0.011213
0.000000
0.000000
0.000000
0.010658
0.000000
0.000000
0.000000
0.018065
0.00000
0.00000
0.00000
Otani, J.
Arita, K.
Kato, T.
Kinoshita, M.
Ariyoshi, M.
Shirakawa, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
89.182
93.829
55.357
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C2 H3 O2 -1
59.044
ACETATE ION
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
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
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
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
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
C
N
39
N
O
N
40
N
O
N
41
N
C
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
N
N
46
S
C
N
47
N
C
N
48
N
O
N
49
N
C
N
50
N
O
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
C
N
65
N
N
N
66
N
C
N
67
N
N
N
68
N
N
N
69
N
O
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
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
N
N
86
S
C
N
87
N
C
N
88
N
O
N
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
O
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
N
N
103
S
C
N
104
N
C
N
105
N
O
N
106
N
C
N
107
N
C
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
N
N
119
R
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
S
N
124
N
O
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
O
N
133
N
P
N
134
N
O
N
135
N
O
N
136
N
O
N
137
N
C
N
138
R
C
N
139
N
O
N
140
S
C
N
141
N
O
N
142
N
C
N
143
R
C
Y
144
N
N
Y
145
N
C
Y
146
N
N
Y
147
N
C
Y
148
N
C
N
149
N
N
Y
150
N
N
Y
151
N
C
Y
152
N
N
Y
153
N
C
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
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
O
N
169
N
P
N
170
N
O
N
171
N
O
N
172
N
O
N
173
N
C
N
174
R
C
N
175
N
O
N
176
S
C
N
177
N
O
N
178
N
C
N
179
R
C
N
180
N
N
N
181
N
C
N
182
N
O
N
183
N
N
N
184
N
C
N
185
N
N
N
186
N
C
N
187
N
C
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
H
N
202
N
O
N
203
N
P
N
204
N
O
N
205
N
O
N
206
N
O
N
207
N
C
N
208
R
C
N
209
N
O
N
210
S
C
N
211
N
O
N
212
N
C
N
213
R
C
Y
214
N
N
Y
215
N
C
Y
216
N
N
Y
217
N
C
N
218
N
C
N
219
N
O
N
220
N
N
N
221
N
C
N
222
N
N
N
223
N
N
Y
224
N
C
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
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
O
N
240
N
P
N
241
N
O
N
242
N
O
N
243
N
O
N
244
N
C
N
245
R
C
N
246
N
O
N
247
S
C
N
248
N
O
N
249
N
C
N
250
R
C
N
251
N
N
N
252
N
C
N
253
N
O
N
254
N
N
N
255
N
C
N
256
N
O
N
257
N
C
N
258
N
C
N
259
N
C
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
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
C
N
276
N
O
N
277
N
C
N
278
N
O
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
N
N
286
S
C
N
287
N
C
N
288
N
O
N
289
N
C
N
290
N
C
N
291
N
C
N
292
N
O
N
293
N
N
N
294
N
O
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
O
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
H
N
323
N
H
N
324
N
N
N
325
N
C
N
326
N
C
N
327
N
O
N
328
N
O
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
Y
339
N
C
Y
340
N
N
Y
341
N
C
Y
342
N
C
Y
343
N
N
N
344
N
O
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
O
N
356
N
H
N
357
N
H
N
358
N
