0.012437
0.007180
0.000000
0.000000
0.014361
0.000000
0.000000
0.000000
0.009428
0.00000
0.00000
0.00000
Decroos, C.
Bowman, C.B.
Moser, J.-A.S.
Christianson, K.E.
Deardorff, M.A.
Christianson, D.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
80.406
80.406
106.063
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C8 H16 N2 O3
188.224
n
N(6)-ACETYLLYSINE
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
K 1
39.098
POTASSIUM ION
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C10 H9 N O2
175.184
7-AMINO-4-METHYL-CHROMEN-2-ONE
7-AMINO-4-METHYLCOUMARIN
non-polymer
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
Zn 2
65.409
ZINC ION
non-polymer
N
1
N
C
N
2
N
O
N
3
N
C
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
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
O
N
22
N
C
N
23
N
C
N
24
N
N
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
C
N
29
S
C
N
30
N
N
N
31
N
C
N
32
N
O
N
33
N
O
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
N
N
51
S
C
N
52
N
C
N
53
N
O
N
54
N
C
N
55
N
C
N
56
N
C
N
57
N
N
N
58
N
C
N
59
N
N
N
60
N
N
N
61
N
O
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
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
N
N
78
S
C
N
79
N
C
N
80
N
O
N
81
N
C
N
82
N
C
N
83
N
O
N
84
N
N
N
85
N
O
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
O
N
101
N
O
N
102
N
O
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
N
N
111
R
C
N
112
N
C
N
113
N
O
N
114
N
C
N
115
N
S
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
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
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
O
N
153
N
O
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
N
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
C
N
174
N
O
N
175
N
C
N
176
N
O
N
177
N
C
N
178
N
O
N
179
N
H
N
180
N
H
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
N
N
188
S
C
N
189
N
C
N
190
N
O
N
191
N
C
Y
192
N
C
Y
193
N
N
Y
194
N
C
Y
195
N
C
Y
196
N
N
N
197
N
O
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
H
N
206
N
H
N
207
N
H
N
208
N
O
N
209
N
H
N
210
N
H
N
211
N
N
N
212
S
C
N
213
N
C
N
214
N
O
N
215
S
C
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
O
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
H
N
231
N
H
N
232
N
H
N
233
N
K
N
234
N
N
N
235
S
C
N
236
N
C
N
237
N
O
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
O
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
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
N
N
257
S
C
N
258
N
C
N
259
N
O
N
260
N
C
N
261
N
C
N
262
N
C
N
263
N
C
N
264
N
N
N
265
N
O
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
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
N
Y
282
N
C
Y
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
N
291
N
C
Y
292
N
O
N
293
N
O
N
294
N
H
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
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
S
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
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
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
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
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
C
N
352
N
C
N
353
N
O
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
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
N
368
N
O
N
369
N
O
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
N
N
378
S
C
N
379
N
C
N
380
N
O
N
381
R
C
N
382
N
O
N
383
N
C
N
384
N
O
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
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
N
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
N
408
N
O
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
N
N
422
S
C
N
423
N
C
N
424
N
O
N
425
N
C
Y
426
N
C
Y
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
C
N
432
N
O
N
433
N
O
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
N
N
446
S
C
N
447
N
C
N
448
N
O
N
449
N
C
N
450
N
C
N
451
N
C
N
452
N
O
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
ZN
N
1
N
doub
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
sing
N
12
N
sing
N
13
N
doub
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
sing
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
doub
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
doub
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
doub
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
doub
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
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
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
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
sing
N
110
N
doub
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
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
doub
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
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
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
doub
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
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
Y
187
N
sing
Y
188
N
doub
Y
189
N
doub
N
190
N
sing
Y
191
N
sing
N
192
N
sing
Y
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
doub
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
sing
N
225
N
sing
N
226
N
doub
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
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
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
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
Y
268
N
doub
Y
269
N
sing
Y
270
N
sing
N
271
N
sing
Y
272
N
doub
Y
273
N
sing
Y
274
N
sing
Y
275
N
sing
N
276
N
doub
Y
277
N
doub
N
278
N
sing
Y
279
N
sing
N
280
N
sing
Y
281
N
sing
Y
282
N
doub
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
doub
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
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
doub
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
Y
318
N
doub
Y
319
N
sing
Y
320
N
sing
N
321
N
sing
Y
322
N
doub
N
323
N
sing
Y
324
N
doub
N
325
N
sing
Y
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
sing
N
335
N
sing
N
336
N
doub
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
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
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
sing
N
365
N
sing
N
366
N
doub
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
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
doub
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
Y
387
N
doub
Y
388
N
sing
Y
389
N
sing
N
390
N
sing
Y
391
N
doub
Y
392
N
sing
Y
393
N
sing
N
394
N
sing
Y
395
N
sing
Y
396
N
doub
N
397
N
sing
Y
398
N
doub
N
399
N
sing
Y
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
doub
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
Y
415
N
doub
Y
416
N
sing
Y
417
N
sing
N
418
N
sing
Y
419
N
doub
N
420
N
sing
Y
421
N
doub
N
422
N
sing
Y
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
doub
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
US
Acs Chem.Biol.
1554-8929
9
2157
2164
10.1021/cb5003762
25075551
Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders.
