0.018136
0.000000
0.000000
-0.000000
0.018136
0.000000
0.000000
-0.000000
0.009478
0.00000
0.00000
0.00000
Kristariyanto, Y.A.
Abdul Rehman, S.A.
Kulathu, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
55.140
55.140
105.510
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
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
H2 O
18.015
WATER
non-polymer
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
C9 H11 N O3
181.189
y
TYROSINE
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
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
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
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
O
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
R
C
N
295
N
O
N
296
N
C
N
297
N
O
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
N
318
N
O
N
319
N
O
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
N
336
N
C
N
337
N
C
N
338
N
O
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
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
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
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
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
sing
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
doub
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
sing
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
doub
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
sing
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
doub
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
sing
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
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
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
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
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
sing
N
282
N
sing
N
283
N
doub
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
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
N
309
N
sing
Y
310
N
doub
N
311
N
sing
Y
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
doub
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
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
UK
EMBO Rep.
1469-3178
18
392
402
10.15252/embr.201643205
28082312
A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains.
2017
10.2210/pdb5mn9/pdb
pdb_00005mn9
100
1
PIXEL
2015-05-01
DECTRIS PILATUS3 2M
single crystal
SINGLE WAVELENGTH
M
x-ray
1
0.96769
1.0
MASSIF-1
ESRF
0.96769
SYNCHROTRON
ESRF BEAMLINE MASSIF-1
8576.831
Ubiquitin-40S ribosomal protein S27a
2
nat
polymer
4939.382
Ubiquitin carboxyl-terminal hydrolase MINDY-1
3.4.19.12
1
man
polymer
18.015
water
3
nat
water
Ubiquitin carboxyl extension protein 80
Deubiquitinating enzyme MINDY-1,Protein FAM63A
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A,B
polypeptide(L)
no
no
GPLGSQVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ
GPLGSQVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ
C
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
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
