0.023794
0.000000
0.004655
0.000000
0.019044
0.000000
0.000000
0.000000
0.019184
0.00000
0.00000
0.00000
Page, R.C.
Pruneda, J.N.
Klevit, R.E.
Misra, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
101.07
90.00
42.027
52.510
53.114
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
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
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
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
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
C
N
138
N
O
N
139
N
C
N
140
N
O
N
141
N
C
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
N
N
152
S
C
N
153
N
C
N
154
N
O
N
155
N
C
Y
156
N
C
Y
157
N
N
Y
158
N
C
Y
159
N
C
Y
160
N
N
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
H
N
171
N
H
N
172
N
O
N
173
N
H
N
174
N
H
N
175
N
N
N
176
S
C
N
177
N
C
N
178
N
O
N
179
S
C
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
O
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
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
N
N
198
S
C
N
199
N
C
N
200
N
O
N
201
N
C
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
O
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
H
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
N
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
N
N
228
N
O
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
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
N
249
N
C
N
250
N
S
N
251
N
C
N
252
N
O
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
H
N
264
N
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
N
275
N
O
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
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
C
N
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
N
309
N
O
N
310
N
O
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
R
C
N
323
N
O
N
324
N
C
N
325
N
O
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
H
N
333
N
H
N
334
N
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
N
Y
344
N
C
Y
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
N
349
N
O
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
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
N
N
363
S
C
N
364
N
C
N
365
N
O
N
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
N
373
N
O
N
374
N
O
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
O
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
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
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
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
Y
153
N
sing
Y
154
N
doub
Y
155
N
doub
N
156
N
sing
Y
157
N
sing
N
158
N
sing
Y
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
doub
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
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
doub
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
sing
N
213
N
doub
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
