0.024349
0.000000
0.000000
0.000000
0.017908
0.000000
0.000000
0.000000
0.010347
0.00000
0.00000
0.00000
Morera, S.
Vigouroux, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.070
55.840
96.650
C5 H11 O6 P
198.111
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
ABASIC DIDEOXYRIBOSE
DNA linking
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
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
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
N
C
N
8
R
C
N
9
N
O
N
10
N
C
N
11
S
C
N
12
N
O
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
N
N
25
S
C
N
26
N
C
N
27
N
O
N
28
N
C
N
29
N
O
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
N
N
38
S
C
N
39
N
C
N
40
N
O
N
41
N
C
N
42
N
C
N
43
N
C
N
44
N
N
N
45
N
C
N
46
N
N
N
47
N
N
N
48
N
O
N
49
N
H
N
50
N
H
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
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
N
N
65
S
C
N
66
N
C
N
67
N
O
N
68
N
C
N
69
N
C
N
70
N
O
N
71
N
N
N
72
N
O
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
N
N
82
S
C
N
83
N
C
N
84
N
O
N
85
N
C
N
86
N
C
N
87
N
O
N
88
N
O
N
89
N
O
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
H
N
97
N
N
N
98
R
C
N
99
N
C
N
100
N
O
N
101
N
C
N
102
N
S
N
103
N
O
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
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
Y
123
N
N
Y
124
N
C
Y
125
N
N
Y
126
N
C
Y
127
N
C
N
128
N
N
Y
129
N
N
Y
130
N
C
Y
131
N
N
Y
132
N
C
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
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
O
N
148
N
P
N
149
N
O
N
150
N
O
N
151
N
O
N
152
N
C
N
153
R
C
N
154
N
O
N
155
S
C
N
156
N
O
N
157
N
C
N
158
R
C
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
N
N
163
N
C
N
164
N
N
N
165
N
C
N
166
N
C
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
O
N
182
N
P
N
183
N
O
N
184
N
O
N
185
N
O
N
186
N
C
N
187
R
C
N
188
N
O
N
189
S
C
N
190
N
O
N
191
N
C
N
192
R
C
Y
193
N
N
Y
194
N
C
Y
195
N
N
Y
196
N
C
N
197
N
C
N
198
N
O
N
199
N
N
N
200
N
C
N
201
N
N
N
202
N
N
Y
203
N
C
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
O
N
219
N
P
N
220
N
O
N
221
N
O
N
222
N
O
N
223
N
C
N
224
R
C
N
225
N
O
N
226
S
C
N
227
N
O
N
228
N
C
N
229
R
C
N
230
N
N
N
231
N
C
N
232
N
O
N
233
N
N
N
234
N
C
N
235
N
O
N
236
N
C
N
237
N
C
N
238
N
C
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
C
N
255
N
O
N
256
N
C
N
257
N
O
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
O
N
272
N
N
N
273
N
O
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
H
N
282
N
H
N
283
N
H
N
284
N
N
N
285
S
C
N
286
N
C
N
287
N
O
N
288
N
C
N
289
N
C
N
290
N
C
N
291
N
O
N
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
N
C
N
305
N
C
N
306
N
O
N
307
N
O
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
N
C
Y
318
N
C
Y
319
N
N
Y
320
N
C
Y
321
N
C
Y
322
N
N
N
323
N
O
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
S
C
N
342
N
C
N
343
N
C
N
344
N
C
N
345
N
O
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
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
C
N
367
N
O
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
H
N
381
N
N
N
382
S
C
N
383
N
C
N
384
N
O
N
385
N
C
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
N
N
390
N
O
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
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
N
N
407
S
C
N
408
N
C
N
409
N
O
N
410
N
C
N
411
N
C
N
412
N
S
N
413
N
C
N
414
N
O
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
N
N
427
S
C
N
428
N
C
N
429
N
O
N
430
N
C
Y
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
N
437
N
O
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
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
N
N
450
S
C
N
451
N
C
N
452
N
O
N
453
N
C
N
454
N
C
N
455
N
C
N
456
N
O
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
H
N
466
N
N
N
467
S
C
N
468
N
C
N
469
N
O
N
470
N
C
N
471
N
O
N
472
N
O
N
473
N
H
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
N
N
481
S
C
N
482
N
C
N
483
N
O
N
484
R
C
N
485
N
O
N
486
N
C
N
487
N
O
N
488
N
H
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
N
N
498
S
C
N
499
N
C
N
500
N
O
N
501
N
C
Y
502