2014
10.2210/pdb4qa7/pdb
pdb_00004qa7
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
2013-08-13
ADSC QUANTUM 315r
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.075
1.0
X29A
NSLS
1.075
SYNCHROTRON
NSLS BEAMLINE X29A
43235.043
Histone deacetylase 8
3.5.1.98
1
man
polymer
679.811
tetrapeptide substrate
1
syn
polymer
65.409
ZINC ION
1
syn
non-polymer
39.098
POTASSIUM ION
2
syn
non-polymer
175.184
7-AMINO-4-METHYL-CHROMEN-2-ONE
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
49
nat
water
HD8
no
no
MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQ
KVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVL
GILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKY
YQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTG
VILGKTLSSEIPDREFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQ
KVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVL
GILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKY
YQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTG
VILGKTLSSEIPDREFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
A
polypeptide(L)
no
yes
(ACE)RH(ALY)(ALY)
XRHKK
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
HDAC8, HDACL1, CDA07
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
plasmid
pHD2-Xa-His
1
2.25
45.42
VAPOR DIFFUSION, SITTING DROP
8.0
0.1 M tris(hydroxymethyl)aminomethane) (TRIS, pH = 8.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 17.5% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
294
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
struct_conn
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
Data collection
Derived calculations
1
0
2014-08-06
1
1
2014-10-01
1
2
2023-09-20
1
3
2023-12-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2014-05-02
REL
REL
ZN
ZINC ION
K
POTASSIUM ION
MCM
7-AMINO-4-METHYL-CHROMEN-2-ONE
GOL
GLYCEROL
HOH
water
synthetic peptide
sample
3EWF
PDB ENTRY 3EWF
PDB
experimental model
ZN
401
3
ZN
ZN
401
A
K
411
4
K
K
402
A
K
412
4
K
K
403
A
MCM
506
5
MCM
MCM
601
B
GOL
201
6
GOL
GOL
602
B
HOH
1
7
HOH
HOH
501
A
HOH
2
7
HOH
HOH
502
A
HOH
3
7
HOH
HOH
503
A
HOH
4
7
HOH
HOH
504
A
HOH
5
7
HOH
HOH
505
A
HOH
6
7
HOH
HOH
506
A
HOH
7
7
HOH
HOH
507
A
HOH
8
7
HOH
HOH
508
A
HOH
9
7
HOH
HOH
509
A
HOH
10
7
HOH
HOH
510
A
HOH
11
7
HOH
HOH
511
A
HOH
12
7
HOH
HOH
512
A
HOH
13
7
HOH
HOH
513
A
HOH
14
7
HOH
HOH
514
A
HOH
15
7
HOH
HOH
515
A
HOH
16
7
HOH
HOH
516
A
HOH
17
7
HOH
HOH
517
A
HOH
18
7
HOH
HOH
518
A
HOH
19
7
HOH
HOH
519
A
HOH
20
7
HOH
HOH
520
A
HOH
21
7
HOH
HOH
521
A
HOH
22
7
HOH
HOH
522
A
HOH
23
7
HOH
HOH
523
A
HOH
24
7
HOH
HOH
524
A
HOH
25
7
HOH
HOH
525
A
HOH
26
7
HOH
HOH
526
A
HOH
27
7
HOH
HOH
527
A
HOH
28
7
HOH
HOH
528
A
HOH
29
7
HOH
HOH
529
A
HOH
30
7
HOH
HOH
530
A
HOH
31
7
HOH
HOH
531
A
HOH
32
7
HOH
HOH
532
A
HOH
33
7
HOH
HOH
533
A
HOH
34
7
HOH
HOH
534
A
HOH
36
7
HOH
HOH
535
A
HOH
37
7
HOH
HOH
536
A
HOH
39
7
HOH
HOH
537
A
HOH
40
7
HOH
HOH
538
A
HOH
41
7
HOH
HOH
539
A
HOH
42
7
HOH
HOH
540
A
HOH
43
7
HOH
HOH
541
A
HOH
44
7
HOH
HOH
542
A
HOH
45
7
HOH
HOH
543
A
HOH
47
7
HOH
HOH
544
A
HOH
48
7
HOH
HOH
545
A
HOH
49
7
HOH
HOH
546
A
HOH
35
7
HOH
HOH
701
B
HOH
38
7
HOH
HOH
702
B
HOH
46
7
HOH
HOH
703
B
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
n
9
9
A
n
10
10
A
n
11
11
A
n
12
12
A
SER
13
n
13
SER
13
A
LEU
14
n
14
LEU
14
A
VAL
15
n
15
VAL
15
A
PRO
16
n
16
PRO
16
A
VAL
17
n
17
VAL
17
A
TYR
18
n
18
TYR
18
A
ILE
19
