
51
ALA
46
A
GLY
47
n
52
GLY
47
A
LYS
48
n
53
LYS
48
A
GLU
49
n
54
GLU
49
A
LEU
50
n
55
LEU
50
A
ARG
51
n
56
ARG
51
A
ASN
52
n
57
ASN
52
A
ASP
53
n
58
ASP
53
A
TRP
54
n
59
TRP
54
A
THR
55
n
60
THR
55
A
VAL
56
n
61
VAL
56
A
GLN
57
n
62
GLN
57
A
ASN
58
n
63
ASN
58
A
CYS
59
n
64
CYS
59
A
ASP
60
n
65
ASP
60
A
LEU
61
n
66
LEU
61
A
ASP
62
n
67
ASP
62
A
GLN
63
n
68
GLN
63
A
GLN
64
n
69
GLN
64
A
SER
65
n
70
SER
65
A
ILE
66
n
71
ILE
66
A
VAL
67
n
72
VAL
67
A
HIS
68
n
73
HIS
68
A
ILE
69
n
74
ILE
69
A
VAL
70
n
75
VAL
70
A
GLN
71
n
76
GLN
71
A
ARG
72
n
77
ARG
72
A
PRO
73
n
78
PRO
73
A
TRP
74
n
79
TRP
74
A
ARG
75
n
80
ARG
75
A
LYS
76
n
81
LYS
76
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
PHE
13
A
O
PHE
18
A
N
VAL
5
A
N
VAL
10
A
N
ARG
6
A
N
ARG
11
A
O
ILE
69
A
O
ILE
74
A
O
VAL
70
A
O
VAL
75
A
N
ARG
42
A
N
ARG
47
A
N
PHE
45
A
N
PHE
50
A
O
LYS
48
A
O
LYS
53
1
A
GLY
-4
A
GLY
1
1
Y
1
A
PRO
-3
A
PRO
2
1
Y
1
A
LEU
-2
A
LEU
3
1
Y
1
A
GLY
-1
A
GLY
4
1
Y
1
A
SER
0
A
SER
5
1
Y
2
A
GLY
-4
A
GLY
1
1
Y
2
A
PRO
-3
A
PRO
2
1
Y
2
A
LEU
-2
A
LEU
3
1
Y
2
A
GLY
-1
A
GLY
4
1
Y
2
A
SER
0
A
SER
5
1
Y
3
A
GLY
-4
A
GLY
1
1
Y
3
A
PRO
-3
A
PRO
2
1
Y
3
A
LEU
-2
A
LEU
3
1
Y
3
A
GLY
-1
A
GLY
4
1
Y
3
A
SER
0
A
SER
5
1
Y
4
A
GLY
-4
A
GLY
1
1
Y
4
A
PRO
-3
A
PRO
2
1
Y
4
A
LEU
-2
A
LEU
3
1
Y
4
A
GLY
-1
A
GLY
4
1
Y
4
A
SER
0
A
SER
5
1
Y
5
A
GLY
-4
A
GLY
1
1
Y
5
A
PRO
-3
A
PRO
2
1
Y
5
A
LEU
-2
A
LEU
3
1
Y
5
A
GLY
-1
A
GLY
4
1
Y
5
A
SER
0
A
SER
5
1
Y
6
A
GLY
-4
A
GLY
1
1
Y
6
A
PRO
-3
A
PRO
2
1
Y
6
A
LEU
-2
A
LEU
3
1
Y
6
A
GLY
-1
A
GLY
4
1
Y
6
A
SER
0
A
SER
5
1
Y
7
A
GLY
-4
A
GLY
1
1
Y
7
A
PRO
-3
A
PRO
2
1
Y
7
A
LEU
-2
A
LEU
3
1
Y
7
A
GLY
-1
A
GLY
4
1
Y
7
A
SER
0
A
SER
5
1
Y
8
A
GLY
-4
A
GLY
1
1
Y
8
A
PRO
-3
A
PRO
2
1
Y
8
A
LEU
-2
A
LEU
3
1
Y
8
A
GLY
-1
A
GLY
4
1
Y
8
A
SER
0
A
SER
5
1
Y
9
A
GLY
-4
A
GLY
1
1
Y
9
A
PRO
-3
A
PRO
2
1
Y
9
A
LEU
-2
A
LEU
3
1
Y
9
A
GLY
-1
A
GLY
4
1
Y
9
A
SER
0
A
SER
5
1
Y
10
A
GLY
-4
A
GLY
1
1
Y
10
A
PRO
-3
A
PRO
2
1
Y
10
A
LEU
-2
A
LEU
3
1
Y
10
A
GLY
-1
A
GLY
4
1
Y
10
A
SER
0
A
SER
5
1
Y
1
A
A
O
H
PHE
SER
7
9
1.55
1
A
A
O
O
ILE
HIS
44
68
2.10
2
A
A
O
H
PHE
SER
7
9
1.56
2
A
A
O
O
ILE
HIS
44
68
2.10
3
A
A
O
H
PHE
LYS
45
48
1.56
3
A
A
O
H
PHE
SER
7
9
1.57
3
A
A
O
O
ILE
HIS
44
68
2.11
4
A
A
O
H
PHE
SER
7
9
1.55
4
A
A
O
H
PHE
LYS
45
48
1.57
4
A
A
O
O
ILE
HIS
44
68
2.10
5
A
A
O
H
PHE
LYS
45
48
1.49
5
A
A
O
H
LEU
ARG
41
72
1.56
5
A
A
O
H
PHE
SER
7
9
1.56
5
A
A
O
O
ILE
HIS
44
68
2.11
6
A
A
O
O
ILE