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
S
C
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
O
N
367
N
H
N
368
N
H
N
369
N
H
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
H
N
378
N
H
N
379
N
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
C
N
388
N
O
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
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
N
C
N
407
N
C
N
408
N
C
N
409
N
C
N
410
N
N
N
411
N
O
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
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
N
N
428
S
C
N
429
N
C
N
430
N
O
N
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
N
438
N
O
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
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
N
455
N
C
N
456
N
C
N
457
N
O
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
H
N
465
N
H
N
466
N
H
N
467
N
N
N
468
S
C
N
469
N
C
N
470
N
O
N
471
N
C
N
472
N
O
N
473
N
O
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
N
N
482
S
C
N
483
N
C
N
484
N
O
N
485
R
C
N
486
N
O
N
487
N
C
N
488
N
O
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
N
N
499
S
C
N
500
N
C
N
501
N
O
N
502
N
C
Y
503
N
C
Y
504
N
C
Y
505
N
C
Y
506
N
N
Y
507
N
C
Y
508
N
C
Y
509
N
C
Y
510
N
C
Y
511
N
C
N
512
N
O
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
N
N
526
S
C
N
527
N
C
N
528
N
O
N
529
N
C
Y
530
N
C
Y
531
N
C
Y
532
N
C
Y
533
N
C
Y
534
N
C
Y
535
N
C
N
536
N
O
N
537
N
O
N
538
N
H
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
N
N
550
S
C
N
551
N
C
N
552
N
O
N
553
N
C
N
554
N
C
N
555
N
C
N
556
N
O
N
557
N
H
N
558
N
H
N
559
N
H
N
560
N
H
N
561
N
H
N
562
N
H
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
N
567
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
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
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
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
sing
N
51
N
doub
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
doub
N
64
N
sing
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
sing
N
77
N
doub
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
doub
N
95
N
sing
N
96
N
sing
N
97
N
sing
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
doub
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
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
Y
150
N
sing
Y
151
N
sing
Y
152
N
doub
N
153
N
sing
Y
154
N
sing
Y
155
N
sing
Y
156
N
doub
N
157
N
sing
Y
158
N
doub
N
159
N
sing
N
160
N
sing
Y
161
N
sing
Y
162
N
doub
N
163
N
sing
Y
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
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
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
doub
N
191
N
sing
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
doub
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
Y
223
N
sing
Y
224
N
sing
Y
225
N
doub
N
226
N
sing
Y
227
N
sing
N
228
N
sing
Y
229
N
doub
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
doub
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
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
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
doub
N
269
