0.041585
0.000000
0.002449
0.000000
0.017700
0.000000
0.000000
0.000000
0.021386
0.00000
0.00000
0.00000
Zhang, D.
LaRonde-LeBlanc, N.
Fushman, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
93.37
90.00
24.047
56.498
46.841
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
C8 H18 N2 O4 S
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
N
C
N
76
N
C
N
77
N
N
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
C
N
82
N
O
N
83
N
C
N
84
N
C
N
85
N
S
N
86
N
O
N
87
N
O
N
88
N
O
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
H
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
N
N
108
S
C
N
109
N
C
N
110
N
O
N
111
N
C
N
112
N
C
N
113
N
C
N
114
N
O
N
115
N
N
N
116
N
O
N
117
N
H
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
S
C
N
129
N
C
N
130
N
O
N
131
N
C
N
132
N
C
N
133
N
C
N
134
N
O
N
135
N
O
N
136
N
O
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
H
N
145
N
H
N
146
N
N
N
147
N
C
N
148
N
C
N
149
N
O
N
150
N
O
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
C
N
157
N
O
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
O
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
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
Y
175
N
C
Y
176
N
N
Y
177
N
C
Y
178
N
C
Y
179
N
N
N
180
N
O
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
O
N
192
N
H
N
193
N
H
N
194
N
N
N
195
S
C
N
196
N
C
N
197
N
O
N
198
S
C
N
199
N
C
N
200
N
C
N
201
N
C
N
202
N
O
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
C
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
H
N
237
N
H
N
238
N
N
N
239
S
C
N
240
N
C
N
241
N
O
N
242
N
C
N
243
N
C
N
244
N
C
N
245
N
C
N
246
N
N
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
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
N
C
N
268
N
C
N
269
N
S
N
270
N
C
N
271
N
O
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
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
N
294
N
O
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
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
N
N
307
S
C
N
308
N
C
N
309
N
O
N
310
N
C
N
311
N
C
N
312
N
C
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
N
328
N
O
N
329
N
O
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
R
C
N
342
N
O
N
343
N
C
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
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
N
365
N
O
N
366
N
O
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
375
N
H
N
376
N
H
N
377
N
H
N
378
N
N
N
379
S
C
N
380
N
C
N
381
N
O
N
382
N
C
N
383
N
C
N
384
N
C
N
385
N
O
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
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
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
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
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
doub
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
sing
N
109
N
doub
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
sing
N
117
N
doub
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
sing
N
127
N
sing
N
128
N
doub
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
sing
N
136
N
doub
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
sing
N
146
N
doub
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
sing
N
167
N
sing
N
168
N
doub
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
Y
173
N
sing
Y
174
N
doub
Y
175
N
doub
N
176
N
sing
Y
177
N
sing
N
178
N
sing
Y
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
doub
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
sing
N
212
N
doub
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
sing
N
233
N
doub
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
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
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
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
Y
281
N
doub
Y
282
N
sing
Y
283
N
sing
N
284
N
sing
Y
285
N
doub
N
286
N
sing
Y
287
N
doub
N
288
N
sing
Y
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
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
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
doub
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
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
doub
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
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
doub
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
Y
350
N
doub
Y
351
N
sing
Y
352
N
sing
N
353
N
sing
Y
354
N
doub
N
355
N
sing
Y
356
N
doub
N
357
N
sing
Y
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
NE
Biochim.Biophys.Acta
BBACAQ
0113
0006-3002
1823
2046
2056
10.1016/j.bbamcr.2012.04.003
22542781
Structural and biochemical studies of the open state of Lys48-linked diubiquitin.
