0.011275
0.000000
0.000000
0.000000
0.010229
0.000000
0.000000
0.000000
0.017945
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
88.693
97.758
55.725
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H16 N3 O8 P
337.223
n
2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
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
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
O
N
58
N
C
N
59
N
O
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
H
N
74
N
H
N
75
N
H
N
76
N
C
N
77
N
O
N
78
N
O
N
79
N
C
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
N
N
84
S
C
N
85
N
C
N
86
N
O
N
87
N
C
N
88
N
O
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
N
N
97
S
C
N
98
N
C
N
99
N
O
N
100
N
C
N
101
N
C
N
102
N
C
N
103
N
N
N
104
N
C
N
105
N
N
N
106
N
N
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
H
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
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
N
C
N
145
N
C
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
N
N
157
R
C
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
S
N
162
N
O
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
O
N
171
N
P
N
172
N
O
N
173
N
O
N
174
N
O
N
175
N
C
N
176
R
C
N
177
N
O
N
178
S
C
N
179
N
O
N
180
N
C
N
181
R
C
Y
182
N
N
Y
183
N
C
Y
184
N
N
Y
185
N
C
Y
186
N
C
N
187
N
N
Y
188
N
N
Y
189
N
C
Y
190
N
N
Y
191
N
C
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
O
N
207
N
P
N
208
N
O
N
209
N
O
N
210
N
O
N
211
N
C
N
212
R
C
N
213
N
O
N
214
S
C
N
215
N
O
N
216
N
C
N
217
R
C
N
218
N
N
N
219
N
C
N
220
N
O
N
221
N
N
N
222
N
C
N
223
N
N
N
224
N
C
N
225
N
C
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
H
N
240
N
O
N
241
N
P
N
242
N
O
N
243
N
O
N
244
N
O
N
245
N
C
N
246
R
C
N
247
N
O
N
248
S
C
N
249
N
O
N
250
N
C
N
251
R
C
Y
252
N
N
Y
253
N
C
Y
254
N
N
Y
255
N
C
N
256
N
C
N
257
N
O
N
258
N
N
N
259
N
C
N
260
N
N
N
261
N
N
Y
262
N
C
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
H
N
276
N
H
N
277
N
O
N
278
N
P
N
279
N
O
N
280
N
O
N
281
N
O
N
282
N
C
N
283
R
C
N
284
N
O
N
285
S
C
N
286
N
O
N
287
N
C
N
288
R
C
N
289
N
N
N
290
N
C
N
291
N
O
N
292
N
N
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
C
N
297
N
C
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
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
C
N
314
N
O
N
315
N
C
N
316
N
O
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
N
328
N
C
N
329
N
C
N
330
N
O
N
331
N
N
N
332
N
O
N
333
N
H
N
334
N
H
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
N
N
344
S
C
N
345
N
C
N
346
N
O
N
347
N
C
N
348
N
C
N
349
N
C
N
350
N
O
N
351
N
O
N
352
N
O
N
353
N
H
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
N
N
363
N
C
N
364
N
C
N
365
N
O
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
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
Y
377
N
C
Y
378
N
N
Y
379
N
C
Y
380
N
C
Y
381
N
N
N
382
N
O
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
O
N
394
N
H
N
395
N
H
N
396
N
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
S
C
N
401
N
C
N
402
N
C
N
403
N
C
N
404
N
O
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
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
N
N
419
S
C
N
420
N
C
N
421
N
O
N
422
N
C
N
423
N
C
N
424
N
C
N
425
N
C
N
426
N
O
