0.015002
0.008661
0.000000
0.000000
0.017323
0.000000
0.000000
0.000000
0.012163
0.00000
0.00000
0.00000
Yin, J.
Bosanac, I.
Ma, X.
Hymowitz, S.
Starovasnik, M.
Cochran, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
66.658
66.658
82.218
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 Se
196.106
n
SELENOMETHIONINE
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
US
Nat.Struct.Mol.Biol.
1545-9993
19
171
175
10.1038/nsmb.2206
22245969
Phosphorylation-dependent activity of the deubiquitinase DUBA.
2012
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
2008-10-07
ADSC QUANTUM 315
a high resolution Si(311) cut and a lower resolution Si(111)
MAD
M
x-ray
1
0.9798
1.0
ID29
ESRF
0.9798
SYNCHROTRON
ESRF BEAMLINE ID29
21598.607
OTU domain-containing protein 5
3.4.19.12
catalytic or OTU domain (Residues 172-351)
3.4.19.12
1
man
polymer
18.015
water
56
nat
water
Deubiquitinating enzyme A, DUBA
no
yes
GSH(MSE)GAGYNSEDEYEAAAARIEA(MSE)DPATVEQQEHWFEKALRDKKGFIIKQ(MSE)KEDGACLFRAVADQVYG
DQD(MSE)HEVVRKHC(MSE)DYL(MSE)KNADYFSNYVTEDFTTYINRKRKNNCHGNHIE(MSE)QA(MSE)AE(MSE)
YNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATIGVGLG
GSHMGAGYNSEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHC
MDYLMKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRV
SYHRNIHYNSVVNPNKATIGVGLG
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
n
n
n
n
n
n
n
n
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
DUBA, OTUD5
9606
Homo sapiens
469008
Escherichia coli
BL21-CodonPlus (DE3)-RIL
PLASMID
pET28B
1
2.44
49.62
THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
VAPOR DIFFUSION, SITTING DROP
7.0
0.8 M succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
repository
Initial release
Database references
1
0
2012-01-11
1
1
2012-02-29
RCSB
Y
RCSB
2011-08-31
REL
REL
HOH
water
HOH
1
2
HOH
HOH
1
A
HOH
2
2
HOH
HOH
2
A
HOH
3
2
HOH
HOH
3
A
HOH
4
2
HOH
HOH
4
A
HOH
5
2
HOH
HOH
5
A
HOH
6
2
HOH
HOH
6
A
HOH
7
2
HOH
HOH
7
A
HOH
8
2
HOH
HOH
8
A
HOH
9
2
HOH
HOH
9
A
HOH
10
2
HOH
HOH
10
A
HOH
11
2
HOH
HOH
11
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
16
2
HOH
HOH
16
A
HOH
17
2
HOH
HOH
17
A
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
21
2
HOH
HOH
21
A
HOH
22
2
HOH
HOH
22
A
