0.009472
0.000000
0.000000
0.000000
0.009472
0.000000
0.000000
0.000000
0.009472
0.00000
0.00000
0.00000
Komander, D.
Reyes-Turcu, F.
Wilkinson, K.D.
Barford, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
105.572
105.572
105.572
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
Cl -1
35.453
CHLORIDE ION
non-polymer
C6 H11 N O3 S
177.221
n
N-FORMYLMETHIONINE
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
Zn 2
65.409
ZINC ION
non-polymer
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
CL
N
75
N
N
N
76
N
C
N
77
N
O
N
78
S
C
N
79
N
C
N
80
N
C
N
81
N
S
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
O
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
H
N
95
N
H
N
96
N
H
N
97
N
N
N
98
S
C
N
99
N
C
N
100
N
O
N
101
N
C
N
102
N
C
N
103
N
C
N
104
N
O
N
105
N
N
N
106
N
O
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
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
N
N
118
S
C
N
119
N
C
N
120
N
O
N
121
N
C
N
122
N
C
N
123
N
C
N
124
N
O
N
125
N
O
N
126
N
O
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
N
N
137
N
C
N
138
N
C
N
139
N
O
N
140
N
O
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
N
N
147
S
C
N
148
N
C
N
149
N
O
N
150
N
C
Y
151
N
C
Y
152
N
N
Y
153
N
C
Y
154
N
C
Y
155
N
N
N
156
N
O
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
O
N
168
N
H
N
169
N
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
S
C
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
O
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
H
N
192
N
N
N
193
S
C
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
C
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
N
N
215
S
C
N
216
N
C
N
217
N
O
N
218
N
C
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
N
N
223
N
O
N
224
N
H
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
H
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
N
C
N
244
N
C
N
245
N
S
N
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
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
N
270
N
O
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
N
N
283
S
C
N
284
N
C
N
285
N
O
N
286
N
C
N
287
N
C
N
288
N
C
N
289
N
O
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
H
N
297
N
H
N
298
N
H
N
299
N
N
N
300
S
C
N
301
N
C
N
302
N
O
N
303
N
C
N
304
N
O
N
305
N
O
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
R
C
N
318
N
O
N
319
N
C
N
320
N
O
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
N
N
331
S
C
N
332
N
C
N
333
N
O
N
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
N
341
N
O
N
342
N
O
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
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
N
359
N
C
N
360
N
C
N
361
N
O
N
362
N
H
N
363
N
H
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
ZN
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
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
doub
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
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
doub
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
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
doub
N
125
N
sing
N
126
N
sing
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
doub
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
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
Y
148
N
sing
Y
149
N
doub
Y
150
N
doub
N
151
N
sing
Y
152
N
sing
N
153
N
sing
Y
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
doub
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
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
sing
N
231
N
sing
N
232
N
doub
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
sing
N
242
N
sing
N
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
doub
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
Y
256
N
doub
Y
257
N
sing
Y
258
N
sing
N
259
N
sing
Y
260
N
doub
N
261
N
sing
Y
262
N
doub
N
263
N
sing
Y
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
doub
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
sing
N
291
N
doub
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
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
doub
N
305
N
sing
N
306
N
sing
N
307
N
sing
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
doub
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
doub
N
330
N
sing
Y
331
N
doub
N
332
N
sing
Y
333
N
sing
N
334
N
sing
N
335
N
sing
N
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
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
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
UK
Embo Rep.
1469-221X
10
466
10.1038/EMBOR.2009.55
19373254
Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains.
2009
10.2210/pdb2w9n/pdb
pdb_00002w9n
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2007-03-12
ADSC CCD
SINGLE WAVELENGTH
M
x-ray
1
0.9537
1.0
ID23-1
ESRF
0.9537
SYNCHROTRON
ESRF BEAMLINE ID23-1
TWO UBIQUITIN MOLECULES FUSED HEAD-TO-TAIL
17163.664
UBIQUITIN
1
man
polymer
65.409
ZINC ION
4
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
26
nat
water
DIUBIQUITIN
no
yes
(FME)QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF
VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A
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
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
9606
HOMO SAPIENS
562
ESCHERICHIA COLI
ROSETTA2 PLYSS
PRSET
1
2.8
55
NONE
7
22% PEG 3350 AND 200 MM ZNOAC, pH 7
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Advisory
Version format compliance
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2009-04-28
1
1
2011-07-13
1
2
2023-12-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_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.ptnr1_symmetry
_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_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
SIMULTANEOUS DETERMINATION OF PROTEIN STRUCTURE AND DYNAMICS
CRYSTAL STRUCTURE OF LYS63-LINKED DI- UBIQUITIN
CRYSTAL STRUCTURE OF THE 9-10 8 GLYCINE INSERTION MUTANT OFUBIQUITIN.