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
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
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
doub
Y
262
N
sing
Y
263
N
sing
N
264
N
sing
Y
265
N
doub
N
266
N
sing
Y
267
N
doub
N
268
N
sing
Y
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
doub
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
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
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
doub
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
sing
N
324
N
sing
N
325
N
doub
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
doub
Y
335
N
sing
Y
336
N
sing
N
337
N
sing
Y
338
N
sing
Y
339
N
doub
N
340
N
sing
Y
341
N
doub
N
342
N
sing
Y
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
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
doub
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
Y
358
N
doub
Y
359
N
sing
Y
360
N
sing
N
361
N
sing
Y
362
N
doub
N
363
N
sing
Y
364
N
doub
N
365
N
sing
Y
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
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
doub
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
51
4175
4187
10.1021/bi300058m
22551455
Structural insights into the conformation and oligomerization of E2~ubiquitin conjugates.
2012
10.2210/pdb3ugb/pdb
pdb_00003ugb
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
113
1
mirrors
CCD
2011-08-09
RIGAKU SATURN 944+
VariMax confocal
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU MICROMAX-007 HF
16690.068
Ubiquitin-conjugating enzyme E2 D3
6.3.2.19
unp residues 1-147
C85S
1
man
polymer
8576.831
Polyubiquitin-C
unp residues 1-76
1
man
polymer
92.094
GLYCEROL
2
syn
non-polymer
18.015
water
128
nat
water
Ubiquitin carrier protein D3, Ubiquitin-conjugating enzyme E2(17)KB 3, Ubiquitin-conjugating enzyme E2-17 kDa 3, Ubiquitin-protein ligase D3
Ubiquitin
no
no
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS
NGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS
NGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
A
polypeptide(L)
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
UBC5C, UBCH5C, UBE2D2, UBE2D3
9606
Homo sapiens
562
Escherichia coli
PLASMID
pET28N
human
sample
UBC
9606
Homo sapiens
562
Escherichia coli
PLASMID
pET24
1
2.28
45.97
VAPOR DIFFUSION, HANGING DROP
7
0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-05-16
1
1
2012-11-14
1
2
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
UbcH5 isoform b (UbcH5b) conjugated to ubiquitin
UbcH5 isoform b (UbcH5b) conjugated to ubiquitin in complex with the NEDD4L HECT domain
E2 enzyme Ubc1 conjugated to ubiquitin
E2 enzyme Ubc13 conjugated to ubiquitin in complex with Mms2
E2 enzyme UbcH8 conjugated by a non-native disulfide bond to ubiquitin(Cys77)
RCSB
Y
RCSB
2011-11-02
REL
REL
GOL
GLYCEROL
HOH
water
3TGD