N
sing
N
270
N
sing
N
271
N
doub
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
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
doub
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
doub
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
doub
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
doub
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
sing
N
337
N
doub
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
Y
342
N
sing
Y
343
N
doub
Y
344
N
doub
N
345
N
sing
Y
346
N
sing
N
347
N
sing
Y
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
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
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
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
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
doub
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
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
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
doub
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
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
doub
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
Y
431
N
doub
Y
432
N
sing
Y
433
N
sing
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
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
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
doub
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
doub
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
doub
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
doub
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
Y
500
N
doub
Y
501
N
sing
Y
502
N
sing
N
503
N
sing
Y
504
N
doub
Y
505
N
sing
Y
506
N
sing
N
507
N
sing
Y
508
N
sing
Y
509
N
doub
N
510
N
sing
Y
511
N
doub
N
512
N
sing
Y
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
doub
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
Y
528
N
doub
Y
529
N
sing
Y
530
N
sing
N
531
N
sing
Y
532
N
doub
N
533
N
sing
Y
534
N
doub
N
535
N
sing
Y
536
N
sing
N
537
N
sing
N
538
N
sing
N
539
N
sing
N
540
N
sing
N
541
N
sing
N
542
N
sing
N
543
N
sing
N
544
N
sing
N
545
N
sing
N
546
N
sing
N
547
N
doub
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
sing
N
552
N
sing
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
sing
N
557
N
sing
N
558
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
288
6351
6362
10.1074/jbc.M112.431098
23316048
Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4
2013
10.2210/pdb3vxx/pdb
pdb_00003vxx
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
95
1
CCD
2009-11-25
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
AR-NW12A
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE AR-NW12A
7829.089
Methyl-CpG-binding domain protein 4
3.2.2.-
methyl CpG binding domain, UNP residues 69-136
1
man
polymer
4263.809
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')
1
syn
polymer
4325.828
DNA (5'-D(*GP*TP*CP*(5CM)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
1
syn
polymer
59.044
ACETATE ION
6
syn
non-polymer
62.068
1,2-ETHANEDIOL
3
syn
non-polymer
18.015
water
123
nat
water
Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase
no
no
SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
A
polypeptide(L)
no
yes
(DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA)
GTCACTACCGGACA
B
polydeoxyribonucleotide
no
yes
(DG)(DT)(DC)(5CM)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT)
GTCCGGTAGTGACT
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
mouse
sample
Mbd4
10090
Mus musculus
562
Escherichia coli
BL21(DE3)
plasmid
1
3.53
65.12
VAPOR DIFFUSION, HANGING DROP
4.4
7% PEG 10000, 0.1M sodium acetate, 0.2M sodium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-24.289
1
19
B
1
C
13
0.991
B_DG1:DC13_C
1
-16.683
-0.204
-0.021
-0.026
-11.881
1
20
B
2
C
12
-3.086
B_DT2:DA12_C
2
-9.124
-0.215
0.085
0.001
-2.031
1
19
B
3
C
11
1.764
B_DC3:DG11_C
3
-7.799
0.105
-0.223
-0.026
2.582
1
20
B
4
C
10
2.068
B_DA4:DT10_C
4
-10.531
0.169
0.075
-0.049
7.609
1
19
B
5
C
9
2.624
B_DC5:DG9_C
5
-16.011
0.554
-0.115
-0.167
-3.137
1
20
B
6
C
8
-0.206
B_DT6:DA8_C
6
-11.306
-0.085
0.022
-0.166
-9.830
1
20
B
7
C
7
1.235
B_DA7:DT7_C
7
-10.211
-0.121
-0.078
-0.107
-3.913
1
19
B
8
C
6
-2.251
B_DC8:DG6_C
8
-7.029
0.402
0.367
-0.124
4.408
1
19
B
9
C
5
-0.814
B_5CM9:DG5_C
9
-7.874
0.524
-0.166
-0.173
3.276
1
19
B
10
C
4
-5.182
B_DG10:5CM4_C
10
6.643
-0.469
0.034
-0.195
19.190
1
19
B
11
C
3
2.071
B_DG11:DC3_C
11
-3.020
-0.334
0.179
0.014
19.492
1
20
B
12
C
2
3.697
B_DA12:DT2_C
12
-21.036
-0.042
0.144
-0.147
13.527
1
19
B
13
C
1
0.915
B_DC13:DG1_C
13
-14.973
0.351
-0.099
-0.031
2.841
31.937
B
B
1
2
8.796
C
C
13
12
2.965
4.822
-0.911
-0.730
BB_DG1DT2:DA12DC13_CC
1
-0.598
1.091
31.574
-2.107
1.558
3.060
38.087
B
B
2
3
2.463
C
C
12
11
3.007
1.604
0.705
0.039
BB_DT2DC3:DG11DA12_CC
2
3.735
-5.733
37.878
-0.129
-0.640
3.031
30.781
B
B
3
4
23.683
C
C
11
10
3.255
12.235
0.055
0.098
BB_DC3DA4:DT10DG11_CC
3
-1.324
2.564
28.268
-2.217
-0.363
3.139
33.599
B
B
4
5
2.367
C
C
10
9
3.131
1.367
0.696
-0.694
BB_DA4DC5:DG9DT10_CC
4
2.241
-3.880
33.499
-1.415
-0.851
3.227
32.580
B
B
5
6
14.919
C
C
9
8
3.508
8.270
-0.040
-0.616
BB_DC5DT6:DA8DG9_CC
5
3.129
-5.644
31.389
-2.611
0.643
3.370
34.005
B
B
6
7
12.672
C
C
8
7
3.503
7.352
0.196
-0.288
BB_DT6DA7:DT7DA8_CC
6
1.923
-3.315
33.169
-1.741
-0.009
3.241
33.451
B
B
7
8
3.967
C
C
7
6
3.251
2.280
-0.563
-0.499
BB_DA7DC8:DG6DT7_CC
7
-2.278
3.964
33.299
-1.241
0.603
3.265
31.331
B
B
8
9
-0.091
C
C
6
5
3.161
-0.049
0.923
0.001
BB_DC85CM9:DG5DG6_CC
8
4.938
-9.181
30.949
0.010
-0.788
3.578
36.545
B
B
9
10
-7.467
C
C
5
4
3.583
-4.665
-0.138
-0.190
BB_5CM9DG10:5CM4DG5_CC
9
-3.169
5.073
36.122
0.406
-0.262
3.090
30.987
B
B
10
11
6.785
C
C
4
3
3.179
3.605
0.045
-0.269
BB_DG10DG11:DC35CM4_CC
10
-4.461
8.397
30.464
-1.175
-0.916
3.246
33.850
B
B
11
12
6.696
C
C
3
2
3.298
3.879
-0.596
-0.735
BB_DG11DA12:DT2DC3_CC
11
-4.679
8.077
33.316
-1.893
0.263
3.240
34.117
B
B
12
13
9.776
C
C
2
1
3.509
5.708
0.279
-1.263
BB_DA12DC13:DG1DT2_CC
12
-1.647
2.821
33.611
-3.094
-0.747
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-01-16
1
1
2013-08-14
1
2
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PDBJ
Y
PDBJ
2012-09-21
REL
REL
ACT
ACETATE ION
EDO
1,2-ETHANEDIOL
HOH