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
32
2
HOH
HOH
32
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
43
2
HOH
HOH
43
A
HOH
44
2
HOH
HOH
44
A
HOH
45
2
HOH
HOH
45
A
HOH
46
2
HOH
HOH
46
A
HOH
47
2
HOH
HOH
47
A
HOH
48
2
HOH
HOH
48
A
HOH
49
2
HOH
HOH
49
A
HOH
50
2
HOH
HOH
50
A
HOH
51
2
HOH
HOH
51
A
HOH
52
2
HOH
HOH
52
A
HOH
53
2
HOH
HOH
53
A
HOH
54
2
HOH
HOH
54
A
HOH
57
2
HOH
HOH
57
A
HOH
58
2
HOH
HOH
58
A
n
1
168
A
n
2
169
A
n
3
170
A
n
4
171
A
n
5
172
A
n
6
173
A
n
7
174
A
n
8
175
A
n
9
176
A
n
10
177
A
n
11
178
A
n
12
179
A
n
13
180
A
n
14
181
A
n
15
182
A
n
16
183
A
n
17
184
A
ALA
185
n
18
ALA
185
A
ALA
186
n
19
ALA
186
A
ARG
187
n
20
ARG
187
A
ILE
188
n
21
ILE
188
A
GLU
189
n
22
GLU
189
A
ALA
190
n
23
ALA
190
A
MSE
191
n
24
MSE
191
A
ASP
192
n
25
ASP
192
A
PRO
193
n
26
PRO
193
A
ALA
194
n
27
ALA
194
A
THR
195
n
28
THR
195
A
VAL
196
n
29
VAL
196
A
GLU
197
n
30
GLU
197
A
GLN
198
n
31
GLN
198
A
GLN
199
n
32
GLN
199
A
GLU
200
n
33
GLU
200
A
HIS
201
n
34
HIS
201
A
TRP
202
n
35
TRP
202
A
PHE
203
n
36
PHE
203
A
GLU
204
n
37
GLU
204
A
LYS
205
n
38
LYS
205
A
ALA
206
n
39
ALA
206
A
LEU
207
n
40
LEU
207
A
ARG
208
n
41
ARG
208
A
ASP
209
n
42
ASP
209
A
LYS
210
n
43
LYS
210
A
LYS
211
n
44
LYS
211
A
GLY
212
n
45
GLY
212
A
PHE
213
n
46
PHE
213
A
ILE
214
n
47
ILE
214
A
ILE
215
n
48
ILE
215
A
LYS
216
n
49
LYS
216
A
GLN
217
n
50
GLN
217
A
MSE
218
n
51
MSE
218
A
LYS
219
n
52
LYS
219
A
GLU
220
n
53
GLU
220
A
ASP
221
n
54
ASP
221
A
GLY
222
n
55
GLY
222
A
ALA
223
n
56
ALA
223
A
CYS
224
n
57
CYS
224
A
LEU
225
n
58
LEU
225
A
PHE
226
n
59
PHE
226
A
ARG
227
n
60
ARG
227
A
ALA
228
n
61
ALA
228
A
VAL
229
n
62
VAL
229
A
ALA
230
n
63
ALA
230
A
ASP
231
n
64
ASP
231
A
GLN
232
n
65
GLN
232
A
VAL
233
n
66
VAL
233
A
TYR
234
n
67
TYR
234
A
GLY
235
n
68
GLY
235
A
ASP
236
n
69
ASP
236
A
GLN
237
n
70
GLN
237
A
ASP
238
n
71
ASP
238
A
MSE
239
n
72
MSE
239
A
HIS
240
n
73
HIS
240
A
GLU
241
n
74
GLU
241
A
VAL
242
n
75
VAL
242
A
VAL
243
n
76
VAL
243
A
ARG
244
n
77
ARG
244
A
LYS
245
n
78
LYS
245
A
HIS
246
n
79
HIS
246
A
CYS
247
n
80
CYS
247
A
MSE
248
n
81
MSE
248
A
ASP
249
n
82
ASP
249
A
TYR
250
n
83
TYR
250
A
LEU
251
n
84
LEU
251
A
MSE
252
n
85
MSE
252
A
LYS
253
n
86
LYS
253
A
ASN
254
n
87
ASN
254
A
ALA
255
n
88
ALA
255
A