sample
1
44
FAM63A, KIAA1390
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
Biological sequence
Bovine
sample
1
76
9913
Bos taurus
1
1.82
32.23
VAPOR DIFFUSION, HANGING DROP
5.4
100 mM sodium acetate pH 5.4 and 18.5 % PEG3350
293.15
diffrn_source
pdbx_audit_support
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ncs_dom_lim
repository
Initial release
Database references
Data collection
Author supporting evidence
Data collection
Database references
Refinement description
1
0
2017-01-25
1
1
2017-03-15
1
2
2017-07-05
1
3
2017-08-30
1
4
2024-01-17
_diffrn_source.pdbx_synchrotron_beamline
_diffrn_source.type
_pdbx_audit_support.funding_organization
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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
United Kingdom
Medical Research Council (United Kingdom)
MC_UU_12016/6
N
PDBE
Y
PDBE
2016-12-13
REL
REL
HOH
water
1UBQ
PDB
experimental model
HOH
2
3
HOH
HOH
101
B
HOH
3
3
HOH
HOH
102
B
HOH
1
3
HOH
HOH
501
C
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
GLU
16
n
16
GLU
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
PRO
19
n
19
PRO
19
A
SER
20
n
20
SER
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
ILE
23
n
23
ILE
23
A
GLU
24
n
24
GLU
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
GLN
31
n
31
GLN
31
A
ASP
32
n
32
ASP
32
A
LYS
33
n
33
LYS
33
A
GLU
34
n
34
GLU
34
A
GLY
35
n
35
GLY
35
A
ILE
36
n
36
ILE
36
A
PRO
37
n
37
PRO
37
A
PRO
38
n
38
PRO
38
A
ASP
39
n
39
ASP
39
A
GLN
40
n
40
GLN
40
A
GLN
41
n
41
GLN
41
A
ARG
42
n
42
ARG
42
A
LEU
43
n
43
LEU
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
LYS
48
n
48
LYS
48
A
GLN
49
n
49
GLN
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
GLY
53
n
53
GLY
53
A
ARG
54
n
54
ARG
54
A
THR
55
n
55
THR
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
ASP
58
n
58
ASP
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
ILE
61
n
61
ILE
61
A
GLN
62
n
62
GLN
62
A
LYS
63
n
63
LYS
63
A
GLU
64
n
64
GLU
64
A
SER
65
n
65
SER
65
A
THR
66
n
66
THR
66
A
LEU
67
n
67
LEU
67
A
HIS
68
n
68
HIS
68
A
LEU
69
n
69
LEU
69
A
VAL
70
n
70
VAL
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
LEU
73
n
73
LEU
73
A
n
74
74
A
n
75
75
A
n
76
76
A
MET
1
n
1
MET
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
PHE
4
n
4
PHE
4
B
VAL
5
n
5
VAL
5
B
LYS
6
n
6
LYS
6
B
THR
7
n
7
THR
7
B
LEU
8
n
8
LEU
8
B
THR
9
n
9
THR
9
B
GLY
10
n
10
GLY
10
B
LYS
11
n
11
LYS
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
THR
14
n
14
THR
14
B
LEU
15
n
15
LEU
15
B
GLU
16
n
16
GLU
16
B
VAL
17
n
17
VAL
17
B
GLU
18
n
18
GLU
18
B
PRO
19
n
19
PRO
19
B
SER
20
n
20
SER
20
B
ASP
21
n
21
ASP
21
B
THR
22
n
22
THR
22
B
ILE
23
n
23
ILE
23
B
GLU
24
n
24
GLU
24
B
ASN
25
n
25
ASN
25
B
VAL
26
n
26
VAL
26
B
LYS
27
n
27
LYS
27
B
ALA
28
n
28
ALA
28
B
LYS
29
n
29
LYS
29
B
ILE
30
n
30
ILE
30
B
GLN
31
n
31
GLN
31
B
ASP
32
n
32
ASP
32
B
LYS
33
n
33
LYS
33
B
GLU
34
n
34
GLU
34
B
GLY
35
n
35
GLY
35
B
ILE
36
n
36
ILE
36
B
PRO
37
n
37
PRO
37
B
PRO
38
n
38
PRO
38
B
ASP
39
n
39
ASP