PDB ENTRIES 3TGD AND 1UBQ
PDB
experimental model
1UBQ
PDB ENTRIES 3TGD AND 1UBQ
PDB
experimental model
GOL
1
3
GOL
GOL
201
A
GOL
2
3
GOL
GOL
202
A
HOH
1
4
HOH
HOH
301
A
HOH
2
4
HOH
HOH
302
A
HOH
3
4
HOH
HOH
303
A
HOH
4
4
HOH
HOH
304
A
HOH
5
4
HOH
HOH
305
A
HOH
6
4
HOH
HOH
306
A
HOH
7
4
HOH
HOH
307
A
HOH
8
4
HOH
HOH
308
A
HOH
9
4
HOH
HOH
309
A
HOH
10
4
HOH
HOH
310
A
HOH
12
4
HOH
HOH
311
A
HOH
13
4
HOH
HOH
312
A
HOH
14
4
HOH
HOH
313
A
HOH
15
4
HOH
HOH
314
A
HOH
16
4
HOH
HOH
315
A
HOH
22
4
HOH
HOH
316
A
HOH
23
4
HOH
HOH
317
A
HOH
24
4
HOH
HOH
318
A
HOH
25
4
HOH
HOH
319
A
HOH
26
4
HOH
HOH
320
A
HOH
27
4
HOH
HOH
321
A
HOH
28
4
HOH
HOH
322
A
HOH
29
4
HOH
HOH
323
A
HOH
34
4
HOH
HOH
324
A
HOH
35
4
HOH
HOH
325
A
HOH
37
4
HOH
HOH
326
A
HOH
40
4
HOH
HOH
327
A
HOH
41
4
HOH
HOH
328
A
HOH
42
4
HOH
HOH
329
A
HOH
43
4
HOH
HOH
330
A
HOH
44
4
HOH
HOH
331
A
HOH
45
4
HOH
HOH
332
A
HOH
46
4
HOH
HOH
333
A
HOH
47
4
HOH
HOH
334
A
HOH
48
4
HOH
HOH
335
A
HOH
49
4
HOH
HOH
336
A
HOH
50
4
HOH
HOH
337
A
HOH
53
4
HOH
HOH
338
A
HOH
54
4
HOH
HOH
339
A
HOH
55
4
HOH
HOH
340
A
HOH
57
4
HOH
HOH
341
A
HOH
59
4
HOH
HOH
342
A
HOH
60
4
HOH
HOH
343
A
HOH
61
4
HOH
HOH
344
A
HOH
63
4
HOH
HOH
345
A
HOH
66
4
HOH
HOH
346
A
HOH
67
4
HOH
HOH
347
A
HOH
68
4
HOH
HOH
348
A
HOH
69
4
HOH
HOH
349
A
HOH
70
4
HOH
HOH
350
A
HOH
71
4
HOH
HOH
351
A
HOH
72
4
HOH
HOH
352
A
HOH
73
4
HOH
HOH
353
A
HOH
75
4
HOH
HOH
354
A
HOH
76
4
HOH
HOH
355
A
HOH
77
4
HOH
HOH
356
A
HOH
78
4
HOH
HOH
357
A
HOH
79
4
HOH
HOH
358
A
HOH
80
4
HOH
HOH
359
A
HOH
81
4
HOH
HOH
360
A
HOH
82
4
HOH
HOH
361
A
HOH
83
4
HOH
HOH
362
A
HOH
84
4
HOH
HOH
363
A
HOH
85
4
HOH
HOH
364
A
HOH
86
4
HOH
HOH
365
A
HOH
87
4
HOH
HOH
366
A
HOH
88
4
HOH
HOH
367
A
HOH
89
4
HOH
HOH
368
A
HOH
90
4
HOH
HOH
369
A
HOH
91
4
HOH
HOH
370
A
HOH
95
4
HOH
HOH
371
A
HOH
101
4
HOH
HOH
372
A
HOH
105
4
HOH
HOH
373
A
HOH
107
4
HOH
HOH
374
A
HOH
108
4
HOH
HOH
375
A
HOH
109
4
HOH
HOH
376
A
HOH
110
4
HOH
HOH
377
A
HOH
111
4
HOH
HOH
378
A
HOH
112
4
HOH
HOH
379
A
HOH
113
4
HOH
HOH
380
A
HOH
115
4
HOH
HOH
381
A
HOH
116
4
HOH
HOH
382
A
HOH
120
4
HOH
HOH
383
A
HOH
121
4
HOH
HOH
384
A
HOH
122
4
HOH
HOH
385
A
HOH
124
4
HOH
HOH
386
A
HOH
126
4
HOH
HOH
387
A
HOH
127
4
HOH
HOH
388
A
HOH
130
4
HOH
HOH
389
A
HOH
131
4
HOH
HOH
390
A
HOH
17
4
HOH
HOH
101
B
HOH
18
4
HOH
HOH
102
B
HOH
19
4
HOH
HOH
103
B
HOH
20
4
HOH
HOH
104
B
HOH
21
4
HOH
HOH
105
B
HOH
30
4
HOH
HOH
106
B
HOH
31
4
HOH
HOH
107
B
HOH
32
4
HOH
HOH
108
B
HOH
33
4
HOH
HOH
109
B
HOH
36
4
HOH
HOH
110
B
HOH
38
4
HOH
HOH
111
B
HOH
39
4
HOH
HOH
112
B
HOH
51
4
HOH
HOH
113
B
HOH
52
4
HOH
HOH
114
B
HOH
56
4
HOH
HOH
115
B
HOH
58
4
HOH
HOH
116
B
HOH
62
4
HOH
HOH
117
B
HOH
64
4
HOH
HOH
118
B
HOH
65
4
HOH
HOH
119
B
HOH
74
4
HOH
HOH
120
B
HOH
92
4
HOH
HOH
121
B
HOH
96
4
HOH
HOH
122
B
HOH
97
4
HOH
HOH
123
B
HOH
98
4
HOH
HOH
124
B
HOH
99
4
HOH
HOH
125
B
HOH
100
4
HOH
HOH
126
B
HOH
102
4
HOH
HOH
127
B
HOH
103
4
HOH
HOH
128
B
HOH
104
4