ASP
256
n
89
ASP
256
A
TYR
257
n
90
TYR
257
A
PHE
258
n
91
PHE
258
A
SER
259
n
92
SER
259
A
ASN
260
n
93
ASN
260
A
TYR
261
n
94
TYR
261
A
n
95
262
A
n
96
263
A
n
97
264
A
n
98
265
A
n
99
266
A
n
100
267
A
n
101
268
A
n
102
269
A
n
103
270
A
n
104
271
A
n
105
272
A
n
106
273
A
n
107
274
A
n
108
275
A
n
109
276
A
n
110
277
A
n
111
278
A
HIS
279
n
112
HIS
279
A
GLY
280
n
113
GLY
280
A
ASN
281
n
114
ASN
281
A
HIS
282
n
115
HIS
282
A
ILE
283
n
116
ILE
283
A
GLU
284
n
117
GLU
284
A
MSE
285
n
118
MSE
285
A
GLN
286
n
119
GLN
286
A
ALA
287
n
120
ALA
287
A
MSE
288
n
121
MSE
288
A
ALA
289
n
122
ALA
289
A
GLU
290
n
123
GLU
290
A
MSE
291
n
124
MSE
291
A
TYR
292
n
125
TYR
292
A
ASN
293
n
126
ASN
293
A
ARG
294
n
127
ARG
294
A
PRO
295
n
128
PRO
295
A
VAL
296
n
129
VAL
296
A
GLU
297
n
130
GLU
297
A
VAL
298
n
131
VAL
298
A
TYR
299
n
132
TYR
299
A
GLN
300
n
133
GLN
300
A
TYR
301
n
134
TYR
301
A
SER
302
n
135
SER
302
A
THR
303
n
136
THR
303
A
GLY
304
n
137
GLY
304
A
THR
305
n
138
THR
305
A
SER
306
n
139
SER
306
A
ALA
307
n
140
ALA
307
A
VAL
308
n
141
VAL
308
A
GLU
309
n
142
GLU
309
A
PRO
310
n
143
PRO
310
A
ILE
311
n
144
ILE
311
A
ASN
312
n
145
ASN
312
A
THR
313
n
146
THR
313
A
PHE
314
n
147
PHE
314
A
HIS
315
n
148
HIS
315
A
GLY
316
n
149
GLY
316
A
ILE
317
n
150
ILE
317
A
HIS
318
n
151
HIS
318
A
GLN
319
n
152
GLN
319
A
ASN
320
n
153
ASN
320
A
GLU
321
n
154
GLU
321
A
ASP
322
n
155
ASP
322
A
GLU
323
n
156
GLU
323
A
PRO
324
n
157
PRO
324
A
ILE
325
n
158
ILE
325
A
ARG
326
n
159
ARG
326
A
VAL
327
n
160
VAL
327
A
SER
328
n
161
SER
328
A
TYR
329
n
162
TYR
329
A
HIS
330
n
163
HIS
330
A
ARG
331
n
164
ARG
331
A
ASN
332
n
165
ASN
332
A
ILE
333
n
166
ILE
333
A
HIS
334
n
167
HIS
334
A
TYR
335
n
168
TYR
335
A
ASN
336
n
169
ASN
336
A
SER
337
n
170
SER
337
A
VAL
338
n
171
VAL
338
A
VAL
339
n
172
VAL
339
A
ASN
340
n
173
ASN
340
A
PRO
341
n
174
PRO
341
A
ASN
342
n
175
ASN
342
A
n
176
343
A
n
177
344
A
n
178
345
A
n
179
346
A
n
180
347
A
n
181
348
A
n
182
349
A
n
183
350
A
n
184
351
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
2
dimeric
5250
-21
15150
A
MSE
191
SELENOMETHIONINE
A
MSE
24
MET
A
MSE
218
SELENOMETHIONINE
A
MSE
51
MET
A
MSE
239
SELENOMETHIONINE
A
MSE
72
MET
A
MSE
248
SELENOMETHIONINE
A
MSE
81
MET
A
MSE
