0.013466
0.007775
0.000000
0.000000
0.015549
0.000000
0.000000
0.000000
0.006285
0.000000
0.000000
0.000000
0000-0002-6471-872X
Rondelet, G.
0000-0002-4920-6857
Wouters, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
74.260
74.260
159.100
C10 H20 N2
168.279
4-(dipropylamino)butanenitrile
non-polymer
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
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
N
C
N
3
N
C
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
C
N
9
N
N
N
10
N
C
N
11
N
C
N
12
N
C
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
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
N
N
34
S
C
N
35
N
C
N
36
N
O
N
37
N
C
N
38
N
O
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
N
N
47
S
C
N
48
N
C
N
49
N
O
N
50
N
C
N
51
N
C
N
52
N
C
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
N
57
N
O
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
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
N
N
74
S
C
N
75
N
C
N
76
N
O
N
77
N
C
N
78
N
C
N
79
N
O
N
80
N
N
N
81
N
O
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
H
N
89
N
H
N
90
N
N
N
91
S
C
N
92
N
C
N
93
N
O
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
O
N
98
N
O
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
N
N
107
S
C
N
108
N
C
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
C
N
113
N
O
N
114
N
N
N
115
N
O
N
116
N
H
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
N
N
127
S
C
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
O
N
134
N
O
N
135
N
O
N
136
N
H
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
N
N
146
N
C
N
147
N
C
N
148
N
O
N
149
N
O
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
N
N
156
S
C
N
157
N
C
N
158
N
O
N
159
N
C
Y
160
N
C
Y
161
N
N
Y
162
N
C
Y
163
N
C
Y
164
N
N
N
165
N
O
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
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
N
N
180
S
C
N
181
N
C
N
182
N
O
N
183
S
C
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
O
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
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
O
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
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
N
N
224
S
C
N
225
N
C
N
226
N
O
N
227
N
C
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
N
N
232
N
O
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
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
S
N
255
N
C
N
256
N
O
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
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
Y
278
N
C
N
279
N
O
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
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
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
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
O
N
314
N
O
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
S
N
323
N
O
N
324
N
O
N
325
N
O
N
326
N
O
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
R
C
N
332
N
O
N
333
N
C
N
334
N
O
N
335
N
H
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
N
N
345
S
C
N
346
N
C
N
347
N
O
N
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
N
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
N
358
N
O
N
359
N
H
N
360
N
H
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
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
Y
381
N
C
N
382
N
O
N
383
N
O
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
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
N
N
396
S
C
N
397
N
C
N
398
N
O
N
399
N
C
N
400
N
C
N
401
N
C
N
402
N
O
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
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
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
trip
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
sing
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
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
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
sing
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
sing
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
doub
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
doub
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
doub
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
doub
N
116
N
sing
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
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
sing
N
144
N
doub
N
145
N
sing
N
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
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
Y
158
N
sing
Y
159
N
doub
Y
160
N
doub
N
161
N
sing
Y
162
N
sing
N
163
N
sing
Y
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
doub
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
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
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
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
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
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
doub
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
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
doub
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
Y
266
N
doub
Y
267
N
sing
Y
268
N
sing
N
269
N
sing
Y
270
N
doub
N
271
N
sing
Y
272
N
doub
N
273
N
sing
Y
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
sing
N
284
N
doub
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
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
doub
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
doub
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
doub
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
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
Y
339
N
doub
Y
340
N
sing
Y
341
N
sing
N
342
N
sing
Y
343
N
doub
Y
344
N
sing
Y
345
N
sing
N
346
N
sing
Y
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
350
N
doub
N
351
N
sing
Y
352
N
sing
N
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
doub
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
Y
367
N
doub
Y
368
N
sing
Y
369
N
sing
N
370
N
sing
Y
371
N
doub
N
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
sing
N
376
N
sing
N
377
N
sing
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
doub
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
To Be Published
0353
Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors
10.2210/pdb5nv0/pdb
pdb_00005nv0
100
1
PIXEL
2015-12-06
DECTRIS PILATUS 6M
channel cut monochromator crystal (Si(111))
SINGLE WAVELENGTH
M
x-ray
1
0.978570
1.0
PROXIMA 1
SOLEIL
0.978570
SYNCHROTRON
SOLEIL BEAMLINE PROXIMA 1
16698.844
DNA (cytosine-5)-methyltransferase 3B
2.1.1.37
2
man
polymer
168.279
4-(dipropylamino)butanenitrile
2
syn
non-polymer
96.063
SULFATE ION
9
syn
non-polymer
18.015
water
73
nat
water
Dnmt3b,DNA methyltransferase HsaIIIB,M.HsaIIIB
no
no
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ
HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ
HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
1
150
DNMT3B
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
PLASMID
Biological sequence
pET28-MHL
1
3.79
67.56
VAPOR DIFFUSION, SITTING DROP
0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
5.7-6.7
298
citation
citation_author
pdbx_database_proc
reflns_shell
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Data collection
Data collection
Database references
Refinement description
1
0
2018-05-30
1
1
2019-03-27
1
2
2019-10-16
1
3
2024-01-17
_citation.journal_abbrev
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Belgium
F.R.S._FNRS_Televie
7.4.532.15.F.