n
19
ILE
19
A
TYR
20
n
20
TYR
20
A
SER
21
n
21
SER
21
A
PRO
22
n
22
PRO
22
A
GLU
23
n
23
GLU
23
A
TYR
24
n
24
TYR
24
A
VAL
25
n
25
VAL
25
A
SER
26
n
26
SER
26
A
MET
27
n
27
MET
27
A
CYS
28
n
28
CYS
28
A
ASP
29
n
29
ASP
29
A
SER
30
n
30
SER
30
A
LEU
31
n
31
LEU
31
A
ALA
32
n
32
ALA
32
A
LYS
33
n
33
LYS
33
A
ILE
34
n
34
ILE
34
A
PRO
35
n
35
PRO
35
A
LYS
36
n
36
LYS
36
A
ARG
37
n
37
ARG
37
A
ALA
38
n
38
ALA
38
A
SER
39
n
39
SER
39
A
MET
40
n
40
MET
40
A
VAL
41
n
41
VAL
41
A
HIS
42
n
42
HIS
42
A
SER
43
n
43
SER
43
A
LEU
44
n
44
LEU
44
A
ILE
45
n
45
ILE
45
A
GLU
46
n
46
GLU
46
A
ALA
47
n
47
ALA
47
A
TYR
48
n
48
TYR
48
A
ALA
49
n
49
ALA
49
A
LEU
50
n
50
LEU
50
A
HIS
51
n
51
HIS
51
A
LYS
52
n
52
LYS
52
A
GLN
53
n
53
GLN
53
A
MET
54
n
54
MET
54
A
ARG
55
n
55
ARG
55
A
ILE
56
n
56
ILE
56
A
VAL
57
n
57
VAL
57
A
LYS
58
n
58
LYS
58
A
PRO
59
n
59
PRO
59
A
LYS
60
n
60
LYS
60
A
VAL
61
n
61
VAL
61
A
ALA
62
n
62
ALA
62
A
SER
63
n
63
SER
63
A
MET
64
n
64
MET
64
A
GLU
65
n
65
GLU
65
A
GLU
66
n
66
GLU
66
A
MET
67
n
67
MET
67
A
ALA
68
n
68
ALA
68
A
THR
69
n
69
THR
69
A
PHE
70
n
70
PHE
70
A
HIS
71
n
71
HIS
71
A
THR
72
n
72
THR
72
A
ASP
73
n
73
ASP
73
A
ALA
74
n
74
ALA
74
A
TYR
75
n
75
TYR
75
A
LEU
76
n
76
LEU
76
A
GLN
77
n
77
GLN
77
A
HIS
78
n
78
HIS
78
A
LEU
79
n
79
LEU
79
A
GLN
80
n
80
GLN
80
A
LYS
81
n
81
LYS
81
A
VAL
82
n
82
VAL
82
A
SER
83
n
83
SER
83
A
GLN
84
n
84
GLN
84
A
GLU
85
n
85
GLU
85
A
GLY
86
n
86
GLY
86
A
ASP
87
n
87
ASP
87
A
ASP
88
n
88
ASP
88
A
ASP
89
n
89
ASP
89
A
HIS
90
n
90
HIS
90
A
PRO
91
n
91
PRO
91
A
ASP
92
n
92
ASP
92
A
SER
93
n
93
SER
93
A
ILE
94
n
94
ILE
94
A
GLU
95
n
95
GLU
95
A
TYR
96
n
96
TYR
96
A
GLY
97
n
97
GLY
97
A
LEU
98
n
98
LEU
98
A
GLY
99
n
99
GLY
99
A
TYR
100
n
100
TYR
100
A
ASP
101
n
101
ASP
101
A
CYS
102
n
102
CYS
102
A
PRO
103
n
103
PRO
103
A
ALA
104
n
104
ALA
104
A
THR
105
n
105
THR
105
A
GLU
106
n
106
GLU
106
A
GLY
107
n
107
GLY
107
A
ILE
108
n
108
ILE
108
A
PHE
109
n
109
PHE
109
A
ASP
110
n
110
ASP
110
A
TYR
111
n
111
TYR
111
A
ALA
112
n
112
ALA
112
A
ALA
113
n
113
ALA
113
A
ALA
114
n
114
ALA
114
A
ILE
115
n
115
ILE
115
A
GLY
116
n
116
GLY
116
A
GLY
117
n
117
GLY
117
A
ALA
118
n
118
ALA
118
A
THR
119
n
119
THR
119
A
ILE
120
n
120
ILE
120
A
THR
121
n
121
THR
121
A
ALA
122
n
122
ALA
122
A
ALA
123
n
123
ALA
123
A
GLN
124
n
124
GLN
124
A
CYS
125
n
125
CYS
125
A
LEU
126
n
126
LEU
126
A
ILE
127
n
127
ILE
127
A
ASP
128
n
128
ASP
128
A
GLY
129
n
129
GLY
129
A
MET
130
n
130
MET
130
A
CYS
131
n
131
CYS
131
A
LYS
132
n
132
LYS
132
A
VAL
133
n
133
VAL
133
A
ALA
134
n
134
ALA
134
A
ILE
135
n
135
ILE
135
A
ASN
136
n
136
ASN
136
A
TRP
137
n
137
TRP
137
A
SER
138
n
138
SER
138
A
GLY
139
n
139
GLY
139
A
GLY
140
n
140
GLY
140
A
TRP
141
n
141
TRP
141
A
HIS
142
n
142
HIS
142
A
HIS
143
n
143
HIS
143
A
ALA
144
n
144
ALA
144
A
LYS
145
n
145
LYS
145
A
LYS
146
n
146
LYS
146
A
ASP
147
n
147
ASP
147
A
GLU
148
n
148
GLU
148
A
ALA
149
n
149
ALA
149
A
SER
150
n
150
SER
150
A
GLY
151
n
151
GLY
151
A
PHE
152
n
152
PHE
152
A
CYS
153
n
153
CYS
153
A
TYR
154
n
154
TYR
154
A
LEU
155
n
155
LEU
155
A
ASN
156
n
156
ASN
156
A
ASP
157
n
157
ASP
157
A
ALA
158
n
158
ALA
158
A
VAL
159
n
159
VAL
159
A
LEU
160
n
160
LEU
160
A
GLY
161
n
161
GLY
161
A
ILE
162
n
162
ILE
162
A
LEU
163
n
163
LEU
163
A
ARG
164
n
164
ARG
164
A
LEU
165
n
165
LEU
165
A
ARG
166
n
166
ARG
166
A
ARG
167
n
167
ARG
167
A
LYS
168
n
168
LYS
168
A
PHE
169
n
169
PHE
