0.031650
0.000000
0.008910
0.000000
0.012335
0.000000
0.000000
0.000000
0.020256
0.00000
0.00000
0.00000
Kalayil, S.
Bhogaraju, S.
Dikic, I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
105.72
90.00
31.596
81.073
51.287
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
C5 H10 O5
150.130
alpha-D-ribofuranose
alpha-D-ribose; D-ribose; ribose
D-saccharide, alpha linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
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
O
N
277
N
C
N
278
R
C
N
279
N
O
N
280
S
C
N
281
N
O
N
282
R
C
N
283
N
O
N
284
S
C
N
285
N
O
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
O
N
302
N
O
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
S
N
311
N
O
N
312
N
O
N
313
N
O
N
314
N
O
N
315
N
N
N
316
S
C
N
317
N
C
N
318
N
O
N
319
R
C
N
320
N
O
N
321
N
C
N
322
N
O
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
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
N
343
N
O
N
344
N
O
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
N
C
N
361
N
C
N
362
N
C
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
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
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
sing
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
doub
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
doub
N
298
N
doub
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
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
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
Y
328
N
doub
Y
329
N
sing
Y
330
N
sing
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
336
N
sing
N
337
N
sing
N
338
N
sing
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
doub
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
Cell
1097-4172
167
1636
1649.e13
10.1016/j.cell.2016.11.019
27912065
Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination.
2016
10.2210/pdb5m93/pdb
pdb_00005m93
100
1
PIXEL
2016-05-27
DECTRIS PILATUS 2M
SINGLE WAVELENGTH
M
x-ray
1
1.00004
1.0
X06DA
SLS
1.00004
SYNCHROTRON
SLS BEAMLINE X06DA
8857.088
Polyubiquitin-B
M1S
3
man
polymer
96.063
SULFATE ION
2
syn
non-polymer
150.130
alpha-D-ribofuranose
2
man
non-polymer
18.015
water
112
nat
water
no
no
GPLGSQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
GPLGSQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A,B,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
Human
sample
1
80
UBB
9606
Homo sapiens
562
Escherichia coli
PGEX-6P1
Biological sequence
1
2.47
50.2
VAPOR DIFFUSION, SITTING DROP
0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
4-5.5
291
atom_site
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2016-12-14
2
0
2020-07-29
2
1
2024-01-17
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.ptnr2_label_atom_id
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Germany
LOEWE program Ubiquitin Networks (Ub-Net
SPP 1580
DRibfa
a-D-ribofuranose
a-D-Ribf
Rib
N
PDBE
Y
PDBE
2016-10-31
REL
REL
SO4
SULFATE ION
RIB
alpha-D-ribofuranose
HOH
water
1UBQ
PDB
experimental model
SO4
1
2
SO4
SO4
101
A
RIB
3
3
RIB
RIB
101
B
SO4
2
2
SO4
SO4
102
B
RIB
2
3
RIB
RIB
101
C
HOH
101
4
HOH
HOH
201
A
HOH
57
4
HOH
HOH
202
A
HOH
38
4
HOH
HOH
203
A
HOH
5
4
HOH
HOH
204
A
HOH
7
4
HOH
HOH
205
A
HOH
13
4
HOH
HOH
206
A
HOH
46
4
HOH
HOH
207
A
HOH
14
4
HOH
HOH
208
A
HOH
50
4
HOH
HOH
209
A
HOH
3
4
HOH
HOH
210
A
HOH
102
4
HOH
HOH
211
A
HOH
39
4
HOH
HOH
212
A
HOH
43
4
HOH
HOH
213
A
HOH
103
4
HOH
HOH
214
A
HOH
12
4
HOH
HOH
215
A
HOH
4
4
HOH
HOH
216
A
HOH
9
4
HOH
HOH
217
A
HOH
2
4
HOH
HOH
218
A
HOH
44
4
HOH
HOH
219
A
HOH
6
4
HOH
HOH
220
A
HOH
8
4
HOH
HOH
221
A
HOH
45
4
HOH
HOH
222
A
HOH
17
4
HOH
HOH
223
A
HOH
56
4
HOH
HOH
224
A
HOH
1
4
HOH
HOH
225
A
HOH
40
4
HOH
HOH
226
A
HOH
16
4
HOH
HOH
227
A
HOH
33
4
HOH
HOH
228
A
HOH
42
4
HOH
HOH
229
A
HOH
32
4
HOH
HOH
230
A
HOH
53
4
HOH
HOH
231
A
HOH
37
4
HOH
HOH
232
A
HOH
54
4
HOH
HOH
233
A
HOH
49
4
HOH
HOH
234
A
HOH
94
4
HOH
HOH
235
A
HOH
41
4
HOH
HOH
236
A
HOH
105
4
HOH
HOH
237
A
HOH
118
4
HOH
HOH
238
A
HOH
63
4
HOH
HOH
239
A
HOH
58
4
HOH
HOH
240
A
HOH
48
4
HOH
HOH
241
A
HOH
91
4
HOH
HOH
201
B
HOH
75
4
HOH
HOH
202
B
HOH
81
4
HOH
HOH
203
B
HOH
11
4
HOH
HOH
204
B
HOH
20
4
HOH
HOH
205
B
HOH
79
4
HOH
HOH
206
B
HOH
21
4
HOH
HOH
207
B
HOH
114
4
HOH
HOH
208
B
HOH
19
4
HOH
HOH
209
B
HOH
77
4
HOH
HOH
210
B
HOH
18
4
HOH
HOH
211
B
HOH
68
4
HOH
HOH
212
B
HOH
110
4
HOH
HOH
213
B
HOH
66
4
HOH
HOH
214
B
HOH
22
4
HOH
HOH
215
B
HOH
112
4
HOH
HOH
216
B
HOH
78
4
HOH
HOH
217
B
HOH
67
4
HOH
HOH
218
B
HOH
74
4
HOH
HOH
219
B
HOH
69
4
HOH
HOH
220
B
HOH
80
4
HOH
HOH
221
B
HOH
108
4
HOH
HOH
222
B
HOH
107
4
HOH
HOH
223
B
HOH
82
4
HOH
HOH
224