N
PDBE
Y
PDBE
2017-05-03
REL
REL
9AH
4-(dipropylamino)butanenitrile
SO4
SULFATE ION
HOH
water
3QKJ
PDB
experimental model
154
2
2
9AH
9AH
401
A
SO4
2
3
SO4
SO4
402
A
SO4
3
3
SO4
SO4
403
A
SO4
6
3
SO4
SO4
404
A
SO4
8
3
SO4
SO4
405
A
SO4
9
3
SO4
SO4
406
A
154
1
2
9AH
9AH
401
B
SO4
1
3
SO4
SO4
402
B
SO4
4
3
SO4
SO4
403
B
SO4
5
3
SO4
SO4
404
B
SO4
7
3
SO4
SO4
405
B
HOH
30
4
HOH
HOH
501
A
HOH
58
4
HOH
HOH
502
A
HOH
4
4
HOH
HOH
503
A
HOH
17
4
HOH
HOH
504
A
HOH
23
4
HOH
HOH
505
A
HOH
45
4
HOH
HOH
506
A
HOH
11
4
HOH
HOH
507
A
HOH
14
4
HOH
HOH
508
A
HOH
79
4
HOH
HOH
509
A
HOH
13
4
HOH
HOH
510
A
HOH
71
4
HOH
HOH
511
A
HOH
69
4
HOH
HOH
512
A
HOH
59
4
HOH
HOH
513
A
HOH
35
4
HOH
HOH
514
A
HOH
5
4
HOH
HOH
515
A
HOH
47
4
HOH
HOH
516
A
HOH
6
4
HOH
HOH
517
A
HOH
33
4
HOH
HOH
518
A
HOH
36
4
HOH
HOH
519
A
HOH
7
4
HOH
HOH
520
A
HOH
68
4
HOH
HOH
521
A
HOH
16
4
HOH
HOH
522
A
HOH
9
4
HOH
HOH
523
A
HOH
70
4
HOH
HOH
524
A
HOH
32
4
HOH
HOH
525
A
HOH
40
4
HOH
HOH
526
A
HOH
41
4
HOH
HOH
527
A
HOH
62
4
HOH
HOH
528
A
HOH
26
4
HOH
HOH
529
A
HOH
25
4
HOH
HOH
530
A
HOH
10
4
HOH
HOH
531
A
HOH
76
4
HOH
HOH
532
A
HOH
22
4
HOH
HOH
533
A
HOH
64
4
HOH
HOH
534
A
HOH
65
4
HOH
HOH
535
A
HOH
52
4
HOH
HOH
536
A
HOH
56
4
HOH
HOH
537
A
HOH
51
4
HOH
HOH
538
A
HOH
63
4
HOH
HOH
539
A
HOH
55
4
HOH
HOH
540
A
HOH
78
4
HOH
HOH
541
A
HOH
77
4
HOH
HOH
542
A
HOH
49
4
HOH
HOH
543
A
HOH
44
4
HOH
HOH
544
A
HOH
53
4
HOH
HOH
545
A
HOH
46
4
HOH
HOH
501
B
HOH
15
4
HOH
HOH
502
B
HOH
8
4
HOH
HOH
503
B
HOH
24
4
HOH
HOH
504
B
HOH
12
4
HOH
HOH
505
B
HOH
50
4
HOH
HOH
506
B
HOH
67
4
HOH
HOH
507
B
HOH
27
4
HOH
HOH
508
B
HOH
42
4
HOH
HOH
509
B
HOH
54
4
HOH
HOH
510
B
HOH
21
4
HOH
HOH
511
B
HOH
19
4
HOH
HOH
512
B
HOH
43
4
HOH
HOH
513
B
HOH
38
4
HOH
HOH
514
B
HOH
61
4
HOH
HOH
515
B
HOH
28
4
HOH
HOH
516
B
HOH
60
4
HOH
HOH
517
B
HOH
72
4
HOH
HOH
518
B
HOH
34
4
HOH
HOH
519
B
HOH
29
4
HOH
HOH
520
B
HOH
74
4
HOH
HOH
521
B
HOH
18
4
HOH
HOH
522
B
HOH
31
4
HOH
HOH
523
B
HOH
81
4
HOH
HOH
524
B
HOH
73
4
HOH
HOH
525
B
HOH
66
4
HOH
HOH
526
B
HOH
75
4
HOH
HOH
527
B
HOH