UBIQUITIN
SOLUTION STRUCTURE OF THE HUMAN MMS2- UBIQUITIN COMPLEX
CO-CRYSTAL STRUCTURE OF ZNF UBP DOMAIN FROM THEDEUBIQUITINATING ENZYME ISOPEPTIDASE T (ISOT) IN COMPLEXWITH UBIQUITIN
CRYSTAL STRUCTURE OF THE 9-10 MOAD INSERTION MUTANT OFUBIQUITIN
CRYSTAL STRUCTURE OF THE UBIQUITIN-SPECIFIC PROTEASE ENCODED BY MURINE CYTOMEGALOVIRUS TEGUMENT PROTEIN M48 IN COMPLEX WITH A UBQUITIN-BASED SUICIDE SUBSTRATE
STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN
NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA
STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTERCOMPLEX
TETRAUBIQUITIN
STRUCTURE OF USP14 BOUND TO UBQUITIN ALDEHYDE
CRYSTAL STRUCTURE OF UCHL3-UBVME COMPLEX
SOLUTION STRUCTURE OF A DIMERIC N-TERMINAL FRAGMENT OF HUMAN UBIQUITIN
UBIQUITIN
STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSEMICELLES
CRYSTAL STRUCTURE OF A UBP-FAMILY DEUBIQUITINATING ENZYMEIN ISOLATION AND IN COMPLEX WITH UBIQUITIN ALDEHYDE
CRYSTAL STRUCTURE OF A MULTIPLE HYDROPHOBIC CORE MUTANT OFUBIQUITIN
UBIQUITIN NMR STRUCTURE
SYNTHETIC UBIQUITIN WITH FLUORO-LEU AT 50 AND 67
CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANTOF UBIQUITIN
CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANTOF UBIQUITIN
SOLUTION STRUCTURE OF S5A UIM-1/UBIQUITIN COMPLEX
ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURALSPECIFICITY
UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS
TSG101(UEV) DOMAIN IN COMPLEX WITH UBIQUITIN
SOLUTION STRUCTURE OF S5A UIM-2/UBIQUITIN COMPLEX
PDBE
Y
PDBE
2009-01-27
REL
REL
ZN
ZINC ION
CL
CHLORIDE ION
HOH
water
TWO COPIES OF ENTRY FUSED HEAD-TO-TAIL
1UBQ
PDB ENTRY 1UBQ
PDB
experimental model
ZN
1150
2
ZN
ZN
1150
A
ZN
1151
2
ZN
ZN
1151
A
ZN
1152
2
ZN
ZN
1152
A
ZN
1153
2
ZN
ZN
1153
A
CL
1154
3
CL
CL
1154
A
HOH
2001
4
HOH
HOH
2001
A
HOH
2002
4
HOH
HOH
2002
A
HOH
2003
4
HOH
HOH
2003
A
HOH
2004
4
HOH
HOH
2004
A
HOH
2005
4
HOH
HOH
2005
A
HOH
2006
4
HOH
HOH
2006
A
HOH
2007
4
HOH
HOH
2007
A
HOH
2008
4
HOH
HOH
2008
A
HOH
2009
4
HOH
HOH
2009
A
HOH
2010
4
HOH
HOH
2010
A
HOH
2011
4
HOH
HOH
2011
A
HOH
2012
4
HOH
HOH
2012
A
HOH
2013
4
HOH
HOH
2013
A
HOH
2014
4
HOH
HOH
2014
A
HOH
2015
4
HOH
HOH
2015
A
HOH
2016
4
HOH
HOH
2016
A
HOH
2017
4
HOH
HOH
2017
A
HOH
2018
4
HOH
HOH
2018
A
HOH
2019