N
C
Y
503
N
C
Y
504
N
C
Y
505
N
N
Y
506
N
C
Y
507
N
C
Y
508
N
C
Y
509
N
C
Y
510
N
C
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
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
N
N
525
S
C
N
526
N
C
N
527
N
O
N
528
N
C
Y
529
N
C
Y
530
N
C
Y
531
N
C
Y
532
N
C
Y
533
N
C
Y
534
N
C
N
535
N
O
N
536
N
O
N
537
N
H
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
N
N
549
S
C
N
550
N
C
N
551
N
O
N
552
N
C
N
553
N
C
N
554
N
C
N
555
N
O
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
H
N
564
N
H
N
565
N
H
N
566
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
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
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
doub
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
doub
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
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
doub
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
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
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
doub
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
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
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
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
Y
129
N
sing
Y
130
N
sing
Y
131
N
doub
N
132
N
sing
Y
133
N
sing
Y
134
N
sing
Y
135
N
doub
N
136
N
sing
Y
137
N
doub
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
N
142
N
sing
Y
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
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
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
sing
N
169
N
doub
N
170
N
sing
N
171
N
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
doub
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
Y
202
N
sing
Y
203
N
sing
Y
204
N
doub
N
205
N
sing
Y
206
N
sing
N
207
N
sing
Y
208
N
doub
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
doub
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
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
doub
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
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
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
doub
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
doub
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
doub
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
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
sing
Y
322
N
doub
Y
323
N
doub
N
324
N
sing
Y
325
N
sing
N
326
N
sing
Y
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
sing
N
337
N
sing
N
338
N
sing
N
339
N
doub
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
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
sing
N
403
N
sing
N
404
N
sing
N
405
N
doub
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
doub
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
Y
429
N
doub
Y
430
N
sing
Y
431
N
sing
N
432
N
sing
Y
433
N
doub
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
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
N
446
N
sing
N
447
N
doub
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
doub
N
465
N
sing
N
466
N
sing
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
doub
N
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
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
doub
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
Y
498
N
doub
Y
499
N
sing
Y
500
N
sing
N
501
N
sing
Y
502
N
doub
Y
503
N
sing
Y
504
N
sing
N
505
N
sing
Y
506
N
sing
Y
507
N
doub
N
508
N
sing
Y
509
N
doub
N
510
N
sing
Y
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
sing
N
519
N
sing
N
520
N
sing
N
521
N
doub
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
Y
526
N
doub
Y
527
N
sing
Y
528
N
sing
N
529
N
sing
Y
530
N
doub
N
531
N
sing
Y
532
N
doub
N
533
N
sing
Y
534
N
sing
N
535
N
sing
N
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
doub
N
546
N
sing
N
547
N
sing
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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
40
9917
9926
10.1093/nar/gks714
22848106
Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.