80
4
HOH
HOH
528
B
n
1
206
A
n
2
207
A
n
3
208
A
n
4
209
A
n
5
210
A
n
6
211
A
n
7
212
A
n
8
213
A
n
9
214
A
SER
215
n
10
SER
215
A
GLU
216
n
11
GLU
216
A
TYR
217
n
12
TYR
217
A
GLN
218
n
13
GLN
218
A
ASP
219
n
14
ASP
219
A
GLY
220
n
15
GLY
220
A
LYS
221
n
16
LYS
221
A
GLU
222
n
17
GLU
222
A
PHE
223
n
18
PHE
223
A
GLY
224
n
19
GLY
224
A
ILE
225
n
20
ILE
225
A
GLY
226
n
21
GLY
226
A
ASP
227
n
22
ASP
227
A
LEU
228
n
23
LEU
228
A
VAL
229
n
24
VAL
229
A
TRP
230
n
25
TRP
230
A
GLY
231
n
26
GLY
231
A
LYS
232
n
27
LYS
232
A
ILE
233
n
28
ILE
233
A
LYS
234
n
29
LYS
234
A
GLY
235
n
30
GLY
235
A
PHE
236
n
31
PHE
236
A
SER
237
n
32
SER
237
A
TRP
238
n
33
TRP
238
A
TRP
239
n
34
TRP
239
A
PRO
240
n
35
PRO
240
A
ALA
241
n
36
ALA
241
A
MET
242
n
37
MET
242
A
VAL
243
n
38
VAL
243
A
VAL
244
n
39
VAL
244
A
SER
245
n
40
SER
245
A
TRP
246
n
41
TRP
246
A
LYS
247
n
42
LYS
247
A
ALA
248
n
43
ALA
248
A
THR
249
n
44
THR
249
A
SER
250
n
45
SER
250
A
LYS
251
n
46
LYS
251
A
ARG
252
n
47
ARG
252
A
GLN
253
n
48
GLN
253
A
ALA
254
n
49
ALA
254
A
MET
255
n
50
MET
255
A
SER
256
n
51
SER
256
A
GLY
257
n
52
GLY
257
A
MET
258
n
53
MET
258
A
ARG
259
n
54
ARG
259
A
TRP
260
n
55
TRP
260
A
VAL
261
n
56
VAL
261
A
GLN
262
n
57
GLN
262
A
TRP
263
n
58
TRP
263
A
PHE
264
n
59
PHE
264
A
GLY
265
n
60
GLY
265
A
ASP
266
n
61
ASP
266
A
GLY
267
n
62
GLY
267
A
LYS
268
n
63
LYS
268
A
PHE
269
n
64
PHE
269
A
SER
270
n
65
SER
270
A
GLU
271
n
66
GLU
271
A
VAL
272
n
67
VAL
272
A
SER
273
n
68
SER
273
A
ALA
274
n
69
ALA
274
A
ASP
275
n
70
ASP
275
A
LYS
276
n
71
LYS
276
A
LEU
277
n
72
LEU
277
A
VAL
278
n
73
VAL
278
A
ALA
279
n
74
ALA
279
A
LEU
280
n
75
LEU
280
A
GLY
281
n
76
GLY
281
A
LEU
282
n
77
LEU
282
A
PHE
283
n
78
PHE
283
A
SER
284
n
79
SER
284
A
GLN
285
n
80
GLN
285
A
HIS
286
n
81
HIS
286
A
PHE
287
n
82
PHE
287
A
ASN
288
n
83
ASN
288
A
LEU
289
n
84
LEU
289
A
ALA
290
n
85
ALA
290
A
THR
291
n
86
THR
291
A
PHE
292
n
87
PHE
292
A
ASN
293
n
88
ASN
293
A
LYS
294
n
89
LYS
294
A
LEU
295
n
90
LEU
295
A
VAL
296
n
91
VAL
296
A
SER
297
n
92
SER
297
A