4
HOH
HOH
2019
A
HOH
2020
4
HOH
HOH
2020
A
HOH
2021
4
HOH
HOH
2021
A
HOH
2022
4
HOH
HOH
2022
A
HOH
2023
4
HOH
HOH
2023
A
HOH
2024
4
HOH
HOH
2024
A
HOH
2025
4
HOH
HOH
2025
A
HOH
2026
4
HOH
HOH
2026
A
FME
1
n
1
FME
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
ARG
74
n
74
ARG
74
A
GLY
75
n
75
GLY
75
A
GLY
76
n
76
GLY
76
A
MET
77
n
77
MET
77
A
GLN
78
n
78
GLN
78
A
ILE
79
n
79
ILE
79
A
PHE
80
n
80
PHE
80
A
VAL
81
n
81
VAL
81
A
LYS
82
n
82
LYS
82
A
THR
83
n
83
THR
83
A
LEU
84
n
84
LEU
84
A
THR
85
n
85
THR
85
A
GLY
86
n
86
GLY
86
A
LYS
87
n
87
LYS
87
A
THR
88
n
88
THR
88
A
ILE
89
n
89
ILE
89
A
THR
90
n
90
THR
90
A
LEU
91
n
91
LEU
91
A
GLU
92
n
92
GLU
92
A
VAL
93
n
93
VAL
93
A
GLU
94
n
94
GLU
94
A
PRO
95
n
95
PRO
95
A
SER
96
n
96
SER
96
A
ASP
97
n
97
ASP
97
A
THR
98
n
98
THR
98
A
ILE
99
n
99
ILE
99
A
GLU
100
n
100
GLU
100
A
ASN
101
n
101
ASN
101
A
VAL
102
n
102
VAL
102
A
LYS
103
n
103
LYS
103
A
ALA
104
n
104
ALA
104
A
LYS
105
n
105
LYS
105
A
ILE
106
n
106
ILE
106
A
GLN
107
n
107
GLN
107
A
ASP
108
n
108
ASP
108
A
LYS
109
n
109
LYS
109
A
GLU
110
n
110
GLU
110
A
GLY
111
n
111
GLY
111
A
ILE
112
n
112
ILE
112
A
PRO
113
n
113
PRO
113
A
PRO
114
n
114
PRO
114
A
ASP
115
n
115
ASP
115
A
GLN
116
n
116
GLN
116
A
GLN
117
n
117
GLN
117
A
ARG
118
n
118
ARG
118
A
LEU
119
n
119
LEU
119
A
ILE
120
n
120
ILE
120
A
PHE
121
n
121
PHE
121
A
ALA
122
n
122
ALA
122
A
GLY
123
n
123
GLY
123
A
LYS
124
n
124
LYS
124
A
GLN
125
n
125
GLN
125
A
LEU
126
n
126
LEU
126
A
GLU
127
n
127
GLU
127
A
ASP
128
n
128
ASP
128
A
GLY
129
n
129
GLY
129
A
ARG
130
n
130
ARG
130
A
THR
131
n
131
THR
131
A
LEU
132
n
132
LEU
132
A
SER
133
n
133
SER
133
A
ASP
134
n
134
ASP
134
A
TYR
135
n
135
TYR
135
A
ASN
136
n
136
ASN
136
A
ILE
137
n
137
ILE
137
A
GLN
138
n
138
GLN
138
A
LYS
139
n
139
LYS
139
A
GLU
140
n
140
GLU
140
A
SER
141
n
141
SER
141
A
THR
142
n
142
THR
142
A
LEU
143
n
143
LEU
143
A
HIS
144
n
144
HIS
144
A
LEU
145
n
145
LEU
145
A
VAL
146
n
146
VAL
146
A
LEU
147
n
147
LEU
147
A
ARG
148
n
148
ARG
148
A
LEU
149
n
149
LEU
149
A
n
150
150
A
n
151
151
A
n
152
152
A
9.0846
3.3463
-0.0458
2.0253
0.1913
0.6035
0.1961
-0.3593
-0.2625
0.0820
-0.0881
-0.3045
-0.0076
0.0864
-0.1080
0.1253
-0.0186
0.0065
0.0273
-0.0099
0.0686
refined
46.5825
74.9048
33.6201