2012
10.2210/pdb4e9f/pdb
pdb_00004e9f
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
PIXEL
2011-08-29
PSI PILATUS 6M
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.9
1.0
ID29
ESRF
0.9
SYNCHROTRON
ESRF BEAMLINE ID29
19416.393
Methyl-CpG-binding domain protein 4
3.2.2.-
glycosylase domain of MBD4 (residues 426-580)
1
man
polymer
DNA fragment with 3DR site
3524.284
DNA (5'-D(*CP*CP*AP*GP*CP*GP*(3DR)P*GP*CP*AP*GP*C)-3')
1
syn
polymer
DNA fragment
3695.390
DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
1
syn
polymer
62.068
1,2-ETHANEDIOL
1
syn
non-polymer
18.015
water
86
nat
water
Methyl-CpG-binding endonuclease 1, Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase
no
no
MLSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP
LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLSHHHHH
H
MLSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP
LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLSHHHHH
H
A
polypeptide(L)
no
yes
(DC)(DC)(DA)(DG)(DC)(DG)(3DR)(DG)(DC)(DA)(DG)(DC)
CCAGCGNGCAGC
C
polydeoxyribonucleotide
no
no
(DG)(DC)(DT)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DG)
GCTGCGCGCTGG
D
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
MBD4, MED1
9606
Homo sapiens
562
Escherichia coli
1
2.08
40.88
VAPOR DIFFUSION, HANGING DROP
8
25% ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
-32.907
1
C
1
D
12
-14.628
C_DC1:DG12_D
1
-9.443
-0.388
0.529
0.519
-10.099
1
C
2
D
11
11.581
C_DC2:DG11_D
2
-0.971
1.907
0.162
-0.254
9.398
1
20
C
3
D
10
-0.959
C_DA3:DT10_D
3
-10.200
0.510
0.199
-0.354
4.109
1
19
C
4
D
9
-2.211
C_DG4:DC9_D
4
-9.659
-0.825
0.188
-0.511
-4.700
1
19
C
5
D
8
1.491
C_DC5:DG8_D
5
-5.342
0.219
0.010
-0.273
8.392
1
19
C
6
D
7
3.491
C_DG6:DC7_D
6
-10.224
-0.577
0.331
-0.226
-16.731
1
19
C
8
D
5
-1.775
C_DG8:DC5_D
7
-7.115
-0.231
-0.508
-0.164
3.438
1
19
C
9
D
4
-1.493
C_DC9:DG4_D
8
-4.113
0.318
-0.001
-0.196
8.086
1
20
C
10
D
3
2.008
C_DA10:DT3_D
9
-11.753
-0.029
0.004
-0.222
7.552
1
19
C
11
D
2
-1.805
C_DG11:DC2_D
10
-14.333
-0.149
0.157
-0.273
10.260
1
19
C
12
D
1
-1.484
C_DC12:DG1_D
11
-9.444
0.073
-0.343
-0.266
2.869
44.440
C
C
1
2
5.870
D
D
12
11
2.899
4.427
0.257
-0.302
CC_DC1DC2:DG11DG12_DD
1
4.331
-5.743
44.028
-0.761
0.014
3.115
30.088
C
C
2
3
9.901
D
D
11
10
2.992
5.114
-0.749
1.251
CC_DC2DA3:DT10DG11_DD