water
chemical synthesis
sample
chemical synthesis
sample
3VXV
PDB ENTRY 3VXV
PDB
experimental model
ACT
1
4
ACT
ACT
201
A
ACT
2
4
ACT
ACT
202
A
ACT
5
4
ACT
ACT
203
A
ACT
6
4
ACT
ACT
204
A
EDO
10
5
EDO
EDO
205
A
EDO
12
5
EDO
EDO
206
A
EDO
13
5
EDO
EDO
207
A
ACT
4
4
ACT
ACT
101
B
ACT
3
4
ACT
ACT
101
C
HOH
2
6
HOH
HOH
301
A
HOH
3
6
HOH
HOH
302
A
HOH
7
6
HOH
HOH
303
A
HOH
11
6
HOH
HOH
304
A
HOH
12
6
HOH
HOH
305
A
HOH
14
6
HOH
HOH
306
A
HOH
16
6
HOH
HOH
307
A
HOH
19
6
HOH
HOH
308
A
HOH
24
6
HOH
HOH
309
A
HOH
26
6
HOH
HOH
310
A
HOH
27
6
HOH
HOH
311
A
HOH
28
6
HOH
HOH
312
A
HOH
34
6
HOH
HOH
313
A
HOH
36
6
HOH
HOH
314
A
HOH
39
6
HOH
HOH
315
A
HOH
40
6
HOH
HOH
316
A
HOH
42
6
HOH
HOH
317
A
HOH
44
6
HOH
HOH
318
A
HOH
46
6
HOH
HOH
319
A
HOH
47
6
HOH
HOH
320
A
HOH
49
6
HOH
HOH
321
A
HOH
52
6
HOH
HOH
322
A
HOH
53
6
HOH
HOH
323
A
HOH
54
6
HOH
HOH
324
A
HOH
58
6
HOH
HOH
325
A
HOH
63
6
HOH
HOH
326
A
HOH
64
6
HOH
HOH
327
A
HOH
65
6
HOH
HOH
328
A
HOH
68
6
HOH
HOH
329
A
HOH
70
6
HOH
HOH
330
A
HOH
72
6
HOH
HOH
331
A
HOH
75
6
HOH
HOH
332
A
HOH
80
6
HOH
HOH
333
A
HOH
83
6
HOH
HOH
334
A
HOH
84
6
HOH
HOH
335
A
HOH
87
6
HOH
HOH
336
A
HOH
94
6
HOH
HOH
337
A
HOH
96
6
HOH
HOH
338
A
HOH
99
6
HOH
HOH
339
A
HOH
100
6
HOH
HOH
340
A
HOH
101
6
HOH
HOH
341
A
HOH
104
6
HOH
HOH
342
A
HOH
105
6
HOH
HOH
343
A
HOH
106
6
HOH
HOH
344
A
HOH
108
6
HOH
HOH
345
A
HOH
109
6
HOH
HOH
346
A
HOH
110
6
HOH
HOH
347
A
HOH
116
6
HOH
HOH
348
A
HOH
119
6
HOH
HOH
349
A
HOH
123
6
HOH
HOH
350
A
HOH
32
6
HOH
HOH
351
A
HOH
15
6
HOH
HOH
352
A
HOH
8
6
HOH
HOH
201
B
HOH
9
6
HOH
HOH
202
B
HOH
10
6
HOH
HOH
203
B
HOH
17
6
HOH
HOH
204
B
HOH
18
6
HOH
HOH
205
B
HOH
20
6
HOH
HOH
206
B
HOH
22
6
HOH
HOH
207
B
HOH
30
6
HOH
HOH
208
B
HOH
38
6
HOH
HOH
209
B
HOH
41
6
HOH
HOH
210
B
HOH
45
6
HOH
HOH
211
B
HOH
48
6
HOH
HOH
212
B
HOH
51
6
HOH
HOH
213
B
HOH
55
6
HOH
HOH
214
B
HOH
61
6
HOH
HOH
215
B
HOH
62
6
HOH
HOH
216
B
HOH
66
6
HOH
HOH
217
B
HOH
69
6
HOH
HOH
218
B
HOH
76
6
HOH
HOH
219
B
HOH
79
6
HOH
HOH
220
B
HOH
88
6
HOH
HOH
221
B
HOH
89
6
HOH
HOH
222
B
HOH
90
6
HOH
HOH
223
B
HOH
93
6
HOH
HOH
224
B
HOH
97
6
HOH
HOH
225
B
HOH
102
6
HOH
HOH
226
B
HOH
111
6
HOH
HOH
227
B
HOH
112
6
HOH
HOH
228
B
HOH
114
6
HOH
HOH
229
B
HOH
115
6
HOH
HOH
230
B
HOH
117
6
HOH
HOH
231
B
HOH
122
6
HOH
HOH
232
B
HOH
92
6
HOH
HOH
201
C
HOH
1
6
HOH
HOH
202
C
HOH
4
6
HOH
HOH
203
C
HOH
5
6
HOH
HOH
204
C
HOH
6
6
HOH
HOH
205
C
HOH
13
6
HOH
HOH
206
C
HOH
21
6
HOH
HOH
207
C
HOH
23
6
HOH
HOH
208
C
HOH
25
6
HOH
HOH
209
C
HOH
29
6
HOH
HOH
210
C
HOH
31
6
HOH
HOH
211
C
HOH
33
6
HOH
HOH
212
C
HOH
35
6
HOH
HOH
213
C
HOH
37
6
HOH
HOH
214
C
HOH
43
6
HOH
HOH
215
C
HOH
50
6
HOH
HOH
216
C
HOH
56
6
HOH
HOH
217
C
HOH
57
6
HOH
HOH
218
C
HOH
59
6
HOH
HOH
219
C
HOH
60
6
HOH
HOH
220
C
HOH
67
6
HOH
HOH
221
C
HOH
71
6
HOH
HOH
222
C
HOH
73
6
HOH
HOH
223
C
HOH
74
6
HOH
HOH
224
C
HOH
77
6
HOH
HOH
225
C
HOH
78
6
HOH
HOH
226
C
HOH
81
6
HOH
HOH
227
C
HOH
82
6
HOH
HOH
228
C
HOH
85
6
HOH
HOH
229
C
HOH
86
6
HOH
HOH
230
C
HOH
91
6
HOH
HOH
231
C
HOH
95
6
HOH
HOH
232
C
HOH
98
6
HOH
HOH
233
C
HOH
103
6
HOH
HOH
234
C
HOH
107
6
HOH
HOH
235
C
HOH
113
6
HOH
HOH
236
C
HOH
118
6
HOH
HOH
237
C
HOH
120