X-RAY DIFFRACTION
A
1
A
149
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PQS
1
monomeric
A
GLU
18
A
OE2
GLU
18
1_555
A
ZN
1150
B
ZN
ZN
1_555
A
ASP
21
A
OD1
ASP
21
6_566
93.0
A
GLU
18
A
OE2
GLU
18
1_555
A
ZN
1150
B
ZN
ZN
1_555
A
CL
1154
F
CL
CL
6_566
121.6
A
ASP
21
A
OD1
ASP
21
6_566
A
ZN
1150
B
ZN
ZN
1_555
A
CL
1154
F
CL
CL
6_566
145.5
A
GLU
94
A
OE1
GLU
94
7_564
A
ZN
1151
C
ZN
ZN
1_555
A
ASP
97
A
OD1
ASP
97
1_555
101.8
A
GLU
94
A
OE1
GLU
94
7_564
A
ZN
1151
C
ZN
ZN
1_555
A
HOH
2026
G
O
HOH
1_555
80.0
A
ASP
97
A
OD1
ASP
97
1_555
A
ZN
1151
C
ZN
ZN
1_555
A
HOH
2026
G
O
HOH
1_555
74.4
A
GLU
140
A
OE2
GLU
140
1_555
A
ZN
1152
D
ZN
ZN
1_555
A
GLU
140
A
OE1
GLU
140
1_555
57.8
A
GLU
140
A
OE2
GLU
140
1_555
A
ZN
1152
D
ZN
ZN
1_555
A
HIS
144
A
NE2
HIS
144
18_554
77.3
A
GLU
140
A
OE1
GLU
140
1_555
A
ZN
1152
D
ZN
ZN
1_555
A
HIS
144
A
NE2
HIS
144
18_554
124.3
A
FME
1
N-FORMYLMETHIONINE
A
FME
1
MET
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
N
LEU
15
A
N
LEU
15
A
O
ILE
3
A
O
ILE
3
A
N
LYS
6
A
N
LYS
6
A
O
LEU
67
A
O
LEU
67
A
N
VAL
70
A
N
VAL
70
A
O
ARG
42
A
O
ARG
42
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
A
N
LEU
91
A
N
LEU
91
A
O
ILE
79
A
O
ILE
79
A
N
LYS
82
A
N
LYS
82
A
O
LEU
143
A
O
LEU
143
A
N
VAL
146
A
N
VAL
146
A
O
ARG
118
A
O
ARG
118
A
N
PHE
121
A
N
PHE
121
A
O
LYS
124
A
O
LYS
124
1
A
ARG
150
A
ARG
150
1
Y
1
A
GLY
151
A
GLY
151
1
Y
1
A
GLY
152
A
GLY
152
1
Y
1
A
A
OE2
O
GLU
HOH
140
2023
2.01
77.15
0.919
0.934
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
0.276
0.259
0.260
2.25
30.00
478
9431
4.800
98.7
16.581
0.207
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.307
0.228
0.80
0.80
1.40
PDB ENTRY 1UBQ
MAXIMUM LIKELIHOOD
MASK
2.25
30.00
26
1216
5
0
1185
0.020
0.022
1198
1.927
2.001
1613
7.510
5.000
148
34.869
25.849
53
19.553
15.000
242
24.087
15.000
7
0.120
0.200
193
0.007
0.020
859
0.226
0.200
435
0.308
0.200
792
0.183
0.200
44
0.261
0.200
53
0.214
0.200
9
0.895
1.500
771
1.441
2.000
1211
2.518
3.000
469
3.940
4.500
402
0.7700
0.4810
2.31
30
630
20
2.25
74.74
2W9N
9985
2.0
0.11
1
27.40
17.1
99.1
0.54
2.25
2.37
2.00
1
5.8
96.9
refinement
REFMAC
5.2.0019
data reduction
MOSFLM
data scaling
SCALA
phasing
PHASER
crystal structure of linear di-ubiquitin