2
1.602
-3.102
29.618
1.425
1.751
3.382
30.063
C
C
3
4
2.425
D
D
10
9
3.357
1.256
-0.579
-0.162
CC_DA3DG4:DC9DT10_DD
3
-2.329
4.496
29.949
-0.577
0.623
3.644
38.838
C
C
4
5
-2.621
D
D
9
8
3.580
-1.741
0.697
-0.521
CC_DG4DC5:DG8DC9_DD
4
3.272
-4.927
38.668
-0.548
-0.608
3.289
33.483
C
C
5
6
5.994
D
D
8
7
3.170
3.443
-0.589
0.959
CC_DC5DG6:DC7DG8_DD
5
-3.054
5.318
33.174
1.102
0.523
2.843
25.760
C
C
8
9
2.806
D
D
5
4
2.839
1.238
-0.365
0.047
CC_DG8DC9:DG4DC5_DD
6
-6.251
14.164
24.972
-0.202
-0.727
3.304
36.900
C
C
9
10
9.178
D
D
4
3
3.233
5.778
0.440
0.540
CC_DC9DA10:DT3DG4_DD
7
3.494
-5.550
36.298
0.065
-0.219
3.408
33.082
C
C
10
11
8.620
D
D
3
2
3.406
4.890
-0.164
0.230
CC_DA10DG11:DC2DT3_DD
8
-1.556
2.743
32.692
-0.462
0.013
3.321
34.871
C
C
11
12
-8.066
D
D
2
1
3.280
-4.792
0.751
0.081
CC_DG11DC12:DG1DC2_DD
9
6.528
-10.987
33.946
0.880
-0.239
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
Structure summary
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-08-08
1
1
2012-11-07
1
2
2016-12-28
1
3
2023-09-13
_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
RCSB
Y
RCSB
2012-03-21
REL
REL
EDO
1,2-ETHANEDIOL
HOH
water
Synthetic DNA
sample
Synthetic DNA
sample
4ENE
PDB ENTRY 4ENE
PDB
experimental model
EGL
1003
4
EDO
EDO
101
C
HOH
1
5
HOH
HOH
601
A
HOH
2
5
HOH
HOH
602
A
HOH
3
5
HOH
HOH
603
A
HOH
4
5
HOH
HOH
604
A
HOH
5
5
HOH
HOH
605
A
HOH
6
5
HOH
HOH
606
A
HOH
7
5
HOH
HOH
607
A
HOH
8
5
HOH
HOH
608
A
HOH
10
5
HOH
HOH
609
A
HOH
11
5
HOH
HOH
610
A
HOH
12
5
HOH
HOH
611
A
HOH
13
5
HOH
HOH
612
A
HOH
15
5
HOH
HOH
613
A
HOH
16
5
HOH
HOH
614
A
HOH
17
5
HOH
HOH
615
A
HOH
18
5
HOH
HOH
616
A
HOH
19
5
HOH
HOH
617
A
HOH
20
5
HOH
HOH
618
A
HOH
21
5
HOH
HOH
619
A
HOH
22
5
HOH
HOH
620
A
HOH
23
5
HOH
HOH
621
A
HOH
24
5
HOH
HOH
622
A
HOH
25
5
HOH
HOH
623
A
HOH
26
5
HOH
HOH
624
A
HOH
27
5
HOH
HOH
625
A
HOH
28
5
HOH
HOH
626
A
HOH
29
5
HOH
HOH
627
A
HOH
30
5
HOH
HOH
628
A
HOH
31
5
HOH
HOH
629
A
HOH
32
5
HOH
HOH
630
A
HOH
35
5
HOH
HOH
631
A
HOH
36
5
HOH
HOH
632
A
HOH
37
5
HOH
HOH
633
A
HOH
39
5
HOH
HOH
634
A
HOH
40
5
HOH
HOH
635
A
HOH
41
5
HOH
HOH
636
A
HOH
42
5
HOH
HOH
637
A
HOH
43
5
HOH
HOH
638
A
HOH
44
5
HOH
HOH
639
A
HOH
45
5
HOH
HOH
640
A
HOH
46
5
HOH
HOH
641
A
HOH
53
5
HOH
HOH
642
A
HOH
54
5
HOH
HOH
643
A
HOH
56
5
HOH
HOH
644
A
HOH
57
5
HOH
HOH
645
A
HOH
58
5
HOH
HOH