TYR
298
n
93
TYR
298
A
ARG
299
n
94
ARG
299
A
LYS
300
n
95
LYS
300
A
ALA
301
n
96
ALA
301
A
MET
302
n
97
MET
302
A
TYR
303
n
98
TYR
303
A
HIS
304
n
99
HIS
304
A
ALA
305
n
100
ALA
305
A
LEU
306
n
101
LEU
306
A
GLU
307
n
102
GLU
307
A
LYS
308
n
103
LYS
308
A
ALA
309
n
104
ALA
309
A
ARG
310
n
105
ARG
310
A
VAL
311
n
106
VAL
311
A
ARG
312
n
107
ARG
312
A
ALA
313
n
108
ALA
313
A
GLY
314
n
109
GLY
314
A
LYS
315
n
110
LYS
315
A
THR
316
n
111
THR
316
A
PHE
317
n
112
PHE
317
A
PRO
318
n
113
PRO
318
A
SER
319
n
114
SER
319
A
n
115
320
A
n
116
321
A
n
117
322
A
n
118
323
A
SER
324
n
119
SER
324
A
LEU
325
n
120
LEU
325
A
GLU
326
n
121
GLU
326
A
ASP
327
n
122
ASP
327
A
GLN
328
n
123
GLN
328
A
LEU
329
n
124
LEU
329
A
LYS
330
n
125
LYS
330
A
PRO
331
n
126
PRO
331
A
MET
332
n
127
MET
332
A
LEU
333
n
128
LEU
333
A
GLU
334
n
129
GLU
334
A
TRP
335
n
130
TRP
335
A
ALA
336
n
131
ALA
336
A
HIS
337
n
132
HIS
337
A
GLY
338
n
133
GLY
338
A
GLY
339
n
134
GLY
339
A
PHE
340
n
135
PHE
340
A
LYS
341
n
136
LYS
341
A
PRO
342
n
137
PRO
342
A
THR
343
n
138
THR
343
A
GLY
344
n
139
GLY
344
A
ILE
345
n
140
ILE
345
A
GLU
346
n
141
GLU
346
A
GLY
347
n
142
GLY
347
A
LEU
348
n
143
LEU
348
A
LYS
349
n
144
LYS
349
A
PRO
350
n
145
PRO
350
A
ASN
351
n
146
ASN
351
A
n
147
352
A
n
148
353
A
n
149
354
A
n
150
355
A
n
1
206
B
n
2
207
B
n
3
208
B
n
4
209
B
n
5
210
B
n
6
211
B
n
7
212
B
n
8
213
B
n
9
214
B
SER
215
n
10
SER
215
B
GLU
216
n
11
GLU
216
B
TYR
217
n
12
TYR
217
B
GLN
218
n
13
GLN
218
B
ASP
219
n
14
ASP
219
B
GLY
220
n
15
GLY
220
B
LYS
221
n
16
LYS
221
B
GLU
222
n
17
GLU
222
B
PHE
223
n
18
PHE
223
B
GLY
224
n
19
GLY
224
B
ILE
225
n
20
ILE
225
B
GLY
226
n
21
GLY
226
B
ASP
227
n
22
ASP
227
B
LEU
228
n
23
LEU
228
B
VAL
229
n
24
VAL
229
B
TRP
230
n
25
TRP
230
B
GLY
231
n
26
GLY
231
B
LYS
232
n
27
LYS
232
B
ILE
233
n
28
ILE
233
B
LYS
234
n
29
LYS
234
B
GLY
235
n
30
GLY
235
B
PHE
236
n
31
PHE
236
B
SER
237
n
32
SER
237
B
TRP
238
n
33
TRP
238
B
TRP
239
n
34
TRP
239
B
PRO
240
n
35
PRO
240
B
ALA
241
n
36
ALA
241
B
MET
242
n
37
MET
242