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
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
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
N
445
N
C
N
446
N
C
N
447
N
C
N
448
N
N
N
449
N
O
N
450
N
H
N
451
N
H
N
452
N
H
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
H
N
465
N
N
N
466
S
C
N
467
N
C
N
468
N
O
N
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
C
Y
474
N
C
Y
475
N
C
N
476
N
O
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
N
N
489
S
C
N
490
N
C
N
491
N
O
N
492
N
C
N
493
N
C
N
494
N
C
N
495
N
O
N
496
N
H
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
N
N
506
S
C
N
507
N
C
N
508
N
O
N
509
N
C
N
510
N
O
N
511
N
O
N
512
N
H
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
N
N
520
S
C
N
521
N
C
N
522
N
O
N
523
R
C
N
524
N
O
N
525
N
C
N
526
N
O
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
H
N
532
N
H
N
533
N
H
N
534
N
H
N
535
N
H
N
536
N
N
N
537
S
C
N
538
N
C
N
539
N
O
N
540
N
C
Y
541
N
C
Y
542
N
C
Y
543
N
C
Y
544
N
N
Y
545
N
C
Y
546
N
C
Y
547
N
C
Y
548
N
C
Y
549
N
C
N
550
N
O
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
H
N
555
N
H
N
556
N
H
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
N
N
564
S
C
N
565
N
C
N
566
N
O
N
567
N
C
Y
568
N
C
Y
569
N
C
Y
570
N
C
Y
571
N
C
Y
572
N
C
Y
573
N
C
N
574
N
O
N
575
N
O
N
576
N
H
N
577
N
H
N
578
N
H
N
579
N
H
N
580
N
H
N
581
N
H
N
582
N
H
N
583
N
H
N
584
N
H
N
585
N
H
N
586
N
H
N
587
N
N
N
588
S
C
N
589
N
C
N
590
N
O
N
591
N
C
N
592
N
C
N
593
N
C
N
594
N
O
N
595
N
H
N
596
N
H
N
597
N
H
N
598
N
H
N
599
N
H
N
600
N
H
N
601
N
H
N
602
N
H
N
603
N
H
N
604
N
H
N
605
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
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
doub
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
doub
N
54
N
sing
N
55
N
doub
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
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
sing
N
78
N
doub
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
sing
N
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
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
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
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
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
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
Y
189
N
sing
Y
190
N
sing
Y
191
N
doub
N
192
N
sing
Y
193
N
sing
Y
194
N
sing
Y
195
N
doub
N
196
N
sing
Y
197
N
doub
N
198
N
sing
N
199
N
sing
Y
200
N
sing
Y
201
N
doub
N
202
N
sing
Y
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
doub
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
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
doub
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
Y
262
N
sing
Y
263
N
sing
Y
264
N
doub
N
265
N
sing
Y
266
N
sing
N
267
N
sing
Y
268
N
doub
N
269
N
doub
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
doub
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
doub
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
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
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
doub
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
sing
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
doub