646
A
HOH
59
5
HOH
HOH
647
A
HOH
62
5
HOH
HOH
648
A
HOH
64
5
HOH
HOH
649
A
HOH
65
5
HOH
HOH
650
A
HOH
66
5
HOH
HOH
651
A
HOH
71
5
HOH
HOH
652
A
HOH
80
5
HOH
HOH
653
A
HOH
81
5
HOH
HOH
654
A
HOH
82
5
HOH
HOH
655
A
HOH
85
5
HOH
HOH
656
A
HOH
87
5
HOH
HOH
657
A
HOH
89
5
HOH
HOH
658
A
HOH
90
5
HOH
HOH
659
A
HOH
93
5
HOH
HOH
660
A
HOH
97
5
HOH
HOH
661
A
HOH
98
5
HOH
HOH
662
A
HOH
103
5
HOH
HOH
663
A
HOH
105
5
HOH
HOH
664
A
HOH
9
5
HOH
HOH
201
C
HOH
38
5
HOH
HOH
202
C
HOH
47
5
HOH
HOH
203
C
HOH
48
5
HOH
HOH
204
C
HOH
67
5
HOH
HOH
205
C
HOH
88
5
HOH
HOH
206
C
HOH
91
5
HOH
HOH
207
C
HOH
92
5
HOH
HOH
208
C
HOH
107
5
HOH
HOH
209
C
HOH
14
5
HOH
HOH
101
D
HOH
68
5
HOH
HOH
102
D
HOH
69
5
HOH
HOH
103
D
HOH
72
5
HOH
HOH
104
D
HOH
77
5
HOH
HOH
105
D
HOH
78
5
HOH
HOH
106
D
HOH
79
5
HOH
HOH
107
D
HOH
86
5
HOH
HOH
108
D
HOH
95
5
HOH
HOH
109
D
HOH
99
5
HOH
HOH
110
D
HOH
104
5
HOH
HOH
111
D
HOH
106
5
HOH
HOH
112
D
HOH
108
5
HOH
HOH
113
D
n
1
426
A
n
2
427
A
n
3
428
A
n
4
429
A
n
5
430
A
n
6
431
A
n
7
432
A
n
8
433
A
n
9
434
A
n
10
435
A
n
11
436
A
LYS
437
n
12
LYS
437
A
TRP
438
n
13
TRP
438
A
THR
439
n
14
THR
439
A
PRO
440
n
15
PRO
440
A
PRO
441
n
16
PRO
441
A
ARG
442
n
17
ARG
442
A
SER
443
n
18
SER
443
A
PRO
444
n
19
PRO
444
A
PHE
445
n
20
PHE
445
A
ASN
446
n
21
ASN
446
A
LEU
447
n
22
LEU
447
A
VAL
448
n
23
VAL
448
A
GLN
449
n
24
GLN
449
A
GLU
450
n
25
GLU
450
A
THR
451
n
26
THR
451
A
LEU
452
n
27
LEU
452
A
PHE
453
n
28
PHE
453
A
HIS
454
n
29
HIS
454
A
ASP
455
n
30
ASP
455
A
PRO
456
n
31
PRO
456
A
TRP
457
n
32
TRP
457
A
LYS
458
n
33
LYS
458
A
LEU
459
n
34
LEU
459
A
LEU
460
n
35
LEU
460
A
ILE
461
n
36
ILE
461
A
ALA
462
n
37
ALA
462
A
THR
463
n
38
THR
463
A
ILE
464
n
39
ILE
464
A
PHE
465
n
40
PHE
465
A
LEU
466
n
41
LEU
466
A
ASN
467
n
42
ASN
467
A
ARG
468
n
43
ARG
468
A
THR
469
n
44
THR
469
A
SER
470
n
45
SER
470
A
GLY
471
n
46
GLY
471
A
LYS
472
n
47
LYS
472
A
MET
473
n
48
MET
473
A
ALA
474
n
49
ALA
474
A
ILE
475
n
50
ILE
475
A
PRO
476
n
51
PRO
476
A
VAL
477
n
52
VAL
477
A
LEU
478
n
53
LEU
478
A
TRP
479
n
54
TRP
479
A
LYS
480
n
55
LYS
480
A
PHE
481
n
56
PHE
481
A
LEU
482
n
57
LEU
482
A
GLU
483
n
58
GLU
483
A
LYS
484
n
59
LYS
484
A
TYR
485
n
60
TYR
485
A
PRO
486
n
61
PRO
486
A
SER
487
n
62
SER
487
A
ALA
488
n
63
ALA
488
A
GLU
489
n
64
GLU
489
A
VAL
490
n
65
VAL
490
A
ALA
491
n
66
ALA
491
A