B
HOH
113
4
HOH
HOH
225
B
HOH
109
4
HOH
HOH
226
B
HOH
64
4
HOH
HOH
227
B
HOH
71
4
HOH
HOH
201
C
HOH
92
4
HOH
HOH
202
C
HOH
24
4
HOH
HOH
203
C
HOH
15
4
HOH
HOH
204
C
HOH
27
4
HOH
HOH
205
C
HOH
28
4
HOH
HOH
206
C
HOH
119
4
HOH
HOH
207
C
HOH
35
4
HOH
HOH
208
C
HOH
70
4
HOH
HOH
209
C
HOH
60
4
HOH
HOH
210
C
HOH
62
4
HOH
HOH
211
C
HOH
121
4
HOH
HOH
212
C
HOH
55
4
HOH
HOH
213
C
HOH
65
4
HOH
HOH
214
C
HOH
100
4
HOH
HOH
215
C
HOH
115
4
HOH
HOH
216
C
HOH
116
4
HOH
HOH
217
C
HOH
59
4
HOH
HOH
218
C
HOH
88
4
HOH
HOH
219
C
HOH
61
4
HOH
HOH
220
C
HOH
34
4
HOH
HOH
221
C
HOH
117
4
HOH
HOH
222
C
HOH
83
4
HOH
HOH
223
C
HOH
52
4
HOH
HOH
224
C
HOH
31
4
HOH
HOH
225
C
HOH
97
4
HOH
HOH
226
C
HOH
25
4
HOH
HOH
227
C
HOH
90
4
HOH
HOH
228
C
HOH
104
4
HOH
HOH
229
C
HOH
111
4
HOH
HOH
230
C
HOH
99
4
HOH
HOH
231
C
HOH
98
4
HOH
HOH
232
C
HOH
51
4
HOH
HOH
233
C
HOH
73
4
HOH
HOH
234
C
HOH
95
4
HOH
HOH
235
C
HOH
23
4
HOH
HOH
236
C
HOH
106
4
HOH
HOH
237
C
HOH
93
4
HOH
HOH
238
C
HOH
10
4
HOH
HOH
239
C
HOH
72
4
HOH
HOH
240
C
HOH
96
4
HOH
HOH
241
C
HOH
89
4
HOH
HOH
242
C
HOH
30
4
HOH
HOH
243
C
HOH
36
4
HOH
HOH
244
C
n
1
-3
A
n
2
-2
A
n
3
-1
A
n
4
0
A
SER
1
n
5
SER
1
A
GLN
2
n
6
GLN
2
A
ILE
3
n
7
ILE
3
A
PHE
4
n
8
PHE
4
A
VAL
5
n
9
VAL
5
A
LYS
6
n
10
LYS
6
A
THR
7
n
11
THR
7
A
LEU
8
n
12
LEU
8
A
THR
9
n
13
THR
9
A
GLY
10
n
14
GLY
10
A
LYS
11
n
15
LYS
11
A
THR
12
n
16
THR
12
A
ILE
13
n
17
ILE
13
A
THR
14
n
18
THR
14
A
LEU
15
n
19
LEU
15
A
GLU
16
n
20
GLU
16
A
VAL
17
n
21
VAL
17
A
GLU
18
n
22
GLU
18
A
PRO
19
n
23
PRO
19
A
SER
20
n
24
SER
20
A
ASP
21
n
25
ASP
21
A
THR
22
n
26
THR
22
A
ILE
23
n
27
ILE
23
A
GLU
24
n
28
GLU
24
A
ASN
25
n
29
ASN
25
A
VAL
26
n
30
VAL
26
A
LYS
27
n
31
LYS
27
A
ALA
28
n
32
ALA
28
A
LYS
29
n
33
LYS
29
A
ILE
30
n
34
ILE
30
A
GLN
31
n
35
GLN
31
A
ASP
32
n
36
ASP
32
A
LYS
33
n
37
LYS
33
A
GLU
34
n
38
GLU
34
A
GLY
35
n
39
GLY
35
A
ILE
36
n
40
ILE
36
A
PRO
37
n
41
PRO
37
A
PRO
38
n
42
PRO
38
A
ASP
39
n
43
ASP
39
A
GLN
40
n
44
GLN
40
A
GLN
41
n
45
GLN
41
A
ARG
42
n
46
ARG
42
A
LEU
43
n
47
LEU
43
A
ILE
44
n
48
ILE
44
A
PHE
45
n
49
PHE
45
A
ALA
46
n
50
ALA
46
A
GLY
47
n
51
GLY
47
A
LYS
48
n
52
LYS
48
A
GLN
49
n
53
GLN
49
A
LEU
50
n
54
LEU
50
A
GLU
51
n
55
GLU
51
A
ASP
52
n
56
ASP
52
A
GLY
53
n
57
GLY
53
A
ARG
54
n
58
ARG
54
A
THR
55
n
59
THR
55
A
LEU
56
n
60
LEU
56
A
SER
57
n