6
HOH
HOH
238
C
HOH
121
6
HOH
HOH
239
C
n
1
68
A
n
2
69
A
n
3
70
A
n
4
71
A
PRO
72
n
5
PRO
72
A
VAL
73
n
6
VAL
73
A
PRO
74
n
7
PRO
74
A
CYS
75
n
8
CYS
75
A
GLY
76
n
9
GLY
76
A
TRP
77
n
10
TRP
77
A
GLU
78
n
11
GLU
78
A
ARG
79
n
12
ARG
79
A
VAL
80
n
13
VAL
80
A
VAL
81
n
14
VAL
81
A
LYS
82
n
15
LYS
82
A
GLN
83
n
16
GLN
83
A
ARG
84
n
17
ARG
84
A
LEU
85
n
18
LEU
85
A
SER
86
n
19
SER
86
A
GLY
87
n
20
GLY
87
A
LYS
88
n
21
LYS
88
A
THR
89
n
22
THR
89
A
ALA
90
n
23
ALA
90
A
GLY
91
n
24
GLY
91
A
LYS
92
n
25
LYS
92
A
PHE
93
n
26
PHE
93
A
ASP
94
n
27
ASP
94
A
VAL
95
n
28
VAL
95
A
TYR
96
n
29
TYR
96
A
PHE
97
n
30
PHE
97
A
ILE
98
n
31
ILE
98
A
SER
99
n
32
SER
99
A
PRO
100
n
33
PRO
100
A
GLN
101
n
34
GLN
101
A
GLY
102
n
35
GLY
102
A
LEU
103
n
36
LEU
103
A
LYS
104
n
37
LYS
104
A
PHE
105
n
38
PHE
105
A
ARG
106
n
39
ARG
106
A
SER
107
n
40
SER
107
A
LYS
108
n
41
LYS
108
A
ARG
109
n
42
ARG
109
A
SER
110
n
43
SER
110
A
LEU
111
n
44
LEU
111
A
ALA
112
n
45
ALA
112
A
ASN
113
n
46
ASN
113
A
TYR
114
n
47
TYR
114
A
LEU
115
n
48
LEU
115
A
LEU
116
n
49
LEU
116
A
LYS
117
n
50
LYS
117
A
ASN
118
n
51
ASN
118
A
GLY
119
n
52
GLY
119
A
GLU
120
n
53
GLU
120
A
THR
121
n
54
THR
121
A
PHE
122
n
55
PHE
122
A
LEU
123
n
56
LEU
123
A
LYS
124
n
57
LYS
124
A
PRO
125
n
58
PRO
125
A
GLU
126
n
59
GLU
126
A
ASP
127
n
60
ASP
127
A
PHE
128
n
61
PHE
128
A
ASN
129
n
62
ASN
129
A
PHE
130
n
63
PHE
130
A
THR
131
n
64
THR
131
A
VAL
132
n
65
VAL
132
A
LEU
133
n
66
LEU
133
A
PRO
134
n
67
PRO
134
A
n
68
135
A
n
69
136
A
DG
1
n
1
DG
1
B
DT
2
n
2
DT
2
B
DC
3
n
3
DC
3
B
DA
4
n
4
DA
4
B
DC
5
n
5
DC
5
B
DT
6
n
6
DT
6
B
DA
7
n
7
DA
7
B
DC
8
n
8
DC
8
B
5CM
9
n
9
5CM
9
B
DG
10
n
10
DG
10
B
DG
11
n
11
DG
11
B
DA
12
n
12
DA
12
B
DC
13
n
13
DC
13
B
DA
14
n
14
DA
14
B
DG
1
n
1
DG
1
C
DT
2
n
2
DT
2
C
DC
3
n
3
DC
3
C
5CM
4
n
4
5CM
4
C
DG
5
n
5
DG
5
C
DG
6
n
6
DG
6
C
DT
7
n
7
DT
7
C
DA
8
n
8
DA
8
C
DG
9
n
9
DG
9
C
DT
10
n
10
DT
10
C
DG
11
n
11
DG
11
C
DA
12
n
12
DA
12
C
DC
13
n
13
DC
13
C
DT
14
n
14
DT
14
C
0.1975
-0.2888
0.2369
0.6312
-0.0399
0.7690
0.0093
0.1466
0.0347
-0.1660
0.0460
-0.0066
-0.0516
0.0524
-0.0326
0.2086
-0.0364
-0.0034
0.2184
0.0066
0.1876
refined
3.4960
12.0971
4.4118
X-RAY DIFFRACTION
2.3468
1.4976
0.1516
1.1846
0.3444
0.2642
-0.1097
-0.3115
-0.3255
-0.2639
-0.0099
-0.2258
-0.1719
-0.1087
0.0512
0.2592
-0.0793
-0.0121
0.2831
0.1062
0.3023
refined
18.9353
11.7890
-13.9496
X-RAY DIFFRACTION
1.2729
-0.3261
0.4259
0.5810
-0.5276
0.4689
-0.2826
-0.0808
0.1478
-0.2369
0.1178
-0.1358
0.0670
-0.0054
0.1290
0.2233
-0.0566
0.0195
0.3830
-0.0170
0.2568
refined
22.7568
13.1583
-11.3946
X-RAY DIFFRACTION
A
72
A
134
X-RAY DIFFRACTION
1
(chain 'A' and (resseq 72:134))
B
1
B
14
X-RAY DIFFRACTION
2
(chain 'B' and (resseq 1:14))
C
1
C
14
X-RAY DIFFRACTION
3
(chain 'C' and (resseq 1:14))
author_and_software_defined_assembly
PISA
3
trimeric
5080
-4
10280
B
5CM
9
B
5CM
9
DC
C
5CM
4
C
5CM
4
DC
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
VAL
80
A
N
VAL
13
A
O
TYR
96
A
O
TYR
29
A
N
PHE
97
A
N
PHE
30
A
O
PHE
105
A
O
PHE
38
1
B
HOH
207
N
HOH
1
A
SER
68
A
SER
1
1
Y
1
A
GLY
69
A
GLY
2
1
Y
1
A
HIS
70
A
HIS
3
1
Y
1
A