B
VAL
243
n
38
VAL
243
B
VAL
244
n
39
VAL
244
B
SER
245
n
40
SER
245
B
TRP
246
n
41
TRP
246
B
LYS
247
n
42
LYS
247
B
ALA
248
n
43
ALA
248
B
THR
249
n
44
THR
249
B
SER
250
n
45
SER
250
B
LYS
251
n
46
LYS
251
B
ARG
252
n
47
ARG
252
B
GLN
253
n
48
GLN
253
B
ALA
254
n
49
ALA
254
B
MET
255
n
50
MET
255
B
SER
256
n
51
SER
256
B
GLY
257
n
52
GLY
257
B
MET
258
n
53
MET
258
B
ARG
259
n
54
ARG
259
B
TRP
260
n
55
TRP
260
B
VAL
261
n
56
VAL
261
B
GLN
262
n
57
GLN
262
B
TRP
263
n
58
TRP
263
B
PHE
264
n
59
PHE
264
B
GLY
265
n
60
GLY
265
B
ASP
266
n
61
ASP
266
B
GLY
267
n
62
GLY
267
B
LYS
268
n
63
LYS
268
B
PHE
269
n
64
PHE
269
B
SER
270
n
65
SER
270
B
GLU
271
n
66
GLU
271
B
VAL
272
n
67
VAL
272
B
SER
273
n
68
SER
273
B
ALA
274
n
69
ALA
274
B
ASP
275
n
70
ASP
275
B
LYS
276
n
71
LYS
276
B
LEU
277
n
72
LEU
277
B
VAL
278
n
73
VAL
278
B
ALA
279
n
74
ALA
279
B
LEU
280
n
75
LEU
280
B
GLY
281
n
76
GLY
281
B
LEU
282
n
77
LEU
282
B
PHE
283
n
78
PHE
283
B
SER
284
n
79
SER
284
B
GLN
285
n
80
GLN
285
B
HIS
286
n
81
HIS
286
B
PHE
287
n
82
PHE
287
B
ASN
288
n
83
ASN
288
B
LEU
289
n
84
LEU
289
B
ALA
290
n
85
ALA
290
B
THR
291
n
86
THR
291
B
PHE
292
n
87
PHE
292
B
ASN
293
n
88
ASN
293
B
LYS
294
n
89
LYS
294
B
LEU
295
n
90
LEU
295
B
VAL
296
n
91
VAL
296
B
SER
297
n
92
SER
297
B
TYR
298
n
93
TYR
298
B
ARG
299
n
94
ARG
299
B
LYS
300
n
95
LYS
300
B
ALA
301
n
96
ALA
301
B
MET
302
n
97
MET
302
B
TYR
303
n
98
TYR
303
B
HIS
304
n
99
HIS
304
B
ALA
305
n
100
ALA
305
B
LEU
306
n
101
LEU
306
B
GLU
307
n
102
GLU
307
B
LYS
308
n
103
LYS
308
B
ALA
309
n
104
ALA
309
B
ARG
310
n
105
ARG
310
B
VAL
311
n
106
VAL
311
B
ARG
312
n
107
ARG
312
B
ALA
313
n
108
ALA
313
B
GLY
314
n
109
GLY
314
B
LYS
315
n
110
LYS
315
B
THR
316
n
111
THR
316
B
PHE
317
n
112
PHE
317
B
PRO
318
n
113
PRO
318
B
SER
319
n
114
SER
319
B
n
115
320
B
n
116
321
B
n
117
322
B
n
118
323
B
SER
324
n
119
SER
324
B
LEU
325
n
120
LEU
325
B
GLU
326
n
121
GLU
326
B
ASP
327
n
122
ASP
327
B
GLN
328
n
123
GLN
328
B
LEU
329
n
124
LEU
329
B
LYS
330
n
125
LYS
330
B
PRO
331
n
126