61
SER
57
A
ASP
58
n
62
ASP
58
A
TYR
59
n
63
TYR
59
A
ASN
60
n
64
ASN
60
A
ILE
61
n
65
ILE
61
A
GLN
62
n
66
GLN
62
A
LYS
63
n
67
LYS
63
A
GLU
64
n
68
GLU
64
A
SER
65
n
69
SER
65
A
THR
66
n
70
THR
66
A
LEU
67
n
71
LEU
67
A
HIS
68
n
72
HIS
68
A
LEU
69
n
73
LEU
69
A
VAL
70
n
74
VAL
70
A
LEU
71
n
75
LEU
71
A
ARG
72
n
76
ARG
72
A
LEU
73
n
77
LEU
73
A
ARG
74
n
78
ARG
74
A
GLY
75
n
79
GLY
75
A
n
80
76
A
GLY
-3
n
1
GLY
-3
B
PRO
-2
n
2
PRO
-2
B
LEU
-1
n
3
LEU
-1
B
GLY
0
n
4
GLY
0
B
SER
1
n
5
SER
1
B
GLN
2
n
6
GLN
2
B
ILE
3
n
7
ILE
3
B
PHE
4
n
8
PHE
4
B
VAL
5
n
9
VAL
5
B
LYS
6
n
10
LYS
6
B
THR
7
n
11
THR
7
B
LEU
8
n
12
LEU
8
B
THR
9
n
13
THR
9
B
GLY
10
n
14
GLY
10
B
LYS
11
n
15
LYS
11
B
THR
12
n
16
THR
12
B
ILE
13
n
17
ILE
13
B
THR
14
n
18
THR
14
B
LEU
15
n
19
LEU
15
B
GLU
16
n
20
GLU
16
B
VAL
17
n
21
VAL
17
B
GLU
18
n
22
GLU
18
B
PRO
19
n
23
PRO
19
B
SER
20
n
24
SER
20
B
ASP
21
n
25
ASP
21
B
THR
22
n
26
THR
22
B
ILE
23
n
27
ILE
23
B
GLU
24
n
28
GLU
24
B
ASN
25
n
29
ASN
25
B
VAL
26
n
30
VAL
26
B
LYS
27
n
31
LYS
27
B
ALA
28
n
32
ALA
28
B
LYS
29
n
33
LYS
29
B
ILE
30
n
34
ILE
30
B
GLN
31
n
35
GLN
31
B
ASP
32
n
36
ASP
32
B
LYS
33
n
37
LYS
33
B
GLU
34
n
38
GLU
34
B
GLY
35
n
39
GLY
35
B
ILE
36
n
40
ILE
36
B
PRO
37
n
41
PRO
37
B
PRO
38
n
42
PRO
38
B
ASP
39
n
43
ASP
39
B
GLN
40
n
44
GLN
40
B
GLN
41
n
45
GLN
41
B
ARG
42
n
46
ARG
42
B
LEU
43
n
47
LEU
43
B
ILE
44
n
48
ILE
44
B
PHE
45
n
49
PHE
45
B
ALA
46
n
50
ALA
46
B
GLY
47
n
51
GLY
47
B
LYS
48
n
52
LYS
48
B
GLN
49
n
53
GLN
49
B
LEU
50
n
54
LEU
50
B
GLU
51
n
55
GLU
51
B
ASP
52
n
56
ASP
52
B
GLY
53
n
57
GLY
53
B
ARG
54
n
58
ARG
54
B
THR
55
n
59
THR
55
B
LEU
56
n
60
LEU
56
B
SER
57
n
61
SER
57
B
ASP
58
n
62
ASP
58
B
TYR
59
n
63
TYR
59
B
ASN
60
n
64
ASN
60
B
ILE
61
n
65
ILE
61
B
GLN
62
n
66
GLN
62
B
LYS
63
n
67
LYS
63
B
GLU
64
n
68
GLU
64
B
SER
65
n
69
SER
65
B
THR
66
n
70
THR
66
B
LEU
67
n
71
LEU
67
B
HIS
68
n
72
HIS
68
B
LEU
69
n
73
LEU
69
B
VAL
70
n
74
VAL
70
B
LEU
71
n
75
LEU
71
B
ARG
72
n
76
ARG
72
B
LEU
73
n
77
LEU
73
B
n
78
74
B
n
79
75
B
n
80
76
B
GLY
-3
n
1
GLY
-3
C
PRO
-2
n
2
PRO
-2
C
LEU
-1
n
3
LEU
-1
C
GLY
0
n
4
GLY
0
C
SER
1
n
5
SER
1
C
GLN
2
n
6
GLN
2
C
ILE
3
n
7
ILE
3
C
PHE
4
n
8
PHE
4
C
VAL
5
n
9
VAL
5
C
LYS
6
n
10
LYS
6
C
THR
7
n
11
THR
7
C
LEU
8
n
12
LEU
8
C
THR
9
n
13
THR
9
C
GLY
10
n
14
GLY
10
C
LYS
11