2012
10.2210/pdb3ns8/pdb
pdb_00003ns8
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
2007-06-14
ADSC QUANTUM 315
single crystal Si(111) side bounce monochromator
SINGLE WAVELENGTH
M
x-ray
1
0.97927
1.0
24-ID-E
APS
0.97927
SYNCHROTRON
APS BEAMLINE 24-ID-E
8576.831
Ubiquitin
2
man
polymer
92.094
GLYCEROL
2
syn
non-polymer
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
1
syn
non-polymer
18.015
water
120
nat
water
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A,B
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
human
sample
RPS27A
9606
Homo sapiens
562
Escherichia coli
BL21
PLASMID
1
1.85
33.58
VAPOR DIFFUSION, SITTING DROP
7.5
HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2011-07-20
1
1
2012-10-10
1
2
2012-10-17
1
3
2023-09-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2010-07-01
REL
REL
GOL
GLYCEROL
EPE
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HOH
water
1UBQ
PDB
experimental model
GOL
1
2
GOL
GOL
77
A
GOL
2
2
GOL
GOL
77
B
EPE
3
3
EPE
EPE
78
B
HOH
78
4
HOH
HOH
78
A
HOH
3
4
HOH
HOH
79
A
HOH
4
4
HOH
HOH
80
A
HOH
81
4
HOH
HOH
81
A
HOH
8
4
HOH
HOH
82
A
HOH
10
4
HOH
HOH
83
A
HOH
11
4
HOH
HOH
84
A
HOH
85
4
HOH
HOH
85
A
HOH
86
4
HOH
HOH
86
A
HOH
87
4
HOH
HOH
87
A
HOH
88
4
HOH
HOH
88
A
HOH
13
4
HOH
HOH
89
A
HOH
90
4
HOH
HOH
90
A
HOH
91
4
HOH
HOH
91
A
HOH
92
4
HOH
HOH
92
A
HOH
93
4
HOH
HOH
93
A
HOH
14
4
HOH
HOH
94
A
HOH
15
4
HOH
HOH
95
A
HOH
17
4
HOH
HOH
96
A
HOH
19
4
HOH
HOH
97
A
HOH
98
4
HOH
HOH
98
A
HOH
20
4
HOH
HOH
99
A
HOH
100
4
HOH
HOH
100
A
HOH
21
4
HOH
HOH
101
A
HOH
102
4
HOH
HOH
102
A
HOH
23
4
HOH
HOH
103
A
HOH
24
4
HOH
HOH
104
A
HOH
25
4
HOH
HOH
105
A
HOH
27
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
29
4
HOH
HOH
108
A
HOH
109
4
HOH
HOH
109
A
HOH
110
4
HOH
HOH
110
A
HOH
111
4
HOH
HOH
111
A
HOH
112
4
HOH
HOH
112
A
HOH
31
4
HOH
HOH
113
A
HOH
32
4
HOH
HOH
114
A
HOH
115
4
HOH
HOH
115
A
HOH
116
4
HOH
HOH
116
A
HOH
117
4
HOH
HOH
117
A
HOH
118
4
HOH
HOH
118
A
HOH
34
4
HOH
HOH
119
A
HOH
120
4
HOH
HOH
120
A
HOH
121
4
HOH
HOH
121
A
HOH
122
4
HOH
HOH
122
A
HOH
123
4
HOH
HOH
123
A
HOH
124
4
HOH
HOH
124
A
HOH
35
4
HOH
HOH
125
A
HOH
38
4
HOH
HOH
126
A
HOH
40
4
HOH
HOH
127
A
HOH
42
4
HOH
HOH
128
A
HOH
47
4
HOH
HOH
129
A
HOH
49
4
HOH
HOH
130
A
HOH
50
4
HOH
HOH
131
A
HOH
51
4
HOH
HOH
132
A
HOH
55
4
HOH
HOH
134
A
HOH
56
4
HOH
HOH
135
A
HOH
58
4
HOH
HOH
136
A
HOH
60
4
HOH
HOH
137
A
HOH
63
4
HOH
HOH
138
A
HOH
64
4
HOH
HOH
139
A
HOH
65
4
HOH
HOH
140
A
HOH
66
4
HOH
HOH
141
A
HOH
67
4
HOH
HOH
142
A
HOH
69
4
HOH
HOH
143
A
HOH
70
4
HOH
HOH
144
A
HOH
71
4
HOH
HOH
145
A
HOH
72
4
HOH
HOH
146
A
HOH
73
4
HOH
HOH
147
A
HOH
76
4
HOH
HOH
148
A
HOH
79
4
HOH
HOH
79
B
HOH
80
4
HOH
HOH
80
B
HOH
1
4
HOH
HOH
81
B
HOH
82
4
HOH
HOH
82
B
HOH
83
4
HOH
HOH
83
B
HOH
2
4
HOH
HOH
84
B
HOH
5
4
HOH
HOH
85
B
HOH
6
4
HOH
HOH
86
B
HOH
7
4
HOH
HOH
87
B
HOH
9
4
HOH
HOH
88
B
HOH
12