PRO
331
B
MET
332
n
127
MET
332
B
LEU
333
n
128
LEU
333
B
GLU
334
n
129
GLU
334
B
TRP
335
n
130
TRP
335
B
ALA
336
n
131
ALA
336
B
HIS
337
n
132
HIS
337
B
GLY
338
n
133
GLY
338
B
GLY
339
n
134
GLY
339
B
PHE
340
n
135
PHE
340
B
LYS
341
n
136
LYS
341
B
PRO
342
n
137
PRO
342
B
THR
343
n
138
THR
343
B
GLY
344
n
139
GLY
344
B
ILE
345
n
140
ILE
345
B
GLU
346
n
141
GLU
346
B
GLY
347
n
142
GLY
347
B
LEU
348
n
143
LEU
348
B
LYS
349
n
144
LYS
349
B
PRO
350
n
145
PRO
350
B
ASN
351
n
146
ASN
351
B
n
147
352
B
n
148
353
B
n
149
354
B
n
150
355
B
author_and_software_defined_assembly
PISA
2
dimeric
none
2650
-107
14190
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
VAL
272
A
O
VAL
67
A
N
ARG
259
A
N
ARG
54
A
O
GLN
262
A
O
GLN
57
A
N
MET
242
A
N
MET
37
A
O
TRP
239
A
O
TRP
34
A
N
GLY
231
A
N
GLY
26
A
N
TRP
230
A
N
TRP
25
A
O
VAL
278
A
O
VAL
73
B
O
VAL
272
B
O
VAL
67
B
N
ARG
259
B
N
ARG
54
B
O
GLN
262
B
O
GLN
57
B
N
MET
242
B
N
MET
37
B
O
ALA
241
B
O
ALA
36
B
N
VAL
229
B
N
VAL
24
B
N
TRP
230
B
N
TRP
25
B
O
VAL
278
B
O
VAL
73
1
B
SO4
405
M
SO4
1
A
GLU
206
A
GLU
1
1
Y
1
A
ALA
207
A
ALA
2
1
Y
1
A
ASP
208
A
ASP
3
1
Y
1
A
SER
209
A
SER
4
1
Y
1
A
GLY
210
A
GLY
5
1
Y
1
A
ASP
211
A
ASP
6
1
Y
1
A
GLY
212
A
GLY
7
1
Y
1
A
ASP
213
A
ASP
8
1
Y
1
A
SER
214
A
SER
9
1
Y
1
A
SER
320
A
SER
115
1
Y
1
A
PRO
321
A
PRO
116
1
Y
1
A
GLY
322
A
GLY
117
1
Y
1
A
ASP
323
A
ASP
118
1
Y
1
A
ASN
352
A
ASN
147
1
Y
1
A
THR
353
A
THR
148
1
Y
1
A
GLN
354
A
GLN
149
1
Y
1
A
PRO
355
A
PRO
150
1
Y
1
B
GLU
206
B
GLU
1
1
Y
1
B
ALA
207
B
ALA
2
1
Y
1
B
ASP
208
B
ASP
3
1
Y
1
B
SER
209
B
SER
4
1
Y
1
B
GLY
210
B
GLY
5
1
Y
1
B
ASP
211
B
ASP
6
1
Y
1
B
GLY
212
B
GLY
7
1
Y
1
B
ASP
213
B
ASP
8
1
Y
1
B
SER
214
B
SER
9
1
Y
1
B
SER
320
B
SER
115
1
Y
1
B
PRO
321
B
PRO
116
1
Y
1
B
GLY
322
B
GLY
117
1
Y
1
B
ASP
323
B
ASP
118
1
Y
1
B
ASN
352
B
ASN
147
1
Y
1
B
THR
353
B
THR
148
1
Y
1
B
GLN
354
B
GLN
149
1
Y
1
B
PRO
355
B
PRO
150
1
Y
1
A
A
O
O
ALA
HOH
248
501
2.15
1
A
PHE
223
75.98
123.02
1
A
LYS
251
-113.97
-94.92
1
A
LEU
325
-99.07
-61.37
1
B
LYS
221