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
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
doub
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
doub
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
sing
N
367
N
doub
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
doub
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
Y
381
N
sing
Y
382
N
doub
Y
383
N
doub
N
384
N
sing
Y
385
N
sing
N
386
N
sing
Y
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
doub
N
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
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
doub
N
421
N
sing
N
422
N
sing
N
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
sing
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
doub
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
sing
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
doub
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
Y
470
N
doub
Y
471
N
sing
Y
472
N
sing
N
473
N
sing
Y
474
N
doub
N
475
N
sing
Y
476
N
doub
N
477
N
sing
Y
478
N
sing
N
479
N
sing
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
doub
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
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
doub
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
doub
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
sing
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
doub
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
sing
Y
539
N
doub
Y
540
N
sing
Y
541
N
sing
N
542
N
sing
Y
543
N
doub
Y
544
N
sing
Y
545
N
sing
N
546
N
sing
Y
547
N
sing
Y
548
N
doub
N
549
N
sing
Y
550
N
doub
N
551
N
sing
Y
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
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
doub
N
563
N
sing
N
564
N
sing
N
565
N
sing
N
566
N
sing
Y
567
N
doub
Y
568
N
sing
Y
569
N
sing
N
570
N
sing
Y
571
N
doub
N
572
N
sing
Y
573
N
doub
N
574
N
sing
Y
575
N
sing
N
576
N
sing
N
577
N
sing
N
578
N
sing
N
579
N
sing
N
580
N
sing
N
581
N
sing
N
582
N
sing
N
583
N
sing
N
584
N
sing
N
585
N
sing
N
586
N
doub
N
587
N
sing
N
588
N
sing
N
589
N
sing
N
590
N
sing
N
591
N
sing
N
592
N
sing
N
593
N
sing
N
594
N
sing
N
595
N
sing
N
596
N
sing
N
597
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/pdb3vyb/pdb
pdb_00003vyb
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
2010-10-08
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
BL-17A
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-17A
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
4341.827
DNA (5'-D(*GP*TP*CP*(5HC)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
1
syn
polymer
59.044
ACETATE ION
1
syn
non-polymer
62.068
1,2-ETHANEDIOL
1
syn
non-polymer
18.015
water
71
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)(5HC)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT)
GTCXGGTAGTGACT
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
3.67
66.53
VAPOR DIFFUSION, HANGING DROP
4
8% PEG 1500, 0.1M sodium acetate, 0.1M sodium cacodylate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-26.739
1
19
B
1
C
13
0.231
B_DG1:DC13_C
1
-17.226
-0.319
-0.144
0.038
-10.893
1
20
B
2
C
12
-4.546
B_DT2:DA12_C
2
-10.534
-0.503
-0.011
0.073
-2.889
1
19
B
3
C
11
1.502
B_DC3:DG11_C
3
-3.934
-0.013
