0.020267
0.000000
0.000000
0.000000
0.019890
0.000000
0.000000
0.000000
0.015552
0.00000
0.00000
0.00000
Page, R.C.
Amick, J.
Misra, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
49.342
50.277
64.299
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
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
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
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
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
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
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
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
R
C
N
309
N
O
N
310
N
C
N
311
N
O
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
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
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
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
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
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
doub
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
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
doub
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
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
doub
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
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
doub
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
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
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
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
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
doub
N
365
N
sing
N
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
To be Published
0353
Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b
10.2210/pdb3tgd/pdb
pdb_00003tgd
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
mirrors
CCD
2011-03-15
RIGAKU SATURN 944+
VariMax confocal
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU MICROMAX-007 HF
17158.686
Ubiquitin-conjugating enzyme E2 D2
6.3.2.19
1
man
polymer
18.015
water
232
nat
water
Ubiquitin carrier protein D2, Ubiquitin-conjugating enzyme E2(17)KB 2, Ubiquitin-conjugating enzyme E2-17 kDa 2, Ubiquitin-protein ligase D2
no
no
GAMGSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYH
PNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
GAMGSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYH
PNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
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
UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
9606
Homo sapiens
562
Escherichia coli
Rosetta2(DE3)
PLASMID
pGST-Parallel2
1
2.32
47.07
VAPOR DIFFUSION, SITTING DROP
7.5
0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Data collection
Database references
Refinement description
1
0
2011-08-31
1
1
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
UbcH5b from a different expression construct
UbcH5b in complex with cIAP2 RING domain
UbcH5b(Ile37Ala) from a different expression construct
UbcH5b(Ile88Ala) from a different expression construct
UbcH5b(Ser94Gly) from a different expression construct
RCSB
Y
RCSB
2011-08-17
REL
REL
HOH
water
2ESK
PDB ENTRY 2ESK
PDB
experimental model
HOH
148
2
HOH
HOH
148
A
HOH
149
2
HOH
HOH
149
A
HOH
150
2
HOH
HOH
150
A
HOH
151
2
HOH
HOH
151
A
HOH
152
2
HOH
HOH
152
A
HOH
153
2
HOH
HOH
153
A
HOH
154
2
HOH
HOH
154
A
HOH
155
2
HOH
HOH
155
A
HOH
156
2
HOH
HOH
156
A
HOH
157
2
HOH
HOH
157
A
HOH
158
2
HOH
HOH
158
A
HOH
159
2
HOH
HOH
159
A
HOH
160
2
HOH
HOH
160
A
HOH
161
2
HOH
HOH
161
A
HOH
162
2
HOH
HOH
162
A
HOH
163
2
HOH
HOH
163
A
HOH
164
2
HOH
HOH
164
A
HOH
165
2
HOH
HOH
165
A
HOH
166
2
HOH
HOH
166
A
HOH
167
2
HOH
HOH
167
A
HOH
168
2
HOH
HOH
168
A
HOH
169
2
HOH
HOH
169
A
HOH
170
2
HOH
HOH
170
A
HOH
171
2
HOH
HOH
171
A
HOH
172
2
HOH
HOH
172
A
HOH
173
2
HOH
HOH
173
A
HOH
174
2
HOH
HOH
174
A
HOH
175
2
HOH
HOH
175
A
HOH
176
2
HOH
HOH
176
A
HOH
177
2
HOH
HOH
177
A
HOH
178
2
HOH
HOH
178
A
HOH
179
2
HOH
HOH
179
A
HOH
180
2
HOH
HOH
180
A
HOH
181
2
HOH
HOH
181
A
HOH
182
2
HOH
HOH
182
A
HOH
183
2
HOH
HOH
183
A
HOH
184
2
HOH
HOH
184
A
HOH
185
2
HOH
HOH
185
A
HOH
186
2
HOH
HOH
186
A
HOH
187
2
HOH
HOH
187
A
HOH
188
2
HOH
HOH
188
A
HOH
189
2
HOH
HOH
189
A
HOH
190
2
HOH
HOH
190
A
HOH
191
2
HOH
HOH
191
A
HOH
192
2
HOH
HOH
192
A
HOH
193
2
HOH
HOH
193
A
HOH
194
2
HOH
HOH
194
A
HOH
195
2
HOH
HOH
195
A
HOH
196
2
HOH
HOH
196
A
HOH
197
2
HOH
HOH
197
A
HOH
198
2
HOH
HOH
198
A
HOH
199
2
HOH
HOH
199
A
HOH
200
2
HOH
HOH
200
A
HOH
201
2
HOH
HOH
201
A
HOH
202
2
HOH
HOH
202
A
HOH
203
2
HOH
HOH
203
A
HOH
204
2
HOH
HOH
204
A
HOH
205
2
HOH
HOH
205
A
HOH
206
2
HOH
HOH
206
A
HOH
207
2
HOH
HOH
207
A
HOH
208
2
HOH
HOH
208
A
HOH
209
2
HOH
HOH
209
A
HOH
210
2
HOH
HOH
210
A
HOH
211
2
HOH
HOH
211
A
HOH
212
2
HOH
HOH
212
A
HOH
213
2
HOH
HOH
213
A
HOH
214
2
HOH
HOH
214
A
HOH
215
2
HOH
HOH
215
A
HOH
216
2
HOH
HOH
216
A
HOH
217
2
HOH
HOH
217
A
HOH
218
2
HOH
HOH
218
A
HOH
219
2
HOH
HOH
219
A
HOH
220
2
HOH
HOH
220
A
HOH
221
2
HOH
HOH
221
A
HOH
222
2
HOH
HOH
222
A
HOH
223
2
HOH
HOH
223
A
HOH
224
2
HOH
HOH
224
A
HOH
225
2
HOH
HOH
225
A
HOH
226
2
HOH
HOH
226
A
HOH
227
2
HOH
HOH
227
A
HOH
228
2
HOH
HOH
228
A
HOH
229
2
HOH
HOH