-63.31
-170.14
1
B
PHE
223
75.44
119.50
1
B
LYS
251
-131.92
-127.11
1
B
LEU
325
-85.25
-77.20
98.860
51.3900
25.520
0.2435
0.1944
0.1968
2.3990
40.9160
1027
20539
5.0000
99.8200
0.3100
1
FREE R-VALUE
1.360
MOLECULAR REPLACEMENT
26.5300
0.9000
1.1100
3QKJ
2.3990
40.9160
73
2270
61.69
48.73
69
0
2128
266
0.008
2250
1.211
3022
0.079
292
0.006
366
14.909
800
0.3320
0.0000
0.2882
2.5253
142
2694
2836
7
99.0000
0.3355
0.0000
0.2599
2.6835
145
2760
2905
7
100.0000
0.2945
0.0000
0.2558
2.8906
144
2731
2875
7
100.0000
0.3017
0.0000
0.2507
3.1814
146
2766
2912
7
100.0000
0.3195
0.0000
0.2119
3.6415
145
2781
2926
7
100.0000
0.2403
0.0000
0.1714
4.5870
149
2829
2978
7
100.0000
0.1783
0.0000
0.1651
40.9217
156
2951
3107
7
100.0000
66.450
2.399
40.916
5NV0
20558
1.0
0.041
1
31.99
9.7
99.9
0.88
2.40
2.54
2.68
3229
0.9
1
9.8
99.5
data scaling
XSCALE
refinement
PHENIX
1.8.1_1168
data extraction
PDB_EXTRACT
3.22
data reduction
XDS
phasing
PHASER
N
Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
SER
245
A
SER
40
HELX_P
A
THR
249
A
THR
44
5
AA1
5
A
ASN
288
A
ASN
83
HELX_P
A
LEU
295
A
LEU
90
1
AA2
8
A
LEU
295
A
LEU
90
HELX_P
A
GLY
314
A
GLY
109
1
AA3
20
A
LEU
325
A
LEU
120
HELX_P
A
GLY
338
A
GLY
133
1
AA4
14
A
GLY
344
A
GLY
139
HELX_P
A
LYS
349
A
LYS
144
5
AA5
6
B
SER
245
B
SER
40
HELX_P
B
THR
249
B
THR
44
5
AA6
5
B
LEU
282
B
LEU
77
HELX_P
B
PHE
287
B
PHE
82
1
AA7
6
B
ASN
288
B
ASN
83
HELX_P
B
LEU
295
B
LEU
90
1
AA8
8
B
LEU
295
B
LEU
90
HELX_P
B
GLY
314
B
GLY
109
1
AA9
20
B
LEU
325
B
LEU
120
HELX_P
B
GLY
338
B
GLY
133
1
AB1
14
B
THR
343
B
THR
138
HELX_P
B
LYS
349
B
LYS
144
5
AB2
7
TRANSFERASE
DNMT3B PWWP DOMAIN, HISTONE BINDING, BETA BARREL, LIGAND, TRANSFERASE
A
LYS
341
A
LYS
136
1
A
PRO
342
A
PRO
137
9.64
B
LYS
341
B
LYS
136
1
B
PRO
342
B
PRO
137
9.30
DNM3B_HUMAN
UNP
1
206
Q9UBC3
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQ
HFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
206
355
5NV0
206
355
Q9UBC3
A
1
1
150
206
355
5NV0
206
355
Q9UBC3
B
1
1
150
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