LYS
71
A
LYS
4
1
Y
1
A
LYS
135
A
LYS
68
1
Y
1
A
GLY
136
A
GLY
69
1
Y
1
C
C
O2
O
DT
HOH
7
234
2.17
1
2.26
0.30
108.30
110.56
B
B
B
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
-3.14
0.40
104.50
101.36
C
C
C
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
2.68
0.30
108.30
110.98
C
C
C
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
2.34
0.30
108.30
110.64
C
C
C
O4'
C1'
N9
DA
DA
DA
12
12
12
N
78.830
20.150
-13.1184
0.0000
0.0000
11.4286
-0.0000
1.6898
0.2145
0.1955
0.1965
2.204
28.339
574
12027
4.77
99.54
1.000
0.460
0.34
1
1.34
MOLECULAR REPLACEMENT
25.1500
0.60
0.90
PDB ENTRY 3VXV
ML
FLAT BULK SOLVENT MODEL
42.734
0.347
2.204
28.339
123
1240
36
570
511
0.006
1201
1.193
1727
23.213
471
0.062
183
0.006
126
0.3409
0.2721
2.4257
142
2830
2972
4
100.0000
0.3333
0.2601
2.7764
141
2828
2969
4
100.0000
0.2073
0.1913
3.4970
133
2858
2991
4
100.0000
0.1738
0.1684
28.3414
158
2937
3095
4
99.0000
41.310
2.2
50
3VXX
12096
12048
1.0
1.0
0.078
1
12.4
7.2
99.6
0.477
2.2
2.28
4.5
1
7.3
99.9
data collection
HKL-2000
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.6.4_486)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
4
N
N
4
N
N
6
N
N
6
N
N
6
N
N
A
SER
107
A
SER
40
HELX_P
A
GLY
119
A
GLY
52
1
1
13
A
LYS
124
A
LYS
57
HELX_P
A
PHE
128
A
PHE
61
5
2
5
disulf
2.056
A
CYS
75
A
SG
CYS
8
1_555
A
CYS
75
A
SG
CYS
8
3_555
covale
1.600
both
B
DC
8
B
O3'
DC
8
1_555
B
5CM
9
B
P
5CM
9
1_555
covale
1.606
both
B
5CM
9
B
O3'
5CM
9
1_555
B
DG
10
B
P
DG
10
1_555
covale
1.607
both
C
DC
3
C
O3'
DC
3
1_555
C
5CM
4
C
P
5CM
4
1_555
covale
1.618
both
C
5CM
4
C
O3'
5CM
4
1_555
C
DG
5
C
P
DG
5
1_555
hydrog
WATSON-CRICK
B
DG
1
B
N1
DG
1
1_555
C
DC
13
C
N3
DC
13
1_555
hydrog
WATSON-CRICK
B
DG
1
B
N2
DG
1
1_555
C
DC
13
C
O2
DC
13
1_555
hydrog
WATSON-CRICK
B
DG
1
B
O6
DG
1
1_555
C
DC
13
C
N4
DC
13
1_555
hydrog
WATSON-CRICK
B
DT
2
B
N3
DT
2
1_555
C
DA
12
C
N1
DA
12
1_555
hydrog
WATSON-CRICK
B
DT
2
B
O4
DT
2
1_555
C
DA
12
C
N6
DA
12
1_555
hydrog
WATSON-CRICK
B
DC
3
B
N3
DC
3
1_555
C
DG
11
C
N1
DG
11
1_555
hydrog
WATSON-CRICK
B
DC
3
B
N4
DC
3
1_555
C
DG
11
C
O6
DG
11
1_555
hydrog
WATSON-CRICK
B
DC
3
B
O2
DC
3
1_555
C
DG
11
C
N2
DG
11
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N1
DA
4
1_555
C
DT
10
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N6
DA
4
1_555
C
DT
10
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N3
DC
5
1_555
C
DG
9
C
N1
DG
9
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N4
DC
5
1_555
C
DG
9
C
O6
DG
9
1_555
hydrog
WATSON-CRICK
B
DC
5
B
O2
DC
5
1_555
C
DG
9
C
N2
DG
9
1_555
hydrog
WATSON-CRICK
B
DT
6
B
N3
DT
6
1_555
C
DA
8
C
N1
DA
8
1_555
hydrog
WATSON-CRICK
B
DT
6
B
O4
DT
6
1_555
C
DA
8
C
N6
DA
8
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N1
DA
7
1_555
C
DT
7
C
N3
DT
7
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N6
DA
7
1_555
C
DT
7
C
O4
DT
7
1_555
hydrog
WATSON-CRICK
B
DC
8
B
N3
DC
8
1_555
C
DG
6
C
N1
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
N4
DC
8
1_555
C
DG
6
C
O6
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
O2
DC
8
1_555
C
DG
6
C
N2
DG
6
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N3