229
A
HOH
230
2
HOH
HOH
230
A
HOH
231
2
HOH
HOH
231
A
HOH
232
2
HOH
HOH
232
A
HOH
1
2
HOH
HOH
233
A
HOH
2
2
HOH
HOH
234
A
HOH
3
2
HOH
HOH
235
A
HOH
4
2
HOH
HOH
236
A
HOH
5
2
HOH
HOH
237
A
HOH
6
2
HOH
HOH
238
A
HOH
7
2
HOH
HOH
239
A
HOH
8
2
HOH
HOH
240
A
HOH
9
2
HOH
HOH
241
A
HOH
10
2
HOH
HOH
242
A
HOH
11
2
HOH
HOH
243
A
HOH
12
2
HOH
HOH
244
A
HOH
13
2
HOH
HOH
245
A
HOH
14
2
HOH
HOH
246
A
HOH
15
2
HOH
HOH
247
A
HOH
16
2
HOH
HOH
248
A
HOH
17
2
HOH
HOH
249
A
HOH
18
2
HOH
HOH
250
A
HOH
19
2
HOH
HOH
251
A
HOH
20
2
HOH
HOH
252
A
HOH
21
2
HOH
HOH
253
A
HOH
22
2
HOH
HOH
254
A
HOH
23
2
HOH
HOH
255
A
HOH
24
2
HOH
HOH
256
A
HOH
25
2
HOH
HOH
257
A
HOH
26
2
HOH
HOH
258
A
HOH
27
2
HOH
HOH
259
A
HOH
28
2
HOH
HOH
260
A
HOH
29
2
HOH
HOH
261
A
HOH
30
2
HOH
HOH
262
A
HOH
31
2
HOH
HOH
263
A
HOH
32
2
HOH
HOH
264
A
HOH
33
2
HOH
HOH
265
A
HOH
34
2
HOH
HOH
266
A
HOH
35
2
HOH
HOH
267
A
HOH
36
2
HOH
HOH
268
A
HOH
37
2
HOH
HOH
269
A
HOH
38
2
HOH
HOH
270
A
HOH
39
2
HOH
HOH
271
A
HOH
40
2
HOH
HOH
272
A
HOH
41
2
HOH
HOH
273
A
HOH
42
2
HOH
HOH
274
A
HOH
43
2
HOH
HOH
275
A
HOH
44
2
HOH
HOH
276
A
HOH
45
2
HOH
HOH
277
A
HOH
46
2
HOH
HOH
278
A
HOH
47
2
HOH
HOH
279
A
HOH
48
2
HOH
HOH
280
A
HOH
49
2
HOH
HOH
281
A
HOH
50
2
HOH
HOH
282
A
HOH
51
2
HOH
HOH
283
A
HOH
52
2
HOH
HOH
284
A
HOH
53
2
HOH
HOH
285
A
HOH
54
2
HOH
HOH
286
A
HOH
55
2
HOH
HOH
287
A
HOH
56
2
HOH
HOH
288
A
HOH
57
2
HOH
HOH
289
A
HOH
58
2
HOH
HOH
290
A
HOH
59
2
HOH
HOH
291
A
HOH
60
2
HOH
HOH
292
A
HOH
61
2
HOH
HOH
293
A
HOH
62
2
HOH
HOH
294
A
HOH
63
2
HOH
HOH
295
A
HOH
64
2
HOH
HOH
296
A
HOH
65
2
HOH
HOH
297
A
HOH
66
2
HOH
HOH
298
A
HOH
67
2
HOH
HOH
299
A
HOH
68
2
HOH
HOH
300
A
HOH
69
2
HOH
HOH
301
A
HOH
70
2
HOH
HOH
302
A
HOH
71
2
HOH
HOH
303
A
HOH
72
2
HOH
HOH
304
A
HOH
73
2
HOH
HOH
305
A
HOH
74
2
HOH
HOH
306
A
HOH
75
2
HOH
HOH
307
A
HOH
76
2
HOH
HOH
308
A
HOH
77
2
HOH
HOH
309
A
HOH
78
2
HOH
HOH
310
A
HOH
79
2
HOH
HOH
311
A
HOH
80
2
HOH
HOH
312
A
HOH
81
2
HOH
HOH
313
A
HOH
82
2
HOH
HOH
314
A
HOH
83
2
HOH
HOH
315
A
HOH
84
2
HOH
HOH
316
A
HOH
85
2
HOH
HOH
317
A
HOH
86
2
HOH
HOH
318
A
HOH
87
2
HOH
HOH
319
A
HOH
88
2
HOH
HOH
320
A
HOH
89
2
HOH
HOH
321
A
HOH
90
2
HOH
HOH
322
A
HOH
91
2
HOH
HOH
323
A
HOH
92
2
HOH
HOH
324
A
HOH
93
2
HOH
HOH
325
A
HOH
94
2
HOH
HOH
326
A
HOH
95
2
HOH
HOH
327
A
HOH
96
2
HOH
HOH
328
A
HOH
97
2
HOH
HOH
329
A
HOH
98
2
HOH
HOH
330
A
HOH
99
2
HOH
HOH
331
A
HOH
100
2
HOH
HOH
332
A
HOH
101
2
HOH
HOH
333
A
HOH
102
2
HOH
HOH
334
A
HOH
103
2
HOH
HOH
335
A
HOH
104
2
HOH
HOH
336
A
HOH
105
2
HOH
HOH
337
A
HOH
106
2
HOH
HOH
338
A
HOH
107
2
HOH
HOH
339
A
HOH
108
2
HOH
HOH
340
A
HOH
109
2
HOH
HOH
341