PHE
269
A
PHE
64
A
SER
273
A
SER
68
A
MET
258
A
MET
53
A
TRP
263
A
TRP
58
A
TRP
239
A
TRP
34
A
VAL
244
A
VAL
39
A
LEU
228
A
LEU
23
A
GLY
231
A
GLY
26
A
LEU
277
A
LEU
72
A
ALA
279
A
ALA
74
B
PHE
269
B
PHE
64
B
SER
273
B
SER
68
B
MET
258
B
MET
53
B
TRP
263
B
TRP
58
B
TRP
239
B
TRP
34
B
VAL
244
B
VAL
39
B
LEU
228
B
LEU
23
B
GLY
231
B
GLY
26
B
LEU
277
B
LEU
72
B
ALA
279
B
ALA
74
binding site for residue 9AH A 401
A
9AH
401
Software
7
binding site for residue SO4 A 402
A
SO4
402
Software
5
binding site for residue SO4 A 403
A
SO4
403
Software
3
binding site for residue SO4 A 404
A
SO4
404
Software
3
binding site for residue SO4 A 405
A
SO4
405
Software
3
binding site for residue SO4 A 406
A
SO4
406
Software
2
binding site for residue 9AH B 401
B
9AH
401
Software
5
binding site for residue SO4 B 402
B
SO4
402
Software
2
binding site for residue SO4 B 403
B
SO4
403
Software
2
binding site for residue SO4 B 404
B
SO4
404
Software
3
binding site for residue SO4 B 405
B
SO4
405
Software
2
A
ILE
233
A
ILE
28
7
1_555
A
PHE
236
A
PHE
31
7
1_555
A
TRP
239
A
TRP
34
7
1_555
A
TRP
263
A
TRP
58
7
1_555
A
ASP
266
A
ASP
61
7
1_555
A
SER
297
A
SER
92
7
1_555
A
HOH
532
N
HOH
7
1_555
A
LYS
251
A
LYS
46
5
1_555
A
ARG
252
A
ARG
47
5
1_555
A
SO4
405
G
SO4
5
1_555
A
HOH
530
N
HOH
5
1_555
B
HIS
304
B
HIS
99
5
1_555
A
LYS
308
A
LYS
103
3
1_555
A
ARG
312
A
ARG
107
3
1_555
A
ASN
351
A
ASN
146
3
1_555
A
LYS
232
A
LYS
27
3
1_555
A
LYS
234
A
LYS
29
3
1_555
A
GLY
235
A
GLY
30
3
1_555
A
LYS
251
A
LYS
46
3
1_555
A
ARG
252
A
ARG
47
3
1_555
A
SO4
402
D
SO4
3
1_555
A
LYS
276
A
LYS
71
2
1_555
B
ARG
310
B
ARG
105
2
1_555
B
ILE
233
B
ILE
28
5
1_555
B
TRP
239
B
TRP
34
5
1_555
B
TRP
263
B
TRP
58
5
1_555
B
ASP
266
B
ASP
61
5
1_555
B
SER
297
B
SER
92
5
1_555
A
ARG
310
A
ARG
105
2
4_655
B
LYS
276
B
LYS
71
2
1_555
B
LYS
251
B
LYS
46
2
1_555
B
ARG
252
B
ARG
47
2
1_555
B
LYS
308
B
LYS
103
3
1_555
B
ARG
312
B
ARG
107
3
1_555
B
ASN
351
B
ASN
146
3
1_555
B
TRP
238
B
TRP
33
2
1_555
B
TRP
238
B
TRP
33
2
5_555
154
P 32 2 1