HIS
44
68
2.10
7
A
A
H
HB
ARG
THR
51
55
1.31
7
A
A
O
H
PHE
SER
7
9
1.54
7
A
A
O
O
ILE
HIS
44
68
2.04
8
A
A
O
H
PHE
LYS
45
48
1.59
8
A
A
O
O
ILE
HIS
44
68
2.10
9
A
A
O
H
ARG
THR
51
55
1.55
9
A
A
O
O
ILE
HIS
44
68
2.14
10
A
A
O
O
ILE
HIS
44
68
2.12
10
A
A
O
N
ASN
SER
8
10
2.18
1
A
ASN
8
-63.01
69.22
1
A
HIS
11
-160.52
115.51
1
A
VAL
17
177.10
154.60
1
A
THR
21
-37.18
154.39
1
A
SER
22
-18.26
142.73
1
A
ILE
23
-39.70
-39.43
1
A
VAL
30
-58.46
-71.78
1
A
PRO
37
-65.17
-152.24
1
A
ALA
38
-106.54
-70.44
1
A
LEU
41
-82.67
-143.33
1
A
ALA
46
23.62
36.28
1
A
LEU
50
-9.77
87.81
1
A
VAL
56
-70.66
-133.45
1
A
CYS
59
-81.36
-78.66
1
A
ASP
60
-168.73
76.02
2
A
ASN
8
-63.73
68.90
2
A
VAL
17
178.88
152.40
2
A
THR
21
-33.51
150.58
2
A
SER
22
-17.30
142.99
2
A
ILE
23
-39.69
-39.99
2
A
VAL
30
-58.78
-73.41
2
A
PRO
37
-66.30
-148.87
2
A
ALA
38
-105.31
-68.02
2
A
GLN
40
-53.20
-76.31
2
A
LEU
41
-84.74
-138.36
2
A
ALA
46
26.03
34.90
2
A
LEU
50
-14.52
89.51
2
A
VAL
56
-82.29
-133.53
2
A
CYS
59
-96.71
-76.99
2
A
ASP
60
-169.94
76.65
3
A
ASN
8
-63.91
69.39
3
A
VAL
17
175.41
157.59
3
A
THR
21
-35.19
153.69
3
A
SER
22
-16.62
144.27
3
A
VAL
30
-61.88
-73.53
3
A
PRO
37
-67.04
-147.57
3
A
ALA
38
-105.96
-69.82
3
A
GLN
40
-49.02
-77.32
3
A
LEU
41
-81.94
-124.71
3
A
ALA
46
26.87
37.86
3
A
LEU
50
-25.05
107.64
3
A
VAL
56
-82.26
-135.01
3
A
CYS
59
-106.22
-79.10
3
A
ASP
60
-165.39
76.46
4
A
ASN
8
-64.13
68.53
4
A
VAL
17
178.99
154.71
4
A
THR
21
-34.35
152.42
4
A
SER
22
-18.87
143.14
4
A
VAL
30
-59.05
-74.01
4
A
PRO
37
-68.20
-145.19
4
A
ALA
38
-104.58
-65.68
4
A
GLN
40
-43.95
-85.26
4
A
LEU
41
-94.19
-113.89
4
A
ALA
46
25.21
38.02
4
A
LEU
50
-10.89
87.94
4
A
VAL
56
-78.63
-134.36
4
A
CYS
59
-96.09
-78.17
4
A
ASP
60
-169.27
76.67
5
A
ASN
8
-59.28
71.45
5
A
VAL
17
178.86
152.73
5
A
THR
21
-35.34
154.32
5
A
SER
22
-18.12
142.79
5
A
VAL
30
-57.12
-75.01
5
A
PRO
37
-70.03
-148.35
5
A
GLN
40
-56.27
92.59
5
A
LEU
41
-69.90
-161.16
5
A
ARG
42
70.58
44.74
5
A
ALA
46
27.41
35.79
5
A
LEU
50
-14.14
88.24
5
A
VAL
56
-82.89
-136.88
5
A
CYS
59
-104.08
-78.33
5
A
ASP
60
-167.04
77.60
6
A
ASN
8
-66.38
71.53
6
A
SER
9
-163.93
-160.77
6
A
SER
10
-49.41
177.09
6
A
THR
21
-32.79
153.96
6
A
SER
22
-20.69
143.95
6
A
VAL
30
-67.03
-74.01
6
A
PRO
37
-66.62
-142.36
6
A
ALA
38
-104.68
-73.07
6
A
LEU
41
-83.20
-138.74
6
A
ALA
46
24.25
35.84
6
A
LEU
50
-21.46
97.09
6
A
VAL
56
-83.81
-137.35
6
A
CYS
59
-101.45
-77.47
6
A
ASP
60
-165.68
78.53