39
B
GLN
40
n
40
GLN
40
B
GLN
41
n
41
GLN
41
B
ARG
42
n
42
ARG
42
B
LEU
43
n
43
LEU
43
B
ILE
44
n
44
ILE
44
B
PHE
45
n
45
PHE
45
B
ALA
46
n
46
ALA
46
B
GLY
47
n
47
GLY
47
B
LYS
48
n
48
LYS
48
B
GLN
49
n
49
GLN
49
B
LEU
50
n
50
LEU
50
B
GLU
51
n
51
GLU
51
B
ASP
52
n
52
ASP
52
B
GLY
53
n
53
GLY
53
B
ARG
54
n
54
ARG
54
B
THR
55
n
55
THR
55
B
LEU
56
n
56
LEU
56
B
SER
57
n
57
SER
57
B
ASP
58
n
58
ASP
58
B
TYR
59
n
59
TYR
59
B
ASN
60
n
60
ASN
60
B
ILE
61
n
61
ILE
61
B
GLN
62
n
62
GLN
62
B
LYS
63
n
63
LYS
63
B
GLU
64
n
64
GLU
64
B
SER
65
n
65
SER
65
B
THR
66
n
66
THR
66
B
LEU
67
n
67
LEU
67
B
HIS
68
n
68
HIS
68
B
LEU
69
n
69
LEU
69
B
VAL
70
n
70
VAL
70
B
LEU
71
n
71
LEU
71
B
ARG
72
n
72
ARG
72
B
LEU
73
n
73
LEU
73
B
ARG
74
n
74
ARG
74
B
GLY
75
n
75
GLY
75
B
GLY
76
n
76
GLY
76
B
n
1
383
C
n
2
384
C
n
3
385
C
n
4
386
C
n
5
387
C
n
6
388
C
n
7
389
C
n
8
390
C
n
9
391
C
n
10
392
C
n
11
393
C
n
12
394
C
n
13
395
C
n
14
396
C
n
15
397
C
n
16
398
C
n
17
399
C
n
18
400
C
n
19
401
C
n
20
402
C
n
21
403
C
n
22
404
C
n
23
405
C
n
24
406
C
n
25
407
C
LEU
408
n
26
LEU
408
C
GLY
409
n
27
GLY
409
C
LEU
410
n
28
LEU
410
C
THR
411
n
29
THR
411
C
ASP
412
n
30
ASP
412
C
LEU
413
n
31
LEU
413
C
GLU
414
n
32
GLU
414
C
LEU
415
n
33
LEU
415
C
ALA
416
n
34
ALA
416
C
GLN
417
n
35
GLN
417
C
GLN
418
n
36
GLN
418
C
LEU
419
n
37
LEU
419
C
GLN
420
n
38
GLN
420
C
GLN
421
n
39
GLN
421
C
GLU
422
n
40
GLU
422
C
GLU
423
n
41
GLU
423
C
TYR
424
n
42
TYR
424
C
GLN
425
n
43
GLN
425
C
GLN
426
n
44
GLN
426
C
4.3672
0.3910
0.3667
9.1965
0.7937
3.9392
-0.0981
-0.2760
0.0822
0.0898
0.1216
1.0675
0.1268
-0.3963
-0.0235
0.0106
-0.0017
-0.0054
0.1068
-0.0049
0.1731
refined
14.1410
91.3920
3.0630
X-RAY DIFFRACTION
6.6267
-0.1177
-1.5525
7.7721
-3.1544
6.0599
-0.2436
-0.0716
0.0742
0.0398
0.6059
1.1527
-0.0871
-0.6003
-0.3622
0.0184
0.0389
0.0235
0.1723
0.1804
0.2877
refined
13.6370
118.8300
10.0330
X-RAY DIFFRACTION
5.2680
-3.3551
2.1336
12.7384
-6.4958
7.0560
-0.1961
0.1189
0.1128
-0.0413
0.1210
-0.2621
-0.0023
0.1250
0.0751
0.0345
-0.0136
-0.0055
0.0910
-0.0618
0.0538
refined
24.6760
101.7680
5.9740
X-RAY DIFFRACTION
A
1
A
73
X-RAY DIFFRACTION
1
B
1
B
76
X-RAY DIFFRACTION
2
C
408
C
426
X-RAY DIFFRACTION
3
author_and_software_defined_assembly
PISA
3
trimeric
1870
-11
9280
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
ILE
13
A
O
ILE
13
A
N
VAL
5
A
N
VAL
5
A
N
PHE
4
A
N
PHE
4
A
O
LEU
67
A
O
LEU
67
A
O
VAL
70
A
O
VAL
70
A
N
ARG
42
A
N
ARG
42
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
B
O
ILE
13
B
O
ILE
13
B
N
VAL
5
B
N
VAL
5
B
N
PHE
4
B
N
PHE
4
B
O
LEU
67
B
O
LEU
67
B
O
VAL
70
B
O
VAL
70
B
N
ARG
42
B
N
ARG
42
B
N
PHE
45
B
N
PHE
45
B
O
LYS
48
B
O
LYS
48
1
B
CG
GLU
18
B
CG
GLU
18
1
Y
1
B
CD
GLU
18
B
CD
GLU
18
1
Y
1
B
OE1
GLU
18
B
OE1
GLU
18
1
Y
1
B
OE2
GLU
18
B
OE2
GLU
18
1
Y
1
B
CG
GLU
24
B
CG
GLU
24
1
Y
1
B
CD
GLU
24
B
CD
GLU
24
1
Y
1
B
OE1
GLU
24
B
OE1
GLU
24
1
Y
1
B
OE2
GLU
24
B
OE2
GLU
24
1
Y
1
A
ARG
74
A
ARG
74
1
Y
1
A
GLY
75
A
GLY
75
1
Y
1
A
GLY
76
A
GLY
76
1
Y
1
C
GLY
383
C
GLY
1
1
Y
1
C
PRO
384
C