A
HOH
110
2
HOH
HOH
342
A
HOH
111
2
HOH
HOH
343
A
HOH
112
2
HOH
HOH
344
A
HOH
113
2
HOH
HOH
345
A
HOH
114
2
HOH
HOH
346
A
HOH
115
2
HOH
HOH
347
A
HOH
116
2
HOH
HOH
348
A
HOH
117
2
HOH
HOH
349
A
HOH
118
2
HOH
HOH
350
A
HOH
119
2
HOH
HOH
351
A
HOH
120
2
HOH
HOH
352
A
HOH
121
2
HOH
HOH
353
A
HOH
122
2
HOH
HOH
354
A
HOH
123
2
HOH
HOH
355
A
HOH
124
2
HOH
HOH
356
A
HOH
125
2
HOH
HOH
357
A
HOH
126
2
HOH
HOH
358
A
HOH
127
2
HOH
HOH
359
A
HOH
128
2
HOH
HOH
360
A
HOH
129
2
HOH
HOH
361
A
HOH
130
2
HOH
HOH
362
A
HOH
131
2
HOH
HOH
363
A
HOH
132
2
HOH
HOH
364
A
HOH
133
2
HOH
HOH
365
A
HOH
134
2
HOH
HOH
366
A
HOH
135
2
HOH
HOH
367
A
HOH
136
2
HOH
HOH
368
A
HOH
137
2
HOH
HOH
369
A
HOH
138
2
HOH
HOH
370
A
HOH
139
2
HOH
HOH
371
A
HOH
140
2
HOH
HOH
372
A
HOH
141
2
HOH
HOH
373
A
HOH
142
2
HOH
HOH
374
A
HOH
143
2
HOH
HOH
375
A
HOH
144
2
HOH
HOH
376
A
HOH
145
2
HOH
HOH
377
A
HOH
146
2
HOH
HOH
378
A
HOH
147
2
HOH
HOH
379
A
GLY
-4
n
1
GLY
-4
A
ALA
-3
n
2
ALA
-3
A
MET
-2
n
3
MET
-2
A
GLY
-1
n
4
GLY
-1
A
SER
0
n
5
SER
0
A
MET
1
n
6
MET
1
A
ALA
2
n
7
ALA
2
A
LEU
3
n
8
LEU
3
A
LYS
4
n
9
LYS
4
A
ARG
5
n
10
ARG
5
A
ILE
6
n
11
ILE
6
A
HIS
7
n
12
HIS
7
A
LYS
8
n
13
LYS
8
A
GLU
9
n
14
GLU
9
A
LEU
10
n
15
LEU
10
A
ASN
11
n
16
ASN
11
A
ASP
12
n
17
ASP
12
A
LEU
13
n
18
LEU
13
A
ALA
14
n
19
ALA
14
A
ARG
15
n
20
ARG
15
A
ASP
16
n
21
ASP
16
A
PRO
17
n
22
PRO
17
A
PRO
18
n
23
PRO
18
A
ALA
19
n
24
ALA
19
A
GLN
20
n
25
GLN
20
A
CYS
21
n
26
CYS
21
A
SER
22
n
27
SER
22
A
ALA
23
n
28
ALA
23
A
GLY
24
n
29
GLY
24
A
PRO
25
n
30
PRO
25
A
VAL
26
n
31
VAL
26
A
GLY
27
n
32
GLY
27
A
ASP
28
n
33
ASP
28
A
ASP
29
n
34
ASP
29
A
MET
30
n
35
MET
30
A
PHE
31
n
36
PHE
31
A
HIS
32
n
37
HIS
32
A
TRP
33
n
38
TRP
33
A
GLN
34
n
39
GLN
34
A
ALA
35
n
40
ALA
35
A
THR
36
n
41
THR
36
A
ILE
37
n
42
ILE
37
A
MET
38
n
43
MET
38
A
GLY
39
n
44
GLY
39
A
PRO
40
n
45
PRO
40
A
ASN
41
n
46
ASN
41
A
ASP
42
n
47
ASP
42
A
SER
43
n
48
SER
43
A
PRO
44
n
49
PRO
44
A
TYR
45
n
50
TYR
45
A
GLN
46
n
51
GLN
46
A
GLY
47
n
52
GLY
47
A
GLY
48
n
53
GLY
48
A
VAL
49
n
54
VAL
49
A
PHE
50
n
55
PHE
50
A
PHE
51
n
56
PHE
51
A
LEU
52
n
57
LEU
52
A
THR
53
n
58
THR
53
A
ILE
54
n
59
ILE
54
A
HIS
55
n
60
HIS
55
A
PHE
56
n
61
PHE
56
A
PRO
57
n
62
PRO
57
A
THR
58
n
63
THR
58
A
ASP
59
n
64
ASP
59
A
TYR
60
n
65
TYR
60
A
PRO
61
n
66
PRO
61
A
PHE
62
n
67
PHE
62
A
LYS
63
n
68
LYS
63
A
PRO
64
n
69
PRO
64
A
PRO
65
n
70
PRO
65
A
LYS
66
n
71
LYS
66
A
VAL
67
n
72
VAL
67
A
ALA
68
n
73
ALA
68
A
PHE
69
n
74
PHE
69
A
THR
70
n
75
THR
70
A
THR
71
n
76
THR
71
A
ARG
72
n
77
ARG
72
A
ILE
73
n
78
ILE
73
A
TYR
74
n
79
TYR
74
A
HIS
75
n
80
HIS
75
A
PRO
76
n
81
PRO
76