169
A
GLU
170
n
170
GLU
170
A
ARG
171
n
171
ARG
171
A
ILE
172
n
172
ILE
172
A
LEU
173
n
173
LEU
173
A
TYR
174
n
174
TYR
174
A
VAL
175
n
175
VAL
175
A
ASP
176
n
176
ASP
176
A
LEU
177
n
177
LEU
177
A
ASP
178
n
178
ASP
178
A
LEU
179
n
179
LEU
179
A
HIS
180
n
180
HIS
180
A
HIS
181
n
181
HIS
181
A
GLY
182
n
182
GLY
182
A
ASP
183
n
183
ASP
183
A
GLY
184
n
184
GLY
184
A
VAL
185
n
185
VAL
185
A
GLU
186
n
186
GLU
186
A
ASP
187
n
187
ASP
187
A
ALA
188
n
188
ALA
188
A
PHE
189
n
189
PHE
189
A
SER
190
n
190
SER
190
A
PHE
191
n
191
PHE
191
A
THR
192
n
192
THR
192
A
SER
193
n
193
SER
193
A
LYS
194
n
194
LYS
194
A
VAL
195
n
195
VAL
195
A
MET
196
n
196
MET
196
A
THR
197
n
197
THR
197
A
VAL
198
n
198
VAL
198
A
SER
199
n
199
SER
199
A
LEU
200
n
200
LEU
200
A
HIS
201
n
201
HIS
201
A
LYS
202
n
202
LYS
202
A
PHE
203
n
203
PHE
203
A
SER
204
n
204
SER
204
A
PRO
205
n
205
PRO
205
A
GLY
206
n
206
GLY
206
A
PHE
207
n
207
PHE
207
A
PHE
208
n
208
PHE
208
A
PRO
209
n
209
PRO
209
A
GLY
210
n
210
GLY
210
A
THR
211
n
211
THR
211
A
GLY
212
n
212
GLY
212
A
ASP
213
n
213
ASP
213
A
VAL
214
n
214
VAL
214
A
SER
215
n
215
SER
215
A
ASP
216
n
216
ASP
216
A
VAL
217
n
217
VAL
217
A
GLY
218
n
218
GLY
218
A
LEU
219
n
219
LEU
219
A
GLY
220
n
220
GLY
220
A
LYS
221
n
221
LYS
221
A
GLY
222
n
222
GLY
222
A
ARG
223
n
223
ARG
223
A
TYR
224
n
224
TYR
224
A
TYR
225
n
225
TYR
225
A
SER
226
n
226
SER
226
A
VAL
227
n
227
VAL
227
A
ASN
228
n
228
ASN
228
A
VAL
229
n
229
VAL
229
A
PRO
230
n
230
PRO
230
A
ILE
231
n
231
ILE
231
A
GLN
232
n
232
GLN
232
A
ASP
233
n
233
ASP
233
A
GLY
234
n
234
GLY
234
A
ILE
235
n
235
ILE
235
A
GLN
236
n
236
GLN
236
A
ASP
237
n
237
ASP
237
A
GLU
238
n
238
GLU
238
A
LYS
239
n
239
LYS
239
A
TYR
240
n
240
TYR
240
A
TYR
241
n
241
TYR
241
A
GLN
242
n
242
GLN
242
A
ILE
243
n
243
ILE
243
A
CYS
244
n
244
CYS
244
A
GLU
245
n
245
GLU
245
A
SER
246
n
246
SER
246
A
VAL
247
n
247
VAL
247
A
LEU
248
n
248
LEU
248
A
LYS
249
n
249
LYS
249
A
GLU
250
n
250
GLU
250
A
VAL
251
n
251
VAL
251
A
TYR
252
n
252
TYR
252
A
GLN
253
n
253
GLN
253
A
ALA
254
n
254
ALA
254
A
PHE
255
n
255
PHE
255
A
ASN
256
n
256
ASN
256
A
PRO
257
n
257
PRO
257
A
LYS
258
n
258
LYS
258
A
ALA
259
n
259
ALA
259
A
VAL
260
n
260
VAL
260
A
VAL
261
n
261
VAL
261
A
LEU
262
n
262
LEU
262
A
GLN
263
n
263
GLN
263
A
LEU
264
n
264
LEU
264
A
GLY
265
n
265
GLY
265
A
ALA
266
n
266
ALA
266
A
ASP
267
n
267
ASP
267
A
THR
268
n
268
THR
268
A
ILE
269
n
269
ILE
269
A
ALA
270
n
270
ALA
270
A
GLY
271
n
271
GLY
271
A
ASP
272
n
272
ASP
272
A
PRO
273
n
273
PRO
273
A
MET
274
n
274
MET
274
A
CYS
275
n
275
CYS
275
A
SER
276
n
276
SER
276
A
PHE
277
n
277
PHE
277
A
ASN
278
n
278
ASN
278
A
MET
279
n
279
MET
279
A
THR
280
n
280
THR
280
A
PRO
281
n
281
PRO
281
A
VAL
282
n
282
VAL
282
A
GLY
283
n
283
GLY
283
A
ILE
284
n
284
ILE
284
A
GLY
285
n
285
GLY
285
A
LYS
286
n
286
LYS
286
A
CYS
287
n
287
CYS
287
A
LEU
288
n
288
LEU
288
A
LYS
289
n
289
LYS
289
A
TYR
290
n
290
TYR
290
A
ILE
291
n
291
ILE
291
A
LEU
292
n
292
LEU
292
A
GLN
293
n
293
GLN
293
A
TRP
294
n
294
TRP
294
A
GLN
295
n
295
GLN
295
A
LEU
296
n
296
LEU
296
A
ALA
297
n
297
ALA
297
A
THR
298
n
298
THR
298
A
LEU
299
n
299
LEU
299
A
ILE
300
n
300
ILE
300
A
LEU
301
n
301
LEU
301
A
GLY
302
n
302
GLY
302
A
GLY
303
n
303
GLY
303
A
GLY
304
n
304
GLY
304
A
GLY
305
n
305
GLY
305
A
PHE
306
n
306
PHE
306
A
ASN
307
n
307
ASN
307
A
LEU
308
n
308
LEU
308
A
ALA
309
n
309
ALA
309
A
ASN