-0.177
-0.037
0.282
1
20
B
4
C
10
5.729
B_DA4:DT10_C
4
-12.127
0.589
-0.064
0.115
5.967
1
19
B
5
C
9
5.404
B_DC5:DG9_C
5
-17.236
0.564
0.052
-0.092
-0.578
1
20
B
6
C
8
0.891
B_DT6:DA8_C
6
-13.758
-0.282
-0.043
-0.037
-5.904
1
20
B
7
C
7
1.699
B_DA7:DT7_C
7
-13.062
0.266
-0.043
0.014
-5.070
1
19
B
8
C
6
0.695
B_DC8:DG6_C
8
-5.702
0.441
0.318
0.060
7.480
1
19
B
9
C
5
-1.535
B_5CM9:DG5_C
9
-6.857
0.380
-0.169
-0.059
28.458
1
19
B
11
C
3
0.983
B_DG11:DC3_C
10
4.535
-0.221
0.286
-0.034
20.432
1
20
B
12
C
2
-0.320
B_DA12:DT2_C
11
-17.314
-0.041
0.442
-0.119
14.465
1
19
B
13
C
1
4.603
B_DC13:DG1_C
12
-14.451
0.273
-0.071
-0.005
2.833
30.733
B
B
1
2
4.160
C
C
13
12
2.883
2.203
-1.046
-0.787
BB_DG1DT2:DA12DC13_CC
1
-0.374
0.706
30.654
-1.862
1.910
3.121
40.721
B
B
2
3
5.655
C
C
12
11
3.078
3.926
0.784
0.070
BB_DT2DC3:DG11DA12_CC
2
3.127
-4.505
40.423
-0.312
-0.798
3.221
32.536
B
B
3
4
19.197
C
C
11
10
3.263
10.570
0.010
0.397
BB_DC3DA4:DT10DG11_CC
3
0.525
-0.953
30.811
-1.174
0.075
3.111
29.442
B
B
4
5
3.887
C
C
10
9
3.171
1.974
0.519
-0.574
BB_DA4DC5:DG9DT10_CC
4
-0.794
1.564
29.367
-1.535
-1.185
3.203
31.087
B
B
5
6
13.680
C
C
9
8
3.435
7.246
-0.191
-0.382
BB_DC5DT6:DA8DG9_CC
5
4.160
-7.855
29.970
-2.149
1.180
3.452
37.340
B
B
6
7
9.125
C
C
8
7
3.480
5.817
0.290
0.008
BB_DT6DA7:DT7DA8_CC
6
2.196
-3.445
36.837
-0.808
-0.143
3.275
34.283
B
B
7
8
8.087
C
C
7
6
3.346
4.750
-0.266
-0.370
BB_DA7DC8:DG6DT7_CC
7
-2.082
3.545
33.900
-1.387
0.118
3.139
30.152
B
B
8
9
0.267
C
C
6
5
3.074
0.138
0.661
0.166
BB_DC85CM9:DG5DG6_CC
8
4.744
-9.155
29.785
0.292
-0.347
6.471
66.436
B
B
9
11
-3.336
C
C
5
3
6.650
-3.637
0.487
-0.080
BB_5CM9DG11:DC3DG5_CC
9
-12.511
11.477
65.290
0.220
-1.455
3.521
36.182
B
B
11
12
6.670
C
C
3
2
3.451
4.098
-1.268
-0.970
BB_DG11DA12:DT2DC3_CC
10
-8.451
13.755
34.981
-2.187
0.751
3.344
33.986
B
B
12
13
5.261
C
C
2
1
3.455
3.070
0.434
-1.287
BB_DA12DC13:DG1DT2_CC
11
1.479
-2.535
33.819
-2.713
-0.497
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
2012-09-22
REL
REL
ACT
ACETATE ION
EDO
1,2-ETHANEDIOL
HOH
water
3VXV
PDB ENTRY 3VXV
PDB
experimental model
ACT
1
4
ACT
ACT
201
A
EDO
10
5
EDO
EDO
202
A
HOH
2
6
HOH
HOH
301
A
HOH
5
6
HOH
HOH
302
A
HOH
8
6
HOH
HOH
303
A
HOH
11
6
HOH
HOH
304
A
HOH
14
6
HOH
HOH
305
A
HOH
16
6
HOH
HOH
306
A
HOH
19
6
HOH
HOH
307
A
HOH
21
6
HOH
HOH
308
A
HOH
22
6
HOH
HOH
309
A
HOH
25
6
HOH
HOH
310
A
HOH
26
6
HOH
HOH
311
A
HOH
30
6
HOH
HOH
312
A
HOH
31
6
HOH
HOH
313
A
HOH
32
6
HOH
HOH
314
A
HOH
36
6
HOH
HOH
315
A
HOH
40
6
HOH
HOH
316
A
HOH
42
6
HOH
HOH
317
A
HOH
43
6
HOH
HOH
318
A
HOH
45
6
HOH
HOH
319
A
HOH
46
6
HOH
HOH
320
A
HOH
47
6
HOH
HOH
321
A
HOH
48
6
HOH
HOH
322
A
HOH
51
6
HOH
HOH
323
A
HOH
52
6
HOH
HOH
324
A
HOH
55
6
HOH
HOH
325
A
HOH
58
6
HOH
HOH
326
A
HOH
66
6
HOH
HOH
327
A
HOH
67
6
HOH
HOH
328
A
HOH
68
6
HOH
HOH
329
A
HOH
69
6
HOH
HOH
330
A
HOH
71
6
HOH
HOH
331
A
HOH
13
6
HOH
HOH
332
A
HOH
9
6
HOH
HOH
101
B
HOH
10
6
HOH
HOH
102
B
HOH
12
6
HOH
HOH
103
B
HOH
17
6
HOH
HOH
104
B
HOH
23
6
HOH
HOH
105
B
HOH
24
6
HOH
HOH
106
B
HOH
27
6
HOH
HOH
107
B
HOH
28
6
HOH
HOH
108
B
HOH
29
6
HOH
HOH
109
B
HOH
35
6
HOH
HOH
110
B
HOH
41
6
HOH
HOH
111
B
HOH
50
6
HOH
HOH
112
B
HOH
56
6
HOH
HOH
113
B
HOH
59
6
HOH
HOH
114
B
HOH
60
6
HOH
HOH
115
B
HOH
61
6
HOH