A
ASN
77
n
82
ASN
77
A
ILE
78
n
83
ILE
78
A
ASN
79
n
84
ASN
79
A
SER
80
n
85
SER
80
A
ASN
81
n
86
ASN
81
A
GLY
82
n
87
GLY
82
A
SER
83
n
88
SER
83
A
ILE
84
n
89
ILE
84
A
CYS
85
n
90
CYS
85
A
LEU
86
n
91
LEU
86
A
ASP
87
n
92
ASP
87
A
ILE
88
n
93
ILE
88
A
LEU
89
n
94
LEU
89
A
ARG
90
n
95
ARG
90
A
SER
91
n
96
SER
91
A
GLN
92
n
97
GLN
92
A
TRP
93
n
98
TRP
93
A
SER
94
n
99
SER
94
A
PRO
95
n
100
PRO
95
A
ALA
96
n
101
ALA
96
A
LEU
97
n
102
LEU
97
A
THR
98
n
103
THR
98
A
ILE
99
n
104
ILE
99
A
SER
100
n
105
SER
100
A
LYS
101
n
106
LYS
101
A
VAL
102
n
107
VAL
102
A
LEU
103
n
108
LEU
103
A
LEU
104
n
109
LEU
104
A
SER
105
n
110
SER
105
A
ILE
106
n
111
ILE
106
A
CYS
107
n
112
CYS
107
A
SER
108
n
113
SER
108
A
LEU
109
n
114
LEU
109
A
LEU
110
n
115
LEU
110
A
CYS
111
n
116
CYS
111
A
ASP
112
n
117
ASP
112
A
PRO
113
n
118
PRO
113
A
ASN
114
n
119
ASN
114
A
PRO
115
n
120
PRO
115
A
ASP
116
n
121
ASP
116
A
ASP
117
n
122
ASP
117
A
PRO
118
n
123
PRO
118
A
LEU
119
n
124
LEU
119
A
VAL
120
n
125
VAL
120
A
PRO
121
n
126
PRO
121
A
GLU
122
n
127
GLU
122
A
ILE
123
n
128
ILE
123
A
ALA
124
n
129
ALA
124
A
ARG
125
n
130
ARG
125
A
ILE
126
n
131
ILE
126
A
TYR
127
n
132
TYR
127
A
LYS
128
n
133
LYS
128
A
THR
129
n
134
THR
129
A
ASP
130
n
135
ASP
130
A
ARG
131
n
136
ARG
131
A
GLU
132
n
137
GLU
132
A
LYS
133
n
138
LYS
133
A
TYR
134
n
139
TYR
134
A
ASN
135
n
140
ASN
135
A
ARG
136
n
141
ARG
136
A
ILE
137
n
142
ILE
137
A
ALA
138
n
143
ALA
138
A
ARG
139
n
144
ARG
139
A
GLU
140
n
145
GLU
140
A
TRP
141
n
146
TRP
141
A
THR
142
n
147
THR
142
A
GLN
143
n
148
GLN
143
A
LYS
144
n
149
LYS
144
A
TYR
145
n
150
TYR
145
A
ALA
146
n
151
ALA
146
A
MET
147
n
152
MET
147
A
0.3461
0.0941
0.0891
0.0300
0.0083
0.0806
-0.0960
0.0677
0.0881
-0.0175
0.1474
0.1069
-0.0159
-0.0110
0.0053
0.0703
0.0117
0.0021
0.0521
0.0119
0.0946
refined
7.6970
-16.9091
-24.2213
X-RAY DIFFRACTION
0.3440
0.1886
0.1000
0.3380
0.2612
0.2239
0.0081
-0.0331
-0.0270
-0.0162
0.0053
-0.0818
0.0137
0.0125
0.0083
0.0345
0.0058
-0.0060
0.0369
0.0068
0.0346
refined
13.2011
-7.5787
-13.0441
X-RAY DIFFRACTION
0.0029
0.0013
-0.0049
0.3179
0.1026
0.0430
0.0192
-0.0498
0.0141
0.1563
-0.0688
0.1600
0.0910
-0.0540
0.0085
0.0672
-0.0082
0.0141
0.1089
-0.0029
0.0896
refined
1.3766
-12.7623
-9.1449
X-RAY DIFFRACTION
0.1113
0.0325
-0.0937
0.1491
0.0627
0.1458
0.0301
-0.0449
0.0374
0.0571
-0.1212
0.0922
0.0087
-0.1594
-0.0064
0.0793
-0.0044
-0.0072
0.0821
0.0023
0.0643
refined
5.5621
1.3987
-5.9204
X-RAY DIFFRACTION
0.5101
0.1964
-0.3929
0.0756
-0.1521
0.3847
0.1407
0.0564
0.1043
-0.0258
-0.0121
0.0817
-0.2203
0.0839
0.0866
0.1024
-0.0169
-0.0069