310
n
310
ASN
310
A
THR
311
n
311
THR
311
A
ALA
312
n
312
ALA
312
A
ARG
313
n
313
ARG
313
A
CYS
314
n
314
CYS
314
A
TRP
315
n
315
TRP
315
A
THR
316
n
316
THR
316
A
TYR
317
n
317
TYR
317
A
LEU
318
n
318
LEU
318
A
THR
319
n
319
THR
319
A
GLY
320
n
320
GLY
320
A
VAL
321
n
321
VAL
321
A
ILE
322
n
322
ILE
322
A
LEU
323
n
323
LEU
323
A
GLY
324
n
324
GLY
324
A
LYS
325
n
325
LYS
325
A
THR
326
n
326
THR
326
A
LEU
327
n
327
LEU
327
A
SER
328
n
328
SER
328
A
SER
329
n
329
SER
329
A
GLU
330
n
330
GLU
330
A
ILE
331
n
331
ILE
331
A
PRO
332
n
332
PRO
332
A
ASP
333
n
333
ASP
333
A
ARG
334
n
334
ARG
334
A
GLU
335
n
335
GLU
335
A
PHE
336
n
336
PHE
336
A
PHE
337
n
337
PHE
337
A
THR
338
n
338
THR
338
A
ALA
339
n
339
ALA
339
A
TYR
340
n
340
TYR
340
A
GLY
341
n
341
GLY
341
A
PRO
342
n
342
PRO
342
A
ASP
343
n
343
ASP
343
A
TYR
344
n
344
TYR
344
A
VAL
345
n
345
VAL
345
A
LEU
346
n
346
LEU
346
A
GLU
347
n
347
GLU
347
A
ILE
348
n
348
ILE
348
A
THR
349
n
349
THR
349
A
PRO
350
n
350
PRO
350
A
SER
351
n
351
SER
351
A
CYS
352
n
352
CYS
352
A
ARG
353
n
353
ARG
353
A
PRO
354
n
354
PRO
354
A
ASP
355
n
355
ASP
355
A
ARG
356
n
356
ARG
356
A
ASN
357
n
357
ASN
357
A
GLU
358
n
358
GLU
358
A
PRO
359
n
359
PRO
359
A
HIS
360
n
360
HIS
360
A
ARG
361
n
361
ARG
361
A
ILE
362
n
362
ILE
362
A
GLN
363
n
363
GLN
363
A
GLN
364
n
364
GLN
364
A
ILE
365
n
365
ILE
365
A
LEU
366
n
366
LEU
366
A
ASN
367
n
367
ASN
367
A
TYR
368
n
368
TYR
368
A
ILE
369
n
369
ILE
369
A
LYS
370
n
370
LYS
370
A
GLY
371
n
371
GLY
371
A
ASN
372
n
372
ASN
372
A
LEU
373
n
373
LEU
373
A
LYS
374
n
374
LYS
374
A
HIS
375
n
375
HIS
375
A
VAL
376
n
376
VAL
376
A
VAL
377
n
377
VAL
377
A
n
378
378
A
n
379
379
A
n
380
380
A
n
381
381
A
n
382
382
A
n
383
383
A
n
384
384
A
n
385
385
A
n
386
386
A
n
387
387
A
n
388
388
A
n
389
389
A
ACE
501
n
1
ACE
501
B
ARG
502
n
2
ARG
502
B
HIS
503
n
3
HIS
503
B
ALY
504
n
4
ALY
504
B
ALY
505
n
5
ALY
505
B
author_and_software_defined_assembly
PISA
2
dimeric
2020
-42
14580
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
A
ASP
176
A
O
ASP
176
1_555
72.7
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
A
ASP
178
A
O
ASP
178
1_555
105.2
A
ASP
176
A
O
ASP
176
1_555
A
K
402
D
K
K
1_555
A
ASP
178
A
O
ASP
178
1_555
105.1
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
A
HIS
180
A
O
HIS
180
1_555
91.8
A
ASP
176
A
O
ASP
176
1_555
A
K
402
D
K
K
1_555
A
HIS
180
A
O
HIS
180
1_555
164.1
A
ASP
178
A
O
ASP
178
1_555
A
K
402
D
K
K
1_555
A
HIS
180
A
O
HIS
180
1_555
81.8
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
A
SER
199
A
OG
SER
199
1_555
104.0
A
ASP
176
A
O
ASP
176
1_555
A
K
402
D
K
K
1_555
A
SER
199
A
OG
SER
199
1_555
85.7
A
ASP
178
A
O
ASP
178
1_555
A
K
402
D
K
K
1_555
A
SER
199
A
OG
SER
199
1_555
150.7
A
HIS
180
A
O
HIS
180
1_555
A
K
402
D
K
K
1_555
A
SER
199
A
OG
SER
199
1_555
95.1
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
A
LEU
200
A
O
LEU
200
1_555
142.3
A
ASP
176
A
O
ASP
176
1_555
A
K
402
D
K
K
1_555
A
LEU
200
A
O
LEU
200
1_555
75.8
A
ASP
178
A
O
ASP
178
1_555
A
K
402
D
K
K
1_555
A
LEU
200
A
O
LEU
200
1_555
63.8
A
HIS
180
A
O
HIS
180
1_555
A
K
402
D
K
K
1_555
A
LEU
200
A
O
LEU
200
1_555
119.9
A
SER
199
A
OG
SER
199
1_555
A
K
402
D
K
K
1_555
A
LEU
200
A
O
LEU
200
1_555
93.7
A
ASP
178
A
OD1
ASP
178
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HIS
180
A
ND1
HIS
180
1_555
102.9
A
ASP
178
A
OD1
ASP
178
1_555
A
ZN
401
C
ZN
ZN
1_555