n
15
LYS
11
C
THR
12
n
16
THR
12
C
ILE
13
n
17
ILE
13
C
THR
14
n
18
THR
14
C
LEU
15
n
19
LEU
15
C
GLU
16
n
20
GLU
16
C
VAL
17
n
21
VAL
17
C
GLU
18
n
22
GLU
18
C
PRO
19
n
23
PRO
19
C
SER
20
n
24
SER
20
C
ASP
21
n
25
ASP
21
C
THR
22
n
26
THR
22
C
ILE
23
n
27
ILE
23
C
GLU
24
n
28
GLU
24
C
ASN
25
n
29
ASN
25
C
VAL
26
n
30
VAL
26
C
LYS
27
n
31
LYS
27
C
ALA
28
n
32
ALA
28
C
LYS
29
n
33
LYS
29
C
ILE
30
n
34
ILE
30
C
GLN
31
n
35
GLN
31
C
ASP
32
n
36
ASP
32
C
LYS
33
n
37
LYS
33
C
GLU
34
n
38
GLU
34
C
GLY
35
n
39
GLY
35
C
ILE
36
n
40
ILE
36
C
PRO
37
n
41
PRO
37
C
PRO
38
n
42
PRO
38
C
ASP
39
n
43
ASP
39
C
GLN
40
n
44
GLN
40
C
GLN
41
n
45
GLN
41
C
ARG
42
n
46
ARG
42
C
LEU
43
n
47
LEU
43
C
ILE
44
n
48
ILE
44
C
PHE
45
n
49
PHE
45
C
ALA
46
n
50
ALA
46
C
GLY
47
n
51
GLY
47
C
LYS
48
n
52
LYS
48
C
GLN
49
n
53
GLN
49
C
LEU
50
n
54
LEU
50
C
GLU
51
n
55
GLU
51
C
ASP
52
n
56
ASP
52
C
GLY
53
n
57
GLY
53
C
ARG
54
n
58
ARG
54
C
THR
55
n
59
THR
55
C
LEU
56
n
60
LEU
56
C
SER
57
n
61
SER
57
C
ASP
58
n
62
ASP
58
C
TYR
59
n
63
TYR
59
C
ASN
60
n
64
ASN
60
C
ILE
61
n
65
ILE
61
C
GLN
62
n
66
GLN
62
C
LYS
63
n
67
LYS
63
C
GLU
64
n
68
GLU
64
C
SER
65
n
69
SER
65
C
THR
66
n
70
THR
66
C
LEU
67
n
71
LEU
67
C
HIS
68
n
72
HIS
68
C
LEU
69
n
73
LEU
69
C
VAL
70
n
74
VAL
70
C
LEU
71
n
75
LEU
71
C
ARG
72
n
76
ARG
72
C
LEU
73
n
77
LEU
73
C
ARG
74
n
78
ARG
74
C
n
79
75
C
n
80
76
C
author_and_software_defined_assembly
PISA
1
monomeric
author_and_software_defined_assembly
PISA
1
monomeric
author_and_software_defined_assembly
PISA
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
LEU
15
A
O
LEU
19
A
N
ILE
3
A
N
ILE
7
A
N
PHE
4
A
N
PHE
8
A
O
LEU
67
A
O
LEU
71
A
O
VAL
70
A
O
VAL
74
A
N
ARG
42
A
N
ARG
46
A
N
PHE
45
A
N
PHE
49
A
O
LYS
48
A
O
LYS
52
B
O
LEU
15
B
O
LEU
19
B
N
ILE
3
B
N
ILE
7
B
N
PHE
4
B
N
PHE
8
B
O
LEU
67
B
O
LEU
71
B
O
HIS
68
B
O
HIS
72
B
N
ILE
44
B
N
ILE
48
B
N
PHE
45
B
N
PHE
49
B
O
LYS
48
B
O
LYS
52
C
O
VAL
17
C
O
VAL
21
C
N
SER
1
C
N
SER
5
C
N
PHE
4
C
N
PHE
8
C
O
LEU
67
C
O
LEU
71
C
O
HIS
68
C
O
HIS
72
C
N
ILE
44
C
N
ILE
48
C
N
PHE
45
C
N
PHE
49
C
O
LYS
48
C
O
LYS
52
1
A
CG
LYS
48
A
CG
LYS
52
1
Y
1
A
CD
LYS
48
A
CD
LYS
52
1
Y
1
A
CE
LYS
48
A
CE
LYS
52
1
Y
1
A
NZ
LYS
48
A
NZ
LYS
52
1
Y
1
A
CG
ARG
74
A
CG
ARG
78
1
Y
1
A
CD
ARG
74
A
CD
ARG
78
1
Y
1
A
NE
ARG
74
A
NE
ARG
78
1
Y
1
A
CZ