252
SELENOMETHIONINE
A
MSE
85
MET
A
MSE
285
SELENOMETHIONINE
A
MSE
118
MET
A
MSE
288
SELENOMETHIONINE
A
MSE
121
MET
A
MSE
291
SELENOMETHIONINE
A
MSE
124
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_665
-x+1,-y+1,z
crystal symmetry operation
33.3290000000
57.7275213655
0.0000000000
A
O
PHE
314
A
O
PHE
147
A
N
VAL
296
A
N
VAL
129
A
N
GLU
297
A
N
GLU
130
A
O
ILE
325
A
O
ILE
158
1
A
GLY
168
A
GLY
1
1
Y
1
A
SER
169
A
SER
2
1
Y
1
A
HIS
170
A
HIS
3
1
Y
1
A
MSE
171
A
MSE
4
1
Y
1
A
GLY
172
A
GLY
5
1
Y
1
A
ALA
173
A
ALA
6
1
Y
1
A
GLY
174
A
GLY
7
1
Y
1
A
TYR
175
A
TYR
8
1
Y
1
A
ASN
176
A
ASN
9
1
Y
1
A
SER
177
A
SER
10
1
Y
1
A
GLU
178
A
GLU
11
1
Y
1
A
ASP
179
A
ASP
12
1
Y
1
A
GLU
180
A
GLU
13
1
Y
1
A
TYR
181
A
TYR
14
1
Y
1
A
GLU
182
A
GLU
15
1
Y
1
A
ALA
183
A
ALA
16
1
Y
1
A
ALA
184
A
ALA
17
1
Y
1
A
VAL
262
A
VAL
95
1
Y
1
A
THR
263
A
THR
96
1
Y
1
A
GLU
264
A
GLU
97
1
Y
1
A
ASP
265
A
ASP
98
1
Y
1
A
PHE
266
A
PHE
99
1
Y
1
A
THR
267
A
THR
100
1
Y
1
A
THR
268
A
THR
101
1
Y
1
A
TYR
269
A
TYR
102
1
Y
1
A
ILE
270
A
ILE
103
1
Y
1
A
ASN
271
A
ASN
104
1
Y
1
A
ARG
272
A
ARG
105
1
Y
1
A
LYS
273
A
LYS
106
1
Y
1
A
ARG
274
A
ARG
107
1
Y
1
A
LYS
275
A
LYS
108
1
Y
1
A
ASN
276
A
ASN
109
1
Y
1
A
ASN
277
A
ASN
110
1
Y
1
A
CYS
278
A
CYS
111
1
Y
1
A
LYS
343
A
LYS
176
1
Y
1
A
ALA
344
A
ALA
177
1
Y
1
A
THR
345
A
THR
178
1
Y
1
A
ILE
346
A
ILE
179
1
Y
1
A
GLY
347
A
GLY
180
1
Y
1
A
VAL
348
A
VAL
181
1
Y
1
A
GLY
349
A
GLY
182
1
Y
1
A
LEU
350
A
LEU
183
1
Y
1
A
GLY
351
A
GLY
184
1
Y
1
A
A
SG
O
CYS
HOH
224
58
1.88
1
A
A
O
O
TYR
HOH
261
32
1.94
1
A
A
O
O
HOH
HOH
24
42
2.10
1
A
SER
306
40.89
81.26
43.351
0.37
0.18
-0.00
0.37
-0.00
-0.55
0.925
0.915
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.27615
0.24308
0.24459
2.20
28.86
503
10073
4.8
99.73
6.184
0.163
RANDOM
1
THROUGHOUT
SAD
0.214
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.20
28.86
56
1213
0
0
1157
0.010
0.021
1185
1.011
1.909
1599
5.165
5.000
139
33.357
24.571
70
15.434
15.000
200
10.701
15.000
7
0.079
0.200
161
0.004
0.021
938
0.797
1.500
702
1.539
2.000
1130
2.105
3.000
483
3.472
4.500
469
0.387
0.287
2.257
39
756
20
99.87
44.7
2.15
50.00
3TMO
22276
21875
0.062
1
19.9
4.5
98.2
2.15
2.23
3.0
1866
0.425
1
4.5
83.8
data collection
HKL-2000
model building