HOH
116
B
HOH
62
6
HOH
HOH
117
B
HOH
63
6
HOH
HOH
118
B
HOH
64
6
HOH
HOH
119
B
HOH
39
6
HOH
HOH
101
C
HOH
1
6
HOH
HOH
102
C
HOH
3
6
HOH
HOH
103
C
HOH
4
6
HOH
HOH
104
C
HOH
6
6
HOH
HOH
105
C
HOH
7
6
HOH
HOH
106
C
HOH
15
6
HOH
HOH
107
C
HOH
18
6
HOH
HOH
108
C
HOH
20
6
HOH
HOH
109
C
HOH
33
6
HOH
HOH
110
C
HOH
34
6
HOH
HOH
111
C
HOH
37
6
HOH
HOH
112
C
HOH
38
6
HOH
HOH
113
C
HOH
44
6
HOH
HOH
114
C
HOH
49
6
HOH
HOH
115
C
HOH
53
6
HOH
HOH
116
C
HOH
54
6
HOH
HOH
117
C
HOH
57
6
HOH
HOH
118
C
HOH
65
6
HOH
HOH
119
C
HOH
70
6
HOH
HOH
120
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
5HM
4
n
4
5HC
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
0.5204
-0.0042
0.5374
0.7592
0.1364
0.8684
-0.0335
0.0180
0.1899
-0.1543
0.1438
0.0997
0.0208
0.0187
-0.1022
0.1781
-0.0150
0.0346
0.2414
0.0650
0.2715
refined
3.7555
12.0077
4.2199
X-RAY DIFFRACTION
2.3511
1.1076
0.2227
0.6930
0.0412
0.6149
-0.0025
-0.4850
-0.5973
-0.2576
-0.0716
-0.4990
-0.1390
-0.1881
0.0227
0.3464
-0.1182
0.0550
0.3574
0.1039
0.5079
refined
18.9074
12.4405
-14.1120
X-RAY DIFFRACTION
1.9438
-0.9158
0.2530
0.4368
-0.2555
0.0450
-0.3740
-0.2072
0.4443
-0.2628
0.2009
-0.3107
0.0173
0.1768
0.1312
0.2686
-0.0809
0.0508
0.5933
-0.0093
0.3734
refined
22.4674
13.8384
-11.5003
X-RAY DIFFRACTION
A
72
A
134
X-RAY DIFFRACTION
1
chain A
B
1
B
14
X-RAY DIFFRACTION
2
chain B
C
1
C
14
X-RAY DIFFRACTION
3
chain C
author_and_software_defined_assembly
PISA
3
trimeric
3250
-8
10580
B
5CM
9
B
5CM
9
DC
C
5HC
4
C
5HC
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
101
G
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
4.66
0.30
108.30
112.96
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
100.750
47.8984
22.030
-11.0243
0.0000
0.0000
8.1093
0.0000
2.9149
0.2199
0.1906
0.1924
2.400
34.700
456
9351
4.88
95.52
1.000
0.500
0.43
RANDOM
1
0.00
MOLECULAR REPLACEMENT
24.3500
0.72
1.00
PDB ENTRY 3VXV
ML
FLAT BULK SOLVENT MODEL
39.965
0.329
2.400
34.700
71
1161
8
571
511
0.004
1171
1.008
1694
26.872
475
0.056
182
0.003
118
0.3224
0.2838
2.7472
133
2712
3
89.00
0.2278
0.1948
3.4607
170
3013
3
99.00
0.1968
0.1716
34.7032
153
3170
3
99.00
48.250
2.19
50
3VYB
11517
1.0
1.0
0.052
1
14.7
6.5
89.6
0.317
2.19
2.27
701
1
4.1
54.7
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/hmCG sequence
1
N
N
2
N
N
3
N
N
4
N
N
5
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
2.029
A
CYS
75
A
SG
CYS
8
1_555
A
CYS
75
A
SG
CYS
8
3_555
covale
1.604
both
B
DC
8
B
O3'
DC
8
1_555
B
5CM
9
B
P
5CM
9
1_555
covale
1.603
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
5HC
4
C
P
5HC
4
1_555
covale
1.610
both
C
5HC
4
C
O3'
5HC
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
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
3VYB
PDB
2
3VYB
3VYB
PDB
3
3VYB
69
136
3VYB
69
136
Q9Z2D7
A
1
2
69
1
14
3VYB
1
14
3VYB
B
2
1
14
1
14
3VYB
1
14
3VYB
C
3
1
14
1
expression tag
SER
68
3VYB
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
4
BINDING SITE FOR RESIDUE EDO A 202
A
EDO
202
Software
6
A
GLU
120
A
GLU
53
4
1_555
A
GLU
120
A
GLU
53
4
3_555
C
DT
14
C
DT
14
4
6_555
C
DT
14
C
DT
14
4
8_455
A
GLN
83
A
GLN
16
6
1_555
A
ARG
84
A
ARG
17
6
1_555
A
HOH
323
F
HOH
6
1_555
C
DC
3
C
DC
3
6
1_555
C
5HC
4
C
5HC
4
6
1_555
C
HOH
106
H
HOH
6
1_555
20
C 2 2 21