ARG
74
A
CZ
ARG
78
1
Y
1
A
NH1
ARG
74
A
NH1
ARG
78
1
Y
1
A
NH2
ARG
74
A
NH2
ARG
78
1
Y
1
B
CG
LEU
8
B
CG
LEU
12
1
Y
1
B
CD1
LEU
8
B
CD1
LEU
12
1
Y
1
B
CD2
LEU
8
B
CD2
LEU
12
1
Y
1
B
CG
LYS
11
B
CG
LYS
15
1
Y
1
B
CD
LYS
11
B
CD
LYS
15
1
Y
1
B
CE
LYS
11
B
CE
LYS
15
1
Y
1
B
NZ
LYS
11
B
NZ
LYS
15
1
Y
1
C
CG
ARG
74
C
CG
ARG
78
1
Y
1
C
CD
ARG
74
C
CD
ARG
78
1
Y
1
C
NE
ARG
74
C
NE
ARG
78
1
Y
1
C
CZ
ARG
74
C
CZ
ARG
78
1
Y
1
C
NH1
ARG
74
C
NH1
ARG
78
1
Y
1
C
NH2
ARG
74
C
NH2
ARG
78
1
Y
1
A
GLY
-3
A
GLY
1
1
Y
1
A
PRO
-2
A
PRO
2
1
Y
1
A
LEU
-1
A
LEU
3
1
Y
1
A
GLY
0
A
GLY
4
1
Y
1
A
GLY
76
A
GLY
80
1
Y
1
B
ARG
74
B
ARG
78
1
Y
1
B
GLY
75
B
GLY
79
1
Y
1
B
GLY
76
B
GLY
80
1
Y
1
C
GLY
75
C
GLY
79
1
Y
1
C
GLY
76
C
GLY
80
1
Y
1
A
A
O
O
HOH
HOH
235
240
1.46
1
C
C
O
O
HOH
HOH
201
206
1.60
1
C
C
O
O
HOH
HOH
214
218
1.65
1
A
A
O
O
HOH
HOH
203
222
1.67
1
C
C
O
O
HOH
HOH
210
238
1.67
1
C
C
O
O
HOH
HOH
220
241
1.90
1
C
C
O
O
HOH
HOH
240
242
1.95
1
B
B
O
O
HOH
HOH
221
225
2.01
1
C
C
O
O
HOH
HOH
210
241
2.06
1
A
A
O
O
HOH
HOH
231
238
2.09
1
C
C
O
O
HOH
HOH
238
241
2.12
1
A
A
O1
O
SO4
HOH
101
201
2.17
1
B
B
O
O
GLY
HOH
35
201
2.18
1
C
C
O
O
GLY
HOH
35
201
2.18
1
7.13
0.90
118.30
125.43
C
C
C
CB
CG
OD1
ASP
ASP
ASP
52
52
52
N
1
-5.48
0.90
118.30
112.82
C
C
C
CB
CG
OD2
ASP
ASP
ASP
52
52
52
N
1
B
C
O
O
HOH
HOH
202
202
1.56
1_555
1_556
1
B
C
O
O
HOH
HOH
201
209
1.59
1_555
1_656
1
A
ARG
74
179.53
-41.25
19.991
-0.45
0.00
-0.28
1.41
0.00
-0.69
0.953
0.922
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.23104
0.18857
0.19070
1.793
49.37
1147
21807
5.0
98.30
3.387
0.102
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.129
0.127
0.80
0.80
1.20
1UBQ
MAXIMUM LIKELIHOOD
MASK
1.793
49.37
112
1929
28
0
1789
0.019
0.019
1861
0.001
0.020
1840
2.038
2.013
2524
0.897
3.000
4270
6.828
5.000
235
37.819
26.203
79
13.986
15.000
355
18.989
15.000
9
0.113
0.200
309
0.009
0.021
2053
0.001
0.020
360
1.929
1.740
931
1.925
1.740
930
2.874
2.594
1163
2.873
2.595
1164
3.257
2.165
930
3.244
2.144
922
5.053
3.071
1348
7.165
14.308
1993
7.164
14.325
1994
0.338
0.311
1.840
83
1586
20
96.03
1.793
49.37
5M93
22956
0.995
0.1224
1
8.24
3.4
98
0.7956
1.793
1.857
1.38
0.535
1
3.1
96
refinement
REFMAC
5.8.0073
data reduction
XDS
data scaling
SCALA
phasing
PHASER
N
Crystal structure of SdeA-modified ubiquitin.