HOH
HOH
129
B
HOH
106
4
HOH
HOH
130
B
HOH
114
4
HOH
HOH
131
B
HOH
117
4
HOH
HOH
132
B
HOH
118
4
HOH
HOH
133
B
HOH
119
4
HOH
HOH
134
B
HOH
123
4
HOH
HOH
135
B
HOH
125
4
HOH
HOH
136
B
HOH
128
4
HOH
HOH
137
B
HOH
129
4
HOH
HOH
138
B
n
1
1
A
ALA
2
n
2
ALA
2
A
LEU
3
n
3
LEU
3
A
LYS
4
n
4
LYS
4
A
ARG
5
n
5
ARG
5
A
ILE
6
n
6
ILE
6
A
ASN
7
n
7
ASN
7
A
LYS
8
n
8
LYS
8
A
GLU
9
n
9
GLU
9
A
LEU
10
n
10
LEU
10
A
SER
11
n
11
SER
11
A
ASP
12
n
12
ASP
12
A
LEU
13
n
13
LEU
13
A
ALA
14
n
14
ALA
14
A
ARG
15
n
15
ARG
15
A
ASP
16
n
16
ASP
16
A
PRO
17
n
17
PRO
17
A
PRO
18
n
18
PRO
18
A
ALA
19
n
19
ALA
19
A
GLN
20
n
20
GLN
20
A
CYS
21
n
21
CYS
21
A
SER
22
n
22
SER
22
A
ALA
23
n
23
ALA
23
A
GLY
24
n
24
GLY
24
A
PRO
25
n
25
PRO
25
A
VAL
26
n
26
VAL
26
A
GLY
27
n
27
GLY
27
A
ASP
28
n
28
ASP
28
A
ASP
29
n
29
ASP
29
A
MET
30
n
30
MET
30
A
PHE
31
n
31
PHE
31
A
HIS
32
n
32
HIS
32
A
TRP
33
n
33
TRP
33
A
GLN
34
n
34
GLN
34
A
ALA
35
n
35
ALA
35
A
THR
36
n
36
THR
36
A
ILE
37
n
37
ILE
37
A
MET
38
n
38
MET
38
A
GLY
39
n
39
GLY
39
A
PRO
40
n
40
PRO
40
A
ASN
41
n
41
ASN
41
A
ASP
42
n
42
ASP
42
A
SER
43
n
43
SER
43
A
PRO
44
n
44
PRO
44
A
TYR
45
n
45
TYR
45
A
GLN
46
n
46
GLN
46
A
GLY
47
n
47
GLY
47
A
GLY
48
n
48
GLY
48
A
VAL
49
n
49
VAL
49
A
PHE
50
n
50
PHE
50
A
PHE
51
n
51
PHE
51
A
LEU
52
n
52
LEU
52
A
THR
53
n
53
THR
53
A
ILE
54
n
54
ILE
54
A
HIS
55
n
55
HIS
55
A
PHE
56
n
56
PHE
56
A
PRO
57
n
57
PRO
57
A
THR
58
n
58
THR
58
A
ASP
59
n
59
ASP
59
A
TYR
60
n
60
TYR
60
A
PRO
61
n
61
PRO
61
A
PHE
62
n
62
PHE
62
A
LYS
63
n
63
LYS
63
A
PRO
64
n
64
PRO
64
A
PRO
65
n
65
PRO
65
A
LYS
66
n
66
LYS
66
A
VAL
67
n
67
VAL
67
A
ALA
68
n
68
ALA
68
A
PHE
69
n
69
PHE
69
A
THR
70
n
70
THR
70
A
THR
71
n
71
THR
71
A
ARG
72
n
72
ARG
72
A
ILE
73
n
73
ILE
73
A
TYR
74
n
74
TYR
74
A
HIS
75
n
75
HIS
75
A
PRO
76
n
76
PRO
76
A
ASN
77
n
77
ASN
77
A
ILE
78
n
78
ILE
78
A
ASN
79
n
79
ASN
79
A
SER
80
n
80
SER
80
A
ASN
81
n
81
ASN
81
A
GLY
82
n
82
GLY
82
A
SER
83
n
83
SER
83
A
ILE
84
n
84
ILE
84
A
SER
85
n
85
SER
85
A
LEU
86
n
86
LEU
86
A
ASP
87
n
87
ASP
87
A
ILE
88
n
88
ILE
88
A
LEU
89
n
89
LEU
89
A
ARG
90
n
90
ARG
90
A
SER
91
n
91
SER
91
A
GLN
92
n
92
GLN
92
A
TRP
93
n
93
TRP
93
A
SER
94
n
94
SER
94
A
PRO
95
n
95
PRO
95
A
ALA
96
n
96
ALA
96
A
LEU
97
n
97
LEU
97
A
THR
98
n
98
THR
98
A
ILE
99
n
99
ILE
99
A
SER
100
n
100
SER
100
A
LYS
101
n
101
LYS
101
A
VAL
102
n
102
VAL
102
A
LEU
103
n
103
LEU
103
A
LEU
104
n
104
LEU
104
A
SER
105
n
105
SER
105
A
ILE
106
n
106
ILE
106
A
CYS
107
n
107
CYS
107
A
SER
108
n
108
SER
108
A
LEU
109
n
109
LEU
109
A
LEU
110
n
110
LEU
110
A
CYS
111
n
111
CYS
111
A
ASP
112
n
112
ASP
112
A
PRO
113
n
113
PRO
113
A
ASN
114
n
114
ASN
114
A
PRO
115
n
115
PRO
115
A
ASP
116
n
116
ASP
116
A
ASP
117
n
117
ASP
117
A
PRO
118
n
118
PRO
118
A
LEU
119
n
119
LEU
119
A
VAL
120
n
120
VAL
120
A
PRO
121
n
121
PRO
121
A
GLU
122
n
122
GLU
122
A
ILE
123
n
123
ILE
123
A
ALA
124
n
124
ALA
124
A
ARG
125