4
HOH
HOH
89
B
HOH
16
4
HOH
HOH
90
B
HOH
18
4
HOH
HOH
91
B
HOH
22
4
HOH
HOH
92
B
HOH
26
4
HOH
HOH
93
B
HOH
94
4
HOH
HOH
94
B
HOH
95
4
HOH
HOH
95
B
HOH
96
4
HOH
HOH
96
B
HOH
28
4
HOH
HOH
97
B
HOH
33
4
HOH
HOH
98
B
HOH
99
4
HOH
HOH
99
B
HOH
36
4
HOH
HOH
100
B
HOH
101
4
HOH
HOH
101
B
HOH
37
4
HOH
HOH
102
B
HOH
39
4
HOH
HOH
103
B
HOH
41
4
HOH
HOH
104
B
HOH
105
4
HOH
HOH
105
B
HOH
106
4
HOH
HOH
106
B
HOH
43
4
HOH
HOH
107
B
HOH
108
4
HOH
HOH
108
B
HOH
44
4
HOH
HOH
109
B
HOH
46
4
HOH
HOH
110
B
HOH
48
4
HOH
HOH
111
B
HOH
52
4
HOH
HOH
112
B
HOH
113
4
HOH
HOH
113
B
HOH
114
4
HOH
HOH
114
B
HOH
54
4
HOH
HOH
115
B
HOH
57
4
HOH
HOH
116
B
HOH
59
4
HOH
HOH
117
B
HOH
61
4
HOH
HOH
118
B
HOH
119
4
HOH
HOH
119
B
HOH
62
4
HOH
HOH
120
B
HOH
68
4
HOH
HOH
121
B
HOH
74
4
HOH
HOH
122
B
HOH
75
4
HOH
HOH
123
B
HOH
77
4
HOH
HOH
124
B
HOH
126
4
HOH
HOH
126
B
HOH
127
4
HOH
HOH
127
B
HOH
128
4
HOH
HOH
128
B
HOH
53
4
HOH
HOH
133
B
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
ALA
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
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
ALA
73
n
73
LEU
73
B
n
74
74
B
n
75
75
B
n
76
76
B
author_defined_assembly
2
dimeric
software_defined_assembly
PISA
1
monomeric
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
15
A
N
ILE
3
A
N
ILE
3
A
N
LYS
6
A
N
LYS
6
A
O
LEU
67
A
O
LEU
67
A
O
HIS
68
A
O
HIS
68
A
N
ILE
44
A
N
ILE
44
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
HIS
68
B
O
HIS
68
B
N
ILE
44
B
N
ILE
44
B
N
PHE
45
B
N
PHE
45
B
O
LYS
48
B
O
LYS
48
1
A
CD
GLU
24
A
CD
GLU
24
1
Y
1
A
OE1
GLU
24
A
OE1
GLU
24
1
Y
1
A
OE2
GLU
24
A
OE2
GLU
24
1
Y
1
A
CG
LEU
73
A
CG
LEU
73
1
Y
1
A
CD1
LEU
73
A
CD1
LEU
73
1
Y
1
A
CD2
LEU
73
A
CD2
LEU
73
1
Y
1
B
CG
LEU
73
B
CG
LEU
73
1
Y
1
B
CD1
LEU
73
B
CD1
LEU
73
1
Y
1
B
CD2
LEU
73
B
CD2
LEU
73
1
Y
1
B
ARG
74
B
ARG
74
1
Y
1
B
GLY
75
B
GLY
75
1
Y
1
B
GLY
76
B
GLY
76
1
Y
21.1
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.2372
0.1861
0.1886
0.1886
1.707
18.293
636
13670
12906
4.93
94.41
0.22
RANDOM
1
Isotropic
THROUGHOUT
1.36
MOLECULAR REPLACEMENT
0.90
1.11
1UBQ
ML
FLAT BULK SOLVENT MODEL
65.935
0.406
0.22
1.707
18.293
120
1321
27
0
1174
0.006
1282
1.115
1736
16.994
515
0.077
200
0.003
226
0.2457
0.1805
1.8385
115
1988
77.00
0.2566
0.1693
2.0233
113
2519
96.00
0.2344
0.1807
2.3156
143
2546
99.00
0.2405
0.1941
2.9155
126
2599
99.00
0.2255
0.1851
18.2937
139
2618
99.00
17.44
1.707
18.3
3NS8
13670
12906
0.0
2.0
0.073
1
17.3
4.5
94.41
1.71
1.76
5.4
968
0.18
1
3.7
72.7
data collection
ADSC
Quantum
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.5_2)
data reduction
HKL-2000
data scaling
HKL-2000
N
Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
4
N
N
The biological unit is two monomers linked by an isopeptide bond between the carboxy-terminal glycine 76 of one monomer, and the lysine 48 side chain of the second monomer.