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
THR
22
A
THR
26
HELX_P
A
GLY
35
A
GLY
39
1
AA1
14
A
PRO
37
A
PRO
41
HELX_P
A
ASP
39
A
ASP
43
5
AA2
3
B
THR
22
B
THR
26
HELX_P
B
GLY
35
B
GLY
39
1
AA3
14
B
PRO
37
B
PRO
41
HELX_P
B
ASP
39
B
ASP
43
5
AA4
3
B
LEU
56
B
LEU
60
HELX_P
B
ASN
60
B
ASN
64
5
AA5
5
C
THR
22
C
THR
26
HELX_P
C
GLY
35
C
GLY
39
1
AA6
14
C
PRO
37
C
PRO
41
HELX_P
C
ASP
39
C
ASP
43
5
AA7
3
covale
1.476
one
B
ARG
42
B
NH1
ARG
46
1_555
B
RIB
101
E
C1
RIB
1_555
covale
1.485
one
C
ARG
42
C
NH1
ARG
46
1_555
C
RIB
101
G
C1
RIB
1_555
SIGNALING PROTEIN
Post translational modification, Ubiquitin, Phosphoribosylation, SdeA, signaling protein
UBB_HUMAN
UNP
1
76
P0CG47
GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
76
152
5M93
0
76
P0CG47
A
1
4
80
76
152
5M93
0
76
P0CG47
B
1
4
80
76
152
5M93
0
76
P0CG47
C
1
4
80
1
expression tag
GLY
-3
5M93
A
P0CG47
UNP
1
1
expression tag
PRO
-2
5M93
A
P0CG47
UNP
2
1
expression tag
LEU
-1
5M93
A
P0CG47
UNP
3
1
MET
conflict
SER
1
5M93
A
P0CG47
UNP
77
5
2
expression tag
GLY
-3
5M93
B
P0CG47
UNP
1
2
expression tag
PRO
-2
5M93
B
P0CG47
UNP
2
2
expression tag
LEU
-1
5M93
B
P0CG47
UNP
3
2
MET
conflict
SER
1
5M93
B
P0CG47
UNP
77
5
3
expression tag
GLY
-3
5M93
C
P0CG47
UNP
1
3
expression tag
PRO
-2
5M93
C
P0CG47
UNP
2
3
expression tag
LEU
-1
5M93
C
P0CG47
UNP
3
3
MET
conflict
SER
1
5M93
C
P0CG47
UNP
77
5
5
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
16
A
GLU
16
A
GLU
20
A
GLN
2
A
GLN
6
A
THR
7
A
THR
11
A
THR
66
A
THR
70
A
LEU
71
A
LEU
75
A
GLN
41
A
GLN
45
A
PHE
45
A
PHE
49
A
LYS
48
A
LYS
52
A
GLN
49
A
GLN
53
B
THR
12
B
THR
16
B
VAL
17
B
VAL
21
B
SER
1
B
SER
5
B
LYS
6
B
LYS
10
B
THR
66
B
THR
70
B
LEU
71
B
LEU
75
B
GLN
41
B
GLN
45
B
PHE
45
B
PHE
49
B
LYS
48
B
LYS
52
B
GLN
49
B
GLN
53
C
THR
12
C
THR
16
C
VAL
17
C
VAL
21
C
SER
1
C
SER
5
C
LYS
6
C
LYS
10
C
THR
66
C
THR
70
C
LEU
71
C
LEU
75
C
GLN
41
C
GLN
45
C
PHE
45
C
PHE
49
C
LYS
48
C
LYS
52
C
GLN
49
C
GLN
53
4
P 1 21 1