PHENIX
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
OTU domain-containing protein 5 (E.C.3.4.19.12)
The catalytic domain of human deubiquitinase DUBA
1
N
N
2
N
N
A
ALA
185
A
ALA
18
HELX_P
A
ASP
192
A
ASP
25
1
1
8
A
ASP
192
A
ASP
25
HELX_P
A
GLY
212
A
GLY
45
1
2
21
A
LEU
225
A
LEU
58
HELX_P
A
GLY
235
A
GLY
68
1
3
11
A
ASP
236
A
ASP
69
HELX_P
A
ASP
238
A
ASP
71
5
4
3
A
MSE
239
A
MSE
72
HELX_P
A
ASN
254
A
ASN
87
1
5
16
A
ASN
254
A
ASN
87
HELX_P
A
SER
259
A
SER
92
1
6
6
A
GLY
280
A
GLY
113
HELX_P
A
TYR
292
A
TYR
125
1
7
13
covale
1.337
A
ALA
190
A
C
ALA
23
1_555
A
MSE
191
A
N
MSE
24
1_555
covale
1.333
A
MSE
191
A
C
MSE
24
1_555
A
ASP
192
A
N
ASP
25
1_555
covale
1.331
A
GLN
217
A
C
GLN
50
1_555
A
MSE
218
A
N
MSE
51
1_555
covale
1.328
A
MSE
218
A
C
MSE
51
1_555
A
LYS
219
A
N
LYS
52
1_555
covale
1.323
A
ASP
238
A
C
ASP
71
1_555
A
MSE
239
A
N
MSE
72
1_555
covale
1.331
A
MSE
239
A
C
MSE
72
1_555
A
HIS
240
A
N
HIS
73
1_555
covale
1.329
A
CYS
247
A
C
CYS
80
1_555
A
MSE
248
A
N
MSE
81
1_555
covale
1.329
A
MSE
248
A
C
MSE
81
1_555
A
ASP
249
A
N
ASP
82
1_555
covale
1.331
A
LEU
251
A
C
LEU
84
1_555
A
MSE
252
A
N
MSE
85
1_555
covale
1.330
A
MSE
252
A
C
MSE
85
1_555
A
LYS
253
A
N
LYS
86
1_555
covale
1.330
A
GLU
284
A
C
GLU
117
1_555
A
MSE
285
A
N
MSE
118
1_555
covale
1.327
A
MSE
285
A
C
MSE
118
1_555
A
GLN
286
A
N
GLN
119
1_555
covale
1.329
A
ALA
287
A
C
ALA
120
1_555
A
MSE
288
A
N
MSE
121
1_555
covale
1.325
A
MSE
288
A
C
MSE
121
1_555
A
ALA
289
A
N
ALA
122
1_555
covale
1.334
A
GLU
290
A
C
GLU
123
1_555
A
MSE
291
A
N
MSE
124
1_555
covale
1.329
A
MSE
291
A
C
MSE
124
1_555
A
TYR
292
A
N
TYR
125
1_555
HYDROLASE
OTU fold, Deubiquitinase, phosphorylation, HYDROLASE
OTUD5_HUMAN
UNP
1
172
Q96G74
GAGYNSEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYL
MKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHR
NIHYNSVVNPNKATIGVGLG
172
351
3TMO
172
351
Q96G74
A
1
5
184
1
EXPRESSION TAG
GLY
168
3TMO
A
Q96G74
UNP
1
1
EXPRESSION TAG
SER
169
3TMO
A
Q96G74
UNP
2
1
EXPRESSION TAG
HIS
170
3TMO
A
Q96G74
UNP
3
1
EXPRESSION TAG
MSE
171
3TMO
A
Q96G74
UNP
4
3
anti-parallel
parallel
A
ASN
312
A
ASN
145
A
PHE
314
A
PHE
147
A
VAL
296
A
VAL
129
A
GLN
300
A
GLN
133
A
ILE
325
A
ILE
158
A
TYR
329
A
TYR
162
172
P 64