6
A
VAL
70
-104.09
74.31
7
A
ASN
8
-58.43
70.44
7
A
VAL
17
-167.37
-169.33
7
A
THR
21
-40.19
175.92
7
A
SER
22
-40.18
154.93
7
A
GLN
25
-58.82
-71.30
7
A
VAL
30
-62.09
-74.57
7
A
PRO
37
-65.48
-140.42
7
A
ALA
38
-110.80
-74.89
7
A
LEU
41
-91.83
-136.25
7
A
ALA
46
77.21
31.85
7
A
LEU
50
-14.64
82.16
7
A
VAL
56
-51.65
-129.49
7
A
CYS
59
-63.73
-72.15
7
A
ASP
60
-166.40
74.94
7
A
GLN
71
-118.57
60.51
8
A
ASN
8
-64.46
72.72
8
A
SER
9
-163.76
-161.15
8
A
SER
10
-49.38
175.59
8
A
VAL
17
179.61
156.03
8
A
THR
21
-33.17
154.75
8
A
SER
22
-20.63
143.67
8
A
VAL
30
-55.42
-72.48
8
A
PRO
37
-66.72
-149.79
8
A
ALA
38
-105.83
-69.90
8
A
GLN
40
-52.26
-73.01
8
A
LEU
41
-82.13
-135.03
8
A
ALA
46
22.53
37.91
8
A
LEU
50
-22.70
97.46
8
A
VAL
56
-81.81
-133.47
8
A
CYS
59
-95.90
-78.03
8
A
ASP
60
-168.41
76.01
9
A
ASN
8
-66.76
71.92
9
A
SER
9
-163.91
-159.43
9
A
SER
10
-48.95
175.80
9
A
VAL
17
-167.84
-166.43
9
A
THR
21
-36.14
169.45
9
A
SER
22
-33.88
148.20
9
A
VAL
30
-57.67
-75.75
9
A
PRO
37
-63.51
-147.30
9
A
ALA
38
-108.79
-77.78
9
A
GLN
40
-46.43
-71.10
9
A
LEU
41
-90.12
-138.60
9
A
ALA
46
40.61
28.69
9
A
VAL
56
-79.88
-140.55
9
A
CYS
59
-84.72
-73.67
9
A
ASP
60
-170.66
84.14
10
A
ASN
8
-42.76
178.09
10
A
SER
9
-49.17
79.86
10
A
VAL
17
176.39
156.35
10
A
THR
21
-34.09
151.27
10
A
SER
22
-17.96
143.92
10
A
VAL
30
-62.53
-74.09
10
A
PRO
37
-66.93
-144.20
10
A
ALA
38
-107.09
-68.05
10
A
GLN
40
-48.53
-81.96
10
A
LEU
41
-87.33
-126.18
10
A
ALA
46
26.62
37.89
10
A
LEU
50
-21.66
103.14
10
A
VAL
56
-80.75
-132.82
10
A
CYS
59
-97.21
-78.24
10
A
ASP
60
-168.68
76.39
10
A
GLN
71
-117.39
70.69
Solution structure of ubiquitin-like domain of human parkin
1
N
N
A
SER
22
A
SER
27
HELX_P
A
GLN
34
A
GLN
39
1
1
13
A
VAL
56
A
VAL
61
HELX_P
A
LEU
61
A
LEU
66
1
2
6
LIGASE
Ubiquitin fold, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, LIGASE
PRKN2_HUMAN
UNP
1
1
O60260
MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRK
1
76
1IYF
1
76
O60260
A
1
6
81
1
cloning artifact
GLY
-4
1IYF
A
O60260
UNP
1
1
cloning artifact
PRO
-3
1IYF
A
O60260
UNP
2
1
cloning artifact
LEU
-2
1IYF
A
O60260
UNP
3
1
cloning artifact
GLY
-1
1IYF
A
O60260
UNP
4
1
cloning artifact
SER
0
1IYF
A
O60260
UNP
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
A
HIS
11
A
HIS
16
A
VAL
15
A
VAL
20
A
ILE
2
A
ILE
7
A
PHE
7
A
PHE
12
A
GLN
64
A
GLN
69
A
VAL
70
A
VAL
75
A
ARG
42
A
ARG
47
A
PHE
45
A
PHE
50
A
LYS
48
A
LYS
53
A
GLU
49
A
GLU
54
1
P 1