5CM
9
1_555
C
DG
5
C
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N4
5CM
9
1_555
C
DG
5
C
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
O2
5CM
9
1_555
C
DG
5
C
N2
DG
5
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N1
DG
10
1_555
C
5CM
4
C
N3
5CM
4
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N2
DG
10
1_555
C
5CM
4
C
O2
5CM
4
1_555
hydrog
WATSON-CRICK
B
DG
10
B
O6
DG
10
1_555
C
5CM
4
C
N4
5CM
4
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N1
DG
11
1_555
C
DC
3
C
N3
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N2
DG
11
1_555
C
DC
3
C
O2
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
O6
DG
11
1_555
C
DC
3
C
N4
DC
3
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N1
DA
12
1_555
C
DT
2
C
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N6
DA
12
1_555
C
DT
2
C
O4
DT
2
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N3
DC
13
1_555
C
DG
1
C
N1
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N4
DC
13
1_555
C
DG
1
C
O6
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
B
O2
DC
13
1_555
C
DG
1
C
N2
DG
1
1_555
HYDROLASE/DNA
methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex
MBD4_MOUSE
UNP
1
69
Q9Z2D7
GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
3VXX
PDB
2
3VXX
3VXX
PDB
3
3VXX
69
136
3VXX
69
136
Q9Z2D7
A
1
2
69
1
14
3VXX
1
14
3VXX
B
2
1
14
1
14
3VXX
1
14
3VXX
C
3
1
14
1
expression tag
SER
68
3VXX
A
Q9Z2D7
UNP
1
3
anti-parallel
anti-parallel
A
GLU
78
A
GLU
11
A
GLN
83
A
GLN
16
A
PHE
93
A
PHE
26
A
ILE
98
A
ILE
31
A
LYS
104
A
LYS
37
A
PHE
105
A
PHE
38
BINDING SITE FOR RESIDUE ACT A 201
A
ACT
201
Software
7
BINDING SITE FOR RESIDUE ACT A 202
A
ACT
202
Software
6
BINDING SITE FOR RESIDUE ACT A 203
A
ACT
203
Software
4
BINDING SITE FOR RESIDUE ACT A 204
A
ACT
204
Software
3
BINDING SITE FOR RESIDUE EDO A 205
A
EDO
205
Software
6
BINDING SITE FOR RESIDUE EDO A 206
A
EDO
206
Software
5
BINDING SITE FOR RESIDUE EDO A 207
A
EDO
207
Software
2
BINDING SITE FOR RESIDUE ACT B 101
B
ACT
101
Software
5
BINDING SITE FOR RESIDUE ACT C 101
C
ACT
101
Software
3
A
GLU
120
A
GLU
53
7
1_555
A
GLU
120
A
GLU
53
7
3_555
A
PHE
122
A
PHE
55
7
1_555
B
DG
1
B
DG
1
7
8_455
B
ACT
101
K
ACT
7
8_455
C
DT
14
C
DT
14
7
6_555
C
DT
14
C
DT
14
7
8_455
A
LYS
92
A
LYS
25
6
1_555
A
PHE
93
A
PHE
26
6
1_555
A
ASP
94
A
ASP
27
6
1_555
A
HOH
331
M
HOH
6
1_555
B
DC
8
B
DC
8
6
1_555
B
HOH
211
N
HOH
6
1_555
A
VAL
73
A
VAL
6
4
1_555
A
PRO
74
A
PRO
7
4
1_555
A
GLY
76
A
GLY
9
4
1_555
A
TRP
77
A
TRP
10
4
1_555
A
GLN
101
A
GLN
34
3
1_555
A
ASN
118
A
ASN
51
3
1_555
A
GLU
120
A
GLU
53
3
1_555
A
GLN
83
A
GLN
16
6
1_555
A
ARG
84
A
ARG
17
6
1_555
A
LEU
85
A
LEU
18
6
1_555
A
HOH
319
M
HOH
6
1_555
C
DC
3
C
DC
3
6
1_555
C
5CM
4
C
5CM
4
6
1_555
A
PHE
93
A
PHE
26
5
1_555
A
PHE
130
A
PHE
63
5
3_555
A
THR
131
A
THR
64
5
3_555
A
VAL
132
A
VAL
65
5
3_555
B
DA
7
B
DA
7
5
1_555
A
LEU
133
A
LEU
66
2
1_555
A
PRO
134
A
PRO
67
2
1_555
A
ACT
201
D
ACT
5
8_555
B
DT
2
B
DT
2
5
1_555
B
DC
3
B
DC
3
5
1_555
C
DC
13
C
DC
13
5
1_555
C
DT
14
C
DT
14
5
3_654
B
DC
13
B
DC
13
3
1_555
C
DT
2
C
DT
2
3
1_555
C
DC
3
C
DC
3
3
1_555
20
C 2 2 21