PRO
2
1
Y
1
C
LEU
385
C
LEU
3
1
Y
1
C
GLY
386
C
GLY
4
1
Y
1
C
SER
387
C
SER
5
1
Y
1
C
GLN
388
C
GLN
6
1
Y
1
C
VAL
389
C
VAL
7
1
Y
1
C
ASP
390
C
ASP
8
1
Y
1
C
GLN
391
C
GLN
9
1
Y
1
C
ASP
392
C
ASP
10
1
Y
1
C
TYR
393
C
TYR
11
1
Y
1
C
LEU
394
C
LEU
12
1
Y
1
C
ILE
395
C
ILE
13
1
Y
1
C
ALA
396
C
ALA
14
1
Y
1
C
LEU
397
C
LEU
15
1
Y
1
C
SER
398
C
SER
16
1
Y
1
C
LEU
399
C
LEU
17
1
Y
1
C
GLN
400
C
GLN
18
1
Y
1
C
GLN
401
C
GLN
19
1
Y
1
C
GLN
402
C
GLN
20
1
Y
1
C
GLN
403
C
GLN
21
1
Y
1
C
PRO
404
C
PRO
22
1
Y
1
C
ARG
405
C
ARG
23
1
Y
1
C
GLY
406
C
GLY
24
1
Y
1
C
PRO
407
C
PRO
25
1
Y
58.638
0.34
-0.00
-0.00
0.34
-0.00
-0.69
0.971
0.958
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22341
0.18268
0.18484
2.05
48.87
517
9368
5.2
99.97
13.654
0.162
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.221
0.177
0.70
0.70
1.20
1UBQ
2.05
48.87
3
1335
0
0
1332
0.010
0.019
1352
0.002
0.020
1368
1.441
1.997
1819
0.904
3.000
3160
6.100
5.000
165
38.290
26.406
64
14.185
15.000
276
13.893
15.000
7
0.081
0.200
217
0.005
0.020
1496
0.001
0.020
271
3.035
3.426
669
3.014
3.425
668
3.804
5.120
831
3.808
5.123
832
3.950
3.919
681
3.947
3.925
682
6.165
5.709
989
7.303
39.656
1354
7.313
39.683
1355
1
A
1
4160
X-RAY DIFFRACTION
interatomic distance
0.11
0.05
2
B
1
4160
X-RAY DIFFRACTION
interatomic distance
0.11
0.05
0.303
0.255
2.103
39
674
20
100.00
2.05
48.87
5MN9
9899
0.999
0.043
1
19.4
6.6
100
0.544
2.05
2.11
2.9
0.818
1
6.6
100
data reduction
XDS
phasing
PHASER
refinement
REFMAC
5.8.0155
data scaling
XDS
N
Crystal structure of MINDY-1 tMIU in complex with K48-diUb
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
THR
22
A
THR
22
HELX_P
A
GLY
35
A
GLY
35
1
AA1
14
A
PRO
37
A
PRO
37
HELX_P
A
ASP
39
A
ASP
39
5
AA2
3
A
LEU
56
A
LEU
56
HELX_P
A
ASN
60
A
ASN
60
5
AA3
5
B
THR
22
B
THR
22
HELX_P
B
GLY
35
B
GLY
35
1
AA4
14
B
PRO
37
B
PRO
37
HELX_P
B
ASP
39
B
ASP
39
5
AA5
3
B
LEU
56
B
LEU
56
HELX_P
B
ASN
60
B
ASN
60
5
AA6
5
C
LEU
410
C
LEU
28
HELX_P
C
GLN
426
C
GLN
44
1
AA7
17
HYDROLASE
MOTIF INTERACTING WITH UBIQUITIN, UBIQUITIN BINDING DOMAIN, HYDROLASE AND CYSTEINE PROTEASE, HYDROLASE
A
B
A
MET
1
A
MET
1
A
ARG
72
A
ARG
72
0
B
MET
1
B
MET
1
B
ARG
72
B
ARG
72
0
RS27A_BOVIN
UNP
1
1
P62992
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
FA63A_HUMAN
UNP
2
388
Q8N5J2
QVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ
1
76
5MN9
1
76
P62992
A
1
1
76
1
76
5MN9
1
76
P62992
B
1
1
76
388
426
5MN9
388
426
Q8N5J2
C
2
6
44
3
expression tag
GLY
383
5MN9
C
Q8N5J2
UNP
1
3
expression tag
PRO
384
5MN9
C
Q8N5J2
UNP
2
3
expression tag
LEU
385
5MN9
C
Q8N5J2
UNP
3
3
expression tag
GLY
386
5MN9
C
Q8N5J2
UNP
4
3
expression tag
SER
387
5MN9
C
Q8N5J2
UNP
5
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
THR
7
A
THR
7
A
THR
66
A
THR
66
A
LEU
71
A
LEU
71
A
GLN
41
A
GLN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49
B
THR
12
B
THR
12
B
GLU
16
B
GLU
16
B
GLN
2
B
GLN
2
B
THR
7
B
THR
7
B
THR
66
B
THR
66
B
LEU
71
B
LEU
71
B
GLN
41
B
GLN
41
B
PHE
45
B
PHE
45
B
LYS
48
B
LYS
48
B
GLN
49
B
GLN
49
80
I 41