n
125
ARG
125
A
ILE
126
n
126
ILE
126
A
TYR
127
n
127
TYR
127
A
LYS
128
n
128
LYS
128
A
THR
129
n
129
THR
129
A
ASP
130
n
130
ASP
130
A
ARG
131
n
131
ARG
131
A
ASP
132
n
132
ASP
132
A
LYS
133
n
133
LYS
133
A
TYR
134
n
134
TYR
134
A
ASN
135
n
135
ASN
135
A
ARG
136
n
136
ARG
136
A
ILE
137
n
137
ILE
137
A
SER
138
n
138
SER
138
A
ARG
139
n
139
ARG
139
A
GLU
140
n
140
GLU
140
A
TRP
141
n
141
TRP
141
A
THR
142
n
142
THR
142
A
GLN
143
n
143
GLN
143
A
LYS
144
n
144
LYS
144
A
TYR
145
n
145
TYR
145
A
ALA
146
n
146
ALA
146
A
MET
147
n
147
MET
147
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
6.5471
3.2338
0.9008
3.9464
-0.0440
4.4650
-0.0814
-0.0414
-1.0833
-0.3197
0.0609
-0.8688
0.2180
0.6901
0.1054
0.1840
0.0234
0.0034
0.3693
0.0303
0.3211
refined
7.2229
-0.8634
-35.8991
X-RAY DIFFRACTION
3.7968
2.8299
-1.2038
3.4229
-0.2780
2.2792
-0.0827
0.3466
-0.1317
-0.3985
0.0010
-0.1624
-0.0015
-0.0194
0.1016
0.1072
0.0813
-0.0134
0.2544
-0.0038
0.1396
refined
-2.9581
0.8857
-32.5569
X-RAY DIFFRACTION
3.7544
0.5645
-2.2327
5.9118
-3.0206
7.1510
0.3975
0.2436
0.3276
0.0273
-0.2922
0.4697
-0.2389
-0.1844
-0.1135
0.0896
-0.0062
0.0068
0.1716
-0.0092
0.1498
refined
-12.8919
0.6069
-25.6323
X-RAY DIFFRACTION
7.8437
6.6398
0.0979
6.8981
0.7890
2.0924
-0.0475
0.0034
-0.0114
0.0761
-0.3957
-0.3117
-0.2600
0.3003
0.1777
0.1341
-0.0413
-0.0820
0.2627
0.1067
0.1845
refined
0.7943
1.1390
-22.7659
X-RAY DIFFRACTION
2.2101
-0.4857
-2.2421
6.5462
-4.6476
8.5021
-0.0384
-0.2786
0.1360
0.6649
-0.0323
0.3149
-0.2812
0.1963
0.1155
0.2617
-0.0263
0.0367
0.1314
-0.0300
0.2194
refined
-14.8559
-3.6068
-12.6993
X-RAY DIFFRACTION
3.0115
1.2910
0.4936
2.8398
0.8161
2.0611
-0.1264
0.3533
-0.1089
0.0486
-0.1422
0.5036
0.0681
-0.3173
-0.3188
0.1048
-0.0458
-0.0365
0.1724
-0.1249
0.4373
refined
-18.8259
-11.7882
-23.4024
X-RAY DIFFRACTION
4.2478
1.1569
0.0840
5.9909
2.1733
4.3608
0.0105
-0.0368
-0.2206
-0.0273
0.0205
0.6114
0.0515
-0.6504
0.0688
0.2585
-0.0519
-0.0175
0.2702
0.0366
0.2641
refined
-33.8018
8.0583
-5.8649
X-RAY DIFFRACTION
3.2583
-2.9200
-0.7350
3.1493
0.2512
3.3699
-0.0757
-0.4144
-0.0771
0.2075
0.2472
0.0296
0.1384
-0.1141
-0.0810
0.3077
-0.0653
-0.0415
0.2031
0.0002
0.1286
refined
-24.4062
10.5580
-4.9984
X-RAY DIFFRACTION
2.2801
-0.5409
-0.9781
2.4725
0.0986
2.2832
-0.0512
0.2137
0.0385
0.3938
0.0637
0.3388
0.0251
-0.3491
0.0614
0.1823
-0.0797
-0.0055
0.0807
0.0332
0.0889
refined
-28.2688
14.1792
-7.2435
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'A' and (resseq 2:25)
X-RAY DIFFRACTION
2
chain 'A' and (resseq 26:65)
X-RAY DIFFRACTION
3
chain 'A' and (resseq 66:84)
X-RAY DIFFRACTION
4
chain 'A' and (resseq 85:111)
X-RAY DIFFRACTION
5
chain 'A' and (resseq 112:130)
X-RAY DIFFRACTION
6
chain 'A' and (resseq 131:147)
X-RAY DIFFRACTION
7
chain 'B' and (resseq 1:22)
X-RAY DIFFRACTION
8
chain 'B' and (resseq 23:54)
X-RAY DIFFRACTION
9