A
ASP
267
A
OD2
ASP
267
1_555
95.3
A
HIS
180
A
ND1
HIS
180
1_555
A
ZN
401
C
ZN
ZN
1_555
A
ASP
267
A
OD2
ASP
267
1_555
90.3
A
ASP
178
A
OD1
ASP
178
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HOH
522
H
O
HOH
1_555
84.5
A
HIS
180
A
ND1
HIS
180
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HOH
522
H
O
HOH
1_555
99.5
A
ASP
267
A
OD2
ASP
267
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HOH
522
H
O
HOH
1_555
170.0
A
ASP
178
A
OD1
ASP
178
1_555
A
ZN
401
C
ZN
ZN
1_555
B
ALY
505
B
OH
ALY
5
1_555
147.6
A
HIS
180
A
ND1
HIS
180
1_555
A
ZN
401
C
ZN
ZN
1_555
B
ALY
505
B
OH
ALY
5
1_555
107.8
A
ASP
267
A
OD2
ASP
267
1_555
A
ZN
401
C
ZN
ZN
1_555
B
ALY
505
B
OH
ALY
5
1_555
94.5
A
HOH
522
H
O
HOH
1_555
A
ZN
401
C
ZN
ZN
1_555
B
ALY
505
B
OH
ALY
5
1_555
80.7
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
A
THR
192
A
O
THR
192
1_555
74.2
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
A
VAL
195
A
O
VAL
195
1_555
105.1
A
THR
192
A
O
THR
192
1_555
A
K
403
E
K
K
1_555
A
VAL
195
A
O
VAL
195
1_555
84.0
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
A
TYR
225
A
O
TYR
225
1_555
157.8
A
THR
192
A
O
THR
192
1_555
A
K
403
E
K
K
1_555
A
TYR
225
A
O
TYR
225
1_555
125.0
A
VAL
195
A
O
VAL
195
1_555
A
K
403
E
K
K
1_555
A
TYR
225
A
O
TYR
225
1_555
89.3
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
A
HOH
523
H
O
HOH
1_555
84.5
A
THR
192
A
O
THR
192
1_555
A
K
403
E
K
K
1_555
A
HOH
523
H
O
HOH
1_555
94.3
A
VAL
195
A
O
VAL
195
1_555
A
K
403
E
K
K
1_555
A
HOH
523
H
O
HOH
1_555
169.3
A
TYR
225
A
O
TYR
225
1_555
A
K
403
E
K
K
1_555
A
HOH
523
H
O
HOH
1_555
83.1
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
71.4
A
THR
192
A
O
THR
192
1_555
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
145.2
A
VAL
195
A
O
VAL
195
1_555
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
109.2
A
TYR
225
A
O
TYR
225
1_555
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
88.0
A
HOH
523
H
O
HOH
1_555
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
78.1
B
ALY
504
N(6)-ACETYLLYSINE
B
ALY
4
LYS
B
ALY
505
N(6)-ACETYLLYSINE
B
ALY
5
LYS
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
ARG
55
A
O
ARG
55
A
N
TYR
18
A
N
TYR
18
A
N
VAL
17
A
N
VAL
17
A
O
ILE
135
A
O
ILE
135
A
N
ALA
134
A
N
ALA
134
A
O
ILE
300
A
O
ILE
300
A
O
LEU
301
A
O
LEU
301
A
N
LEU
262
A
N
LEU
262
A
O
GLN
263
A
O
GLN
263
A
N
VAL
175
A
N
VAL
175
A
N
ASP
176
A
N
ASP
176
A
O
VAL
198
A
O
VAL
198
A
N
THR
197
A
N
THR
197
A
O
VAL
227
A
O
VAL
227
1
A
CG
LYS
60
A
CG
LYS
60
1
Y
1
A
CD
LYS
60
A
CD
LYS
60
1
Y
1
A
CE
LYS
60
A
CE
LYS
60
1
Y
1
A
NZ
LYS
60
A
NZ
LYS
60
1
Y
1
A
CG
ASP
89
A
CG
ASP
89
1
Y
1
A
OD1
ASP
89
A
OD1
ASP
89
1
Y
1
A
OD2
ASP
89
A
OD2
ASP
89
1
Y
1
A
CG
GLU
170
A
CG
GLU
170
1
Y
1
A
CD
GLU
170
A
CD
GLU
170
1
Y
1
A
OE1
GLU
170
A
OE1
GLU
170
1
Y
1
A
OE2
GLU
170
A
OE2
GLU
170
1
Y
1
A
CG
GLN
253
A
CG
GLN
253
1
Y
1
A
CD
GLN
253
A
CD
GLN
253
1
Y
1
A
OE1
GLN
253
A
OE1
GLN
253
1
Y
1
A
NE2
GLN
253
A
NE2
GLN
253
1
Y
1
A
CG
LYS
258
A
CG
LYS
258
1
Y
1
A
CD
LYS
258
A
CD
LYS
258
1
Y
1
A
CE
LYS
258
A
CE
LYS
258
1
Y
1
A
NZ
LYS
258
A
NZ
LYS
258
1
Y
1
A
CG
LYS
325
A
CG
LYS
325
1
Y
1
A
CD
LYS
325
A
CD
LYS
325
1
Y
1
A
CE
LYS
325
A
CE
LYS
325
1
Y
1
A
NZ
LYS
325
A
NZ
LYS
325
1
Y
1
A
CG
LYS
370
A
CG
LYS
370
1
Y
1
A
CD
LYS
370
A
CD
LYS
370
1
Y
1
A
CE
LYS
370
A
CE
LYS
370
1
Y
1
A
NZ
LYS
370
A
NZ
LYS
370
1
Y
1
A
CG
LYS
374
A
CG
LYS
374
1
Y
1
A
CD
LYS
374