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
THR
55
A
THR
55
HELX_P
A
ASN
60
A
ASN
60
5
3
6
B
THR
22
B
THR
22
HELX_P
B
GLY
35
B
GLY
35
1
4
14
B
PRO
37
B
PRO
37
HELX_P
B
ASP
39
B
ASP
39
5
5
3
B
THR
55
B
THR
55
HELX_P
B
ASN
60
B
ASN
60
5
6
6
covale
1.325
one
A
GLY
76
A
C
GLY
76
1_555
B
LYS
48
B
NZ
LYS
48
1_555
SIGNALING PROTEIN
Diubiquitin, isopeptide bond, SIGNALING PROTEIN
UBIQ_HUMAN
UNP
1
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
1
76
3NS8
1
76
P62988
A
1
1
76
1
76
3NS8
1
76
P62988
B
1
1
76
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
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
B
THR
12
B
THR
12
B
GLU
16
B
GLU
16
B
GLN
2
B
GLN
2
B
LYS
6
B
LYS
6
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
BINDING SITE FOR RESIDUE GOL A 77
A
GOL
77
Software
9
BINDING SITE FOR RESIDUE GOL B 77
B
GOL
77
Software
11
BINDING SITE FOR RESIDUE EPE B 78
B
EPE
78
Software
11
A
GLU
51
A
GLU
51
9
1_555
A
ASP
52
A
ASP
52
9
1_555
A
ARG
72
A
ARG
72
9
1_555
A
HOH
81
F
HOH
9
1_555
A
HOH
102
F
HOH
9
1_555
A
HOH
111
F
HOH
9
1_555
B
GLY
47
B
GLY
47
9
1_555
B
LYS
48
B
LYS
48
9
1_555
B
GLN
49
B
GLN
49
9
1_555
A
LYS
48
A
LYS
48
11
1_455
A
GLN
49
A
GLN
49
11
1_455
A
HOH
90
F
HOH
11
1_455
A
HOH
130
F
HOH
11
1_455
B
LYS
27
B
LYS
27
11
1_555
B
GLN
49
B
GLN
49
11
1_555
B
LEU
50
B
LEU
50
11
1_555
B
GLU
51
B
GLU
51
11
1_555
B
ASP
52
B
ASP
52
11
1_555
B
ARG
72
B
ARG
72
11
1_555
B
HOH
96
G
HOH
11
1_555
B
ASN
25
B
ASN
25
11
1_655
B
ALA
28
B
ALA
28
11
1_655
B
LYS
29
B
LYS
29
11
1_655
B
ASP
32
B
ASP
32
11
1_655
B
PHE
45
B
PHE
45
11
1_555
B
SER
65
B
SER
65
11
1_555
B
THR
66
B
THR
66
11
1_555
B
HIS
68
B
HIS
68
11
1_555
B
HOH
87
G
HOH
11
1_555
B
HOH
95
G
HOH
11
1_555
B
HOH
124
G
HOH
11
1_655
4
P 1 21 1