chain 'B' and (resseq 55:76)
author_defined_assembly
4
tetrameric
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_454
-x-1,y+1/2,-z-1
crystal symmetry operation
-31.8286798368
26.2550000000
-52.1257255283
A
N
GLY
24
A
N
GLY
24
A
O
GLN
34
A
O
GLN
34
A
N
TRP
33
A
N
TRP
33
A
O
ILE
54
A
O
ILE
54
A
N
HIS
55
A
N
HIS
55
A
O
LYS
66
A
O
LYS
66
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
A
MET
1
A
MET
1
1
Y
1
A
ARG
90
-119.42
-92.73
-3.8773
0.0000
3.1039
3.4703
0.0000
0.4070
0.2524
0.2108
0.2130
2.350
29.618
467
9298
9298
5.02
96.95
0.41
1
1.37
MOLECULAR REPLACEMENT
27.10
0.86
1.10
PDB ENTRIES 3TGD AND 1UBQ
ML
FLAT BULK SOLVENT MODEL
36.985
0.324
2.350
29.618
128
1907
12
0
1767
0.014
1819
1.071
2466
14.970
696
0.089
274
0.012
320
2.35
52.51
3UGB
9319
9319
0.048
1
19.2
4.89
97.1
0.204
2.35
2.43
5.0
1
3.11
78.2
data collection
StructureStudio
model building
PHENIX
(phenix 1.7.2_869)
refinement
PHENIX
(phenix.refine: 1.7.2_869)
data reduction
d*TREK
data scaling
d*TREK
phasing
PHENIX
1.7.2_869
N
UbcH5c~Ubiquitin Conjugate
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
ALA
2
A
ALA
2
HELX_P
A
ASP
16
A
ASP
16
1
1
15
A
LEU
86
A
LEU
86
HELX_P
A
ARG
90
A
ARG
90
5
2
5
A
THR
98
A
THR
98
HELX_P
A
ASP
112
A
ASP
112
1
3
15
A
VAL
120
A
VAL
120
HELX_P
A
ASP
130
A
ASP
130
1
4
11
A
ASP
130
A
ASP
130
HELX_P
A
ALA
146
A
ALA
146
1
5
17
B
THR
22
B
THR
22
HELX_P
B
GLY
35
B
GLY
35
1
6
14
B
PRO
37
B
PRO
37
HELX_P
B
GLN
41
B
GLN
41
5
7
5
covale
1.434
one
A
SER
85
A
OG
SER
85
1_555
B
GLY
76
B
C
GLY
76
1_555
LIGASE/PROTEIN BINDING
E2 ubiquitin-conjugating enzyme, ubiquitin, Ubl conjugation pathway, oxyester bond, ubiquitin-protein ligase activity, LIGASE-PROTEIN BINDING complex
A
TYR
60
A
TYR
60
1
A
PRO
61
A
PRO
61
12.20
UB2D3_HUMAN
UNP
1
1
P61077
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS
NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
UBC_HUMAN
UNP
2
1
P0CG48
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
1
147
3UGB
1
147
P61077
A
1
1
147
1
76
3UGB
1
76
P0CG48
B
2
1
76
1
CYS
engineered mutation
SER
85
3UGB
A
P61077
UNP
85
85
4
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
CYS
21
A
CYS
21
A
PRO
25
A
PRO
25
A
HIS
32
A
HIS
32
A
MET
38
A
MET
38
A
VAL
49
A
VAL
49
A
HIS
55
A
HIS
55
A
LYS
66
A
LYS
66
A
PHE
69
A
PHE
69
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
VAL
70
B
VAL
70
B
ARG
42
B
ARG
42
B
PHE
45
B
PHE
45
B
LYS
48
B
LYS
48
B
GLN
49
B
GLN
49
BINDING SITE FOR RESIDUE GOL A 201
A
GOL
201
Software
4
BINDING SITE FOR RESIDUE GOL A 202
A
GOL
202
Software
9
A
HIS
55
A
HIS
55
4
1_555
A
PRO
57
A
PRO
57
4
1_555
A
THR
58
A
THR
58
4
1_555
A
LYS
66
A
LYS
66
4
1_555
A
PRO
44
A
PRO
44
9
1_555
A
LEU
110
A
LEU
110
9
1_555
A
CYS
111
A
CYS
111
9
1_555
A
PRO
113
A
PRO
113
9
1_555
A
TYR
127
A
TYR
127
9
1_555
A
ARG
131
A
ARG
131
9
1_555
A
TYR
134
A
TYR
134
9
1_555
A
ASN
135
A
ASN
135
9
1_555
A
HOH
324
E
HOH
9
1_555
4
P 1 21 1