A
CD
LYS
374
1
Y
1
A
CE
LYS
374
A
CE
LYS
374
1
Y
1
A
NZ
LYS
374
A
NZ
LYS
374
1
Y
1
A
MET
1
A
MET
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
GLU
3
A
GLU
3
1
Y
1
A
PRO
4
A
PRO
4
1
Y
1
A
GLU
5
A
GLU
5
1
Y
1
A
GLU
6
A
GLU
6
1
Y
1
A
PRO
7
A
PRO
7
1
Y
1
A
ALA
8
A
ALA
8
1
Y
1
A
ASP
9
A
ASP
9
1
Y
1
A
SER
10
A
SER
10
1
Y
1
A
GLY
11
A
GLY
11
1
Y
1
A
GLN
12
A
GLN
12
1
Y
1
A
ILE
378
A
ILE
378
1
Y
1
A
GLU
379
A
GLU
379
1
Y
1
A
GLY
380
A
GLY
380
1
Y
1
A
ARG
381
A
ARG
381
1
Y
1
A
GLY
382
A
GLY
382
1
Y
1
A
SER
383
A
SER
383
1
Y
1
A
HIS
384
A
HIS
384
1
Y
1
A
HIS
385
A
HIS
385
1
Y
1
A
HIS
386
A
HIS
386
1
Y
1
A
HIS
387
A
HIS
387
1
Y
1
A
HIS
388
A
HIS
388
1
Y
1
A
HIS
389
A
HIS
389
1
Y
1
A
PHE
70
-135.32
-53.31
1
A
GLU
85
-155.57
-36.41
1
A
THR
105
-69.47
-177.27
1
A
SER
276
-113.62
-71.78
57.99
0.2415
0.2044
0.2083
2.310
42.190
1814
17899
17891
10.14
99.94
0.29
random
1
isotropic
THROUGHOUT
1.34
MOLECULAR REPLACEMENT
28.18
0.90
1.11
PDB ENTRY 3EWF
ML
FLAT BULK SOLVENT MODEL
2.310
42.190
49
2933
22
0
2862
0.002
2964
0.630
4027
11.418
1063
0.042
439
0.003
517
0.3262
0.2860
2.3720
142
1201
100.00
0.3517
0.2788
2.4417
138
1219
100.00
0.2876
0.2596
2.5205
143
1203
100.00
0.3073
0.2575
2.6106
142
1225
100.00
0.3102
0.2366
2.7151
156
1194
100.00
0.3453
0.2550
2.8387
116
1249
100.00
0.3072
0.2366
2.9883
134
1217
100.00
0.2922
0.2359
3.1755
141
1243
100.00
0.2891
0.2213
3.4205
148
1220
100.00
0.2215
0.2032
3.7646
129
1241
100.00
0.1887
0.1851
4.3088
133
1258
100.00
0.2067
0.1800
5.4269
145
1264
100.00
0.2085
0.1750
42.1966
147
1343
100.00
51.85
2.31
50
4QA7
17924
17922
0
-3
0.082
1
26.8
12.0
100
1.597
2.31
2.39
2.0
1740
1
11.5
100
data collection
CBASS
phasing
PHASER
refinement
PHENIX
(phenix.refine: dev_1370)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
6
N
N
7
N
N
7
N
N
A
SER
21
A
SER
21
HELX_P
A
ASP
29
A
ASP
29
1
1
9
A
LYS
36
A
LYS
36
HELX_P
A
TYR
48
A
TYR
48
1
2
13
A
ALA
49
A
ALA
49
HELX_P
A
MET
54
A
MET
54
5
3
6
A
SER
63
A
SER
63
HELX_P
A
ALA
68
A
ALA
68
1
4
6
A
THR
72
A
THR
72
HELX_P
A
GLN
84
A
GLN
84
1
5
13
A
HIS
90
A
HIS
90
HELX_P
A
GLY
97
A
GLY
97
5
6
8
A
GLY
107
A
GLY
107
HELX_P
A
GLY
129
A
GLY
129
1
7
23
A
ASN
156
A
ASN
156
HELX_P
A
ARG
166
A
ARG
166
1
8
11
A
GLY
182
A
GLY
182
HELX_P
A
PHE
189
A
PHE
189
1
9
8
A
GLN
236
A
GLN
236
HELX_P
A
ASN
256
A
ASN
256
1
10
21
A
GLY
265
A
GLY
265
HELX_P
A
ILE
269
A
ILE
269
5
11
5
A
THR
280
A
THR
280
HELX_P
A
GLN
293
A
GLN
293
1
12
14
A
ASN
307
A
ASN
307
HELX_P
A
GLY
324
A
GLY
324
1
13
18
A
PHE
336
A
PHE
336
HELX_P
A
GLY
341
A
GLY
341
5
14
6
A
GLU
358
A
GLU
358
HELX_P
A
LEU
373
A
LEU
373
1
15
16
covale
1.330
both
B
ACE
501
B
C
ACE
1
1_555
B
ARG
502
B
N
ARG
2
1_555
covale
1.328
both
B
HIS
503
B
C
HIS
3
1_555
B
ALY
504
B
N
ALY
4
1_555
covale
1.329
both
B
ALY
504
B
C
ALY
4
1_555
B
ALY
505
B
N
ALY
5
1_555
covale
1.333
both
B
ALY
505
B
C
ALY
5
1_555
B
MCM
601
F
N
MCM
1_555
metalc
2.804
A
ASP
176
A
OD1
ASP
176
1_555
A
K
402
D
K
K
1_555
metalc
2.873
A
ASP
176
A
O
ASP
176
1_555
A
K
402
D
K
K
1_555
metalc
2.059
A
ASP
178
A
OD1
ASP
178
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.749
A
ASP
178
A
O
ASP
178
1_555
A
K
402
D
K
K
1_555
metalc
2.289
A
HIS
180
A
ND1
HIS
180
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.797
A
HIS
180
A
O
HIS
180
1_555
A
K
402
D
K
K
1_555
metalc
2.677
A
PHE
189
A
O
PHE
189
1_555
A
K
403
E
K
K
1_555
metalc
2.906
A
THR
192
A
O
THR
192
1_555
A