0.0848
0.0030
0.0821
refined
15.1789
11.0954
-8.0845
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'A' and (resseq -4:25)
X-RAY DIFFRACTION
2
chain 'A' and (resseq 26:84)
X-RAY DIFFRACTION
3
chain 'A' and (resseq 85:98)
X-RAY DIFFRACTION
4
chain 'A' and (resseq 99:130)
X-RAY DIFFRACTION
5
chain 'A' and (resseq 131:147)
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
N
SER
22
A
N
SER
27
A
O
THR
36
A
O
THR
41
A
N
TRP
33
A
N
TRP
38
A
O
ILE
54
A
O
ILE
59
A
N
HIS
55
A
N
HIS
60
A
O
LYS
66
A
O
LYS
71
1
A
ARG
90
-114.35
-79.69
0.4430
-0.0000
-0.0000
-0.2372
0.0000
-0.2058
0.2028
0.1788
0.1812
1.800
30.887
1518
15004
14979
10.13
97.46
0.35
RANDOM
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
18.28
0.61
0.90
PDB ENTRY 2ESK
MLHL
FLAT BULK SOLVENT MODEL
51.450
0.369
1.800
30.887
232
1437
0
0
1205
0.010
1266
1.192
1733
13.843
482
0.100
186
0.007
227
0.2879
0.2411
1.8581
110
965
78.00
0.2548
0.1965
1.9245
134
1162
96.00
0.2157
0.1902
2.0015
129
1233
99.00
0.2251
0.1824
2.0926
139
1236
100.00
0.1870
0.1704
2.2029
147
1230
100.00
0.2090
0.1789
2.3409
134
1247
100.00
0.2027
0.1764
2.5215
142
1248
100.00
0.1876
0.1828
2.7751
141
1253
100.00
0.2010
0.1770
3.1764
139
1258
100.00
0.1818
0.1660
4.0005
148
1281
100.00
0.2011
0.1763
30.8914
155
1348
100.00
15.38
1.800
30.887
3TGD
15004
15004
0.0
0.0
0.043
1
30.7
6.04
97.6
0.080
1.80
1.86
5.8
1511
1
2.55
80.1
data collection
StructureStudio
model building
PHENIX
1.7_743
refinement
PHENIX
(phenix.refine: 1.7.1_743)
data reduction
d*TREK
data scaling
d*TREK
phasing
PHENIX
1.7_743
N
Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b
1
N
N
2
N
N
A
SER
0
A
SER
5
HELX_P
A
ASP
16
A
ASP
21
1
1
17
A
LEU
86
A
LEU
91
HELX_P
A
ARG
90
A
ARG
95
5
2
5
A
THR
98
A
THR
103
HELX_P
A
ASP
112
A
ASP
117
1
3
15
A
VAL
120
A
VAL
125
HELX_P
A
ASP
130
A
ASP
135
1
4
11
A
ASP
130
A
ASP
135
HELX_P
A
ALA
146
A
ALA
151
1
5
17
LIGASE
UBC-like, ubiqutin-conjugating enzyme, ubiquitin binding, LIGASE
A
TYR
60
A
TYR
65
1
A
PRO
61
A
PRO
66
17.59
UB2D2_HUMAN
UNP
1
1
P62837
MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS
NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
1
147
3TGD
1
147
P62837
A
1
6
152
1
expression tag
GLY
-4
3TGD
A
P62837
UNP
1
1
expression tag
ALA
-3
3TGD
A
P62837
UNP
2
1
expression tag
MET
-2
3TGD
A
P62837
UNP
3
1
expression tag
GLY
-1
3TGD
A
P62837
UNP
4
1
expression tag
SER
0
3TGD
A
P62837
UNP
5
4
anti-parallel
anti-parallel
anti-parallel
A
CYS
21
A
CYS
26
A
PRO
25
A
PRO
30
A
HIS
32
A
HIS
37
A
MET
38
A
MET
43
A
VAL
49
A
VAL
54
A
HIS
55
A
HIS
60
A
LYS
66
A
LYS
71
A
PHE
69
A
PHE
74
19
P 21 21 21