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
THR
22
A
THR
22
HELX_P
A
GLY
35
A
GLY
35
1
1
14
A
PRO
37
A
PRO
37
HELX_P
A
ASP
39
A
ASP
39
5
2
3
A
LEU
56
A
LEU
56
HELX_P
A
ASN
60
A
ASN
60
5
3
5
A
THR
98
A
THR
98
HELX_P
A
GLY
111
A
GLY
111
1
4
14
A
PRO
113
A
PRO
113
HELX_P
A
ASP
115
A
ASP
115
5
5
3
covale
1.336
both
A
FME
1
A
C
FME
1
1_555
A
GLN
2
A
N
GLN
2
1_555
metalc
2.165
A
GLU
18
A
OE2
GLU
18
1_555
A
ZN
1150
B
ZN
ZN
1_555
metalc
2.111
A
ASP
21
A
OD1
ASP
21
6_566
A
ZN
1150
B
ZN
ZN
1_555
metalc
2.012
A
GLU
94
A
OE1
GLU
94
7_564
A
ZN
1151
C
ZN
ZN
1_555
metalc
2.037
A
ASP
97
A
OD1
ASP
97
1_555
A
ZN
1151
C
ZN
ZN
1_555
metalc
2.018
A
ASP
128
A
OD2
ASP
128
1_555
A
ZN
1153
E
ZN
ZN
1_555
metalc
2.333
A
GLU
140
A
OE2
GLU
140
1_555
A
ZN
1152
D
ZN
ZN
1_555
metalc
2.147
A
GLU
140
A
OE1
GLU
140
1_555
A
ZN
1152
D
ZN
ZN
1_555
metalc
2.118
A
HIS
144
A
NE2
HIS
144
18_554
A
ZN
1152
D
ZN
ZN
1_555
metalc
2.300
A
ZN
1150
B
ZN
ZN
1_555
A
CL
1154
F
CL
CL
6_566
metalc
1.827
A
ZN
1151
C
ZN
ZN
1_555
A
HOH
2026
G
O
HOH
1_555
CELL CYCLE
CELL CYCLE, K63, IKK, NEMO, LYS63, LINEAR, UBIQUITIN, SIGNALLING CELL CYCLE
UBIQ_HUMAN
UNP
1
P62988
1
76
2W9N
1
76
P62988
A
1
1
76
1
76
2W9N
77
152
P62988
A
1
77
152
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
LEU
15
A
LEU
15
A
ILE
3
A
ILE
3
A
LYS
6
A
LYS
6
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
A
THR
88
A
THR
88
A
GLU
92
A
GLU
92
A
GLN
78
A
GLN
78
A
LYS
82
A
LYS
82
A
THR
142
A
THR
142
A
LEU
147
A
LEU
147
A
GLN
117
A
GLN
117
A
PHE
121
A
PHE
121
A
LYS
124
A
LYS
124
A
GLN
125
A
GLN
125
BINDING SITE FOR RESIDUE ZN A 1150
A
ZN
1150
Software
4
BINDING SITE FOR RESIDUE ZN A 1151
A
ZN
1151
Software
5
BINDING SITE FOR RESIDUE ZN A 1152
A
ZN
1152
Software
2
BINDING SITE FOR RESIDUE ZN A 1153
A
ZN
1153
Software
2
BINDING SITE FOR RESIDUE CL A 1154
A
CL
1154
Software
3
A
GLU
18
A
GLU
18
4
1_555
A
ASP
21
A
ASP
21
4
6_566
A
CL
1154
F
CL
4
6_566
A
HOH
2003
G
HOH
4
1_555
A
GLU
94
A
GLU
94
5
7_564
A
ASP
97
A
ASP
97
5
1_555
A
LYS
105
A
LYS
105
5
1_555
A
HOH
2025
G
HOH
5
1_555
A
HOH
2026
G
HOH
5
1_555
A
GLU
140
A
GLU
140
2
1_555
A
HIS
144
A
HIS
144
2
18_554
A
LYS
103
A
LYS
103
2
1_555
A
ASP
128
A
ASP
128
2
1_555
A
ASP
21
A
ASP
21
3
1_555
A
ZN
1150
B
ZN
3
12_664
A
HOH
2002
G
HOH
3
1_555
212
P 43 3 2