K
403
E
K
K
1_555
metalc
2.679
A
VAL
195
A
O
VAL
195
1_555
A
K
403
E
K
K
1_555
metalc
3.028
A
SER
199
A
OG
SER
199
1_555
A
K
402
D
K
K
1_555
metalc
2.780
A
LEU
200
A
O
LEU
200
1_555
A
K
402
D
K
K
1_555
metalc
2.847
A
TYR
225
A
O
TYR
225
1_555
A
K
403
E
K
K
1_555
metalc
2.090
A
ASP
267
A
OD2
ASP
267
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.400
A
ZN
401
C
ZN
ZN
1_555
A
HOH
522
H
O
HOH
1_555
metalc
1.968
A
ZN
401
C
ZN
ZN
1_555
B
ALY
505
B
OH
ALY
5
1_555
metalc
2.776
A
K
403
E
K
K
1_555
A
HOH
523
H
O
HOH
1_555
metalc
2.861
A
K
403
E
K
K
1_555
A
HOH
536
H
O
HOH
1_555
HYDROLASE
metalloenzyme, hydrolase, histone deacetylase, enzyme substrate complex, Cornelia de Lange Syndrome, arginase/deacetylase fold
A
PHE
208
A
PHE
208
1
A
PRO
209
A
PRO
209
-2.05
A
GLY
341
A
GLY
341
1
A
PRO
342
A
PRO
342
2.94
HDAC8_HUMAN
UNP
1
1
Q9BY41
MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQ
KVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVL
GILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKY
YQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTG
VILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV
4QA7
PDB
2
4QA7
1
377
4QA7
1
377
Q9BY41
A
1
1
377
501
505
4QA7
501
505
4QA7
B
2
1
5
1
TYR
engineered mutation
PHE
306
4QA7
A
Q9BY41
UNP
306
306
1
HIS
engineered mutation
ARG
334
4QA7
A
Q9BY41
UNP
334
334
1
expression tag
ILE
378
4QA7
A
Q9BY41
UNP
378
1
expression tag
GLU
379
4QA7
A
Q9BY41
UNP
379
1
expression tag
GLY
380
4QA7
A
Q9BY41
UNP
380
1
expression tag
ARG
381
4QA7
A
Q9BY41
UNP
381
1
expression tag
GLY
382
4QA7
A
Q9BY41
UNP
382
1
expression tag
SER
383
4QA7
A
Q9BY41
UNP
383
1
expression tag
HIS
384
4QA7
A
Q9BY41
UNP
384
1
expression tag
HIS
385
4QA7
A
Q9BY41
UNP
385
1
expression tag
HIS
386
4QA7
A
Q9BY41
UNP
386
1
expression tag
HIS
387
4QA7
A
Q9BY41
UNP
387
1
expression tag
HIS
388
4QA7
A
Q9BY41
UNP
388
1
expression tag
HIS
389
4QA7
A
Q9BY41
UNP
389
8
parallel
parallel
parallel
parallel
parallel
parallel
parallel
A
ARG
55
A
ARG
55
A
VAL
57
A
VAL
57
A
VAL
17
A
VAL
17
A
ILE
19
A
ILE
19
A
VAL
133
A
VAL
133
A
ASN
136
A
ASN
136
A
ALA
297
A
ALA
297
A
LEU
301
A
LEU
301
A
ALA
259
A
ALA
259
A
GLN
263
A
GLN
263
A
ILE
172
A
ILE
172
A
ASP
176
A
ASP
176
A
VAL
195
A
VAL
195
A
LYS
202
A
LYS
202
A
SER
226
A
SER
226
A
ILE
231
A
ILE
231
BINDING SITE FOR RESIDUE ZN A 401
A
ZN
401
Software
5
BINDING SITE FOR RESIDUE K A 402
A
K
402
Software
5
BINDING SITE FOR RESIDUE K A 403
A
K
403
Software
6
BINDING SITE FOR RESIDUE MCM B 601
B
MCM
601
Software
8
BINDING SITE FOR RESIDUE GOL B 602
B
GOL
602
Software
6
A
ASP
178
A
ASP
178
5
1_555
A
HIS
180
A
HIS
180
5
1_555
A
ASP
267
A
ASP
267
5
1_555
A
HOH
522
H
HOH
5
1_555
B
ALY
505
B
ALY
5
5
1_555
A
ASP
176
A
ASP
176
5
1_555
A
ASP
178
A
ASP
178
5
1_555
A
HIS
180
A
HIS
180
5
1_555
A
SER
199
A
SER
199
5
1_555
A
LEU
200
A
LEU
200
5
1_555
A
PHE
189
A
PHE
189
6
1_555
A
THR
192
A
THR
192
6
1_555
A
VAL
195
A
VAL
195
6
1_555
A
TYR
225
A
TYR
225
6
1_555
A
HOH
523
H
HOH
6
1_555
A
HOH
536
H
HOH
6
1_555
A
LYS
33
A
LYS
33
8
1_555
A
LYS
33
A
LYS
33
8
6_555
A
TYR
100
A
TYR
100
8
1_555
A
ASP
101
A
ASP
101
8
1_555
A
PHE
152
A
PHE
152
8
6_555
A
PHE
152
A
PHE
152
8
1_555
A
PRO
273
A
PRO
273
8
6_555
B
ALY
505
B
ALY
5
8
1_555
A
LYS
145
A
LYS
145
6
1_555
A
GLU
148
A
GLU
148
6
1_555
A
PHE
208
A
PHE
208
6
1_555
B
ARG
502
B
ARG
2
6
1_555
B
HIS
503
B
HIS
3
6
1_555
B
HOH
702
I
HOH
6
1_555
152
P 31 2 1