ARG
492
n
67
ARG
492
A
THR
493
n
68
THR
493
A
ALA
494
n
69
ALA
494
A
ASP
495
n
70
ASP
495
A
TRP
496
n
71
TRP
496
A
ARG
497
n
72
ARG
497
A
ASP
498
n
73
ASP
498
A
VAL
499
n
74
VAL
499
A
SER
500
n
75
SER
500
A
GLU
501
n
76
GLU
501
A
LEU
502
n
77
LEU
502
A
LEU
503
n
78
LEU
503
A
LYS
504
n
79
LYS
504
A
PRO
505
n
80
PRO
505
A
LEU
506
n
81
LEU
506
A
GLY
507
n
82
GLY
507
A
LEU
508
n
83
LEU
508
A
TYR
509
n
84
TYR
509
A
ASP
510
n
85
ASP
510
A
LEU
511
n
86
LEU
511
A
ARG
512
n
87
ARG
512
A
ALA
513
n
88
ALA
513
A
LYS
514
n
89
LYS
514
A
THR
515
n
90
THR
515
A
ILE
516
n
91
ILE
516
A
VAL
517
n
92
VAL
517
A
LYS
518
n
93
LYS
518
A
PHE
519
n
94
PHE
519
A
SER
520
n
95
SER
520
A
ASP
521
n
96
ASP
521
A
GLU
522
n
97
GLU
522
A
TYR
523
n
98
TYR
523
A
LEU
524
n
99
LEU
524
A
THR
525
n
100
THR
525
A
LYS
526
n
101
LYS
526
A
GLN
527
n
102
GLN
527
A
TRP
528
n
103
TRP
528
A
LYS
529
n
104
LYS
529
A
TYR
530
n
105
TYR
530
A
PRO
531
n
106
PRO
531
A
ILE
532
n
107
ILE
532
A
GLU
533
n
108
GLU
533
A
LEU
534
n
109
LEU
534
A
HIS
535
n
110
HIS
535
A
GLY
536
n
111
GLY
536
A
ILE
537
n
112
ILE
537
A
GLY
538
n
113
GLY
538
A
LYS
539
n
114
LYS
539
A
TYR
540
n
115
TYR
540
A
GLY
541
n
116
GLY
541
A
ASN
542
n
117
ASN
542
A
ASP
543
n
118
ASP
543
A
SER
544
n
119
SER
544
A
TYR
545
n
120
TYR
545
A
ARG
546
n
121
ARG
546
A
ILE
547
n
122
ILE
547
A
PHE
548
n
123
PHE
548
A
CYS
549
n
124
CYS
549
A
VAL
550
n
125
VAL
550
A
ASN
551
n
126
ASN
551
A
GLU
552
n
127
GLU
552
A
TRP
553
n
128
TRP
553
A
LYS
554
n
129
LYS
554
A
GLN
555
n
130
GLN
555
A
VAL
556
n
131
VAL
556
A
HIS
557
n
132
HIS
557
A
PRO
558
n
133
PRO
558
A
GLU
559
n
134
GLU
559
A
ASP
560
n
135
ASP
560
A
HIS
561
n
136
HIS
561
A
LYS
562
n
137
LYS
562
A
LEU
563
n
138
LEU
563
A
ASN
564
n
139
ASN
564
A
LYS
565
n
140
LYS
565
A
TYR
566
n
141
TYR
566
A
HIS
567
n
142
HIS
567
A
ASP
568
n
143
ASP
568
A
TRP
569
n
144
TRP
569
A
LEU
570
n
145
LEU
570
A
TRP
571
n
146
TRP
571
A
GLU
572
n
147
GLU
572
A
ASN
573
n
148
ASN
573
A
HIS
574
n
149
HIS
574
A
n
150
575
A
n
151
576
A
n
152
577
A
n
153
578
A
n
154
579
A
n
155
580
A
n
156
581
A
n
157
582
A
n
158
583
A
n
159
584
A
n
160
585
A
n
161
586
A
C
1
n
1
DC
1
C
C
2
n
2
DC
2
C
A
3
n
3
DA
3
C
G
4
n
4
DG
4
C
C
5
n
5
DC
5
C
G
6
n
6
DG
6
C
3DR
7
n
7
3DR
7
C
G
8
n
8
DG
8
C
C
9
n
9
DC
9
C
A
10
n
10
DA
10
C
G
11
n
11
DG
11
C
C
12
n
12
DC
12
C
G
1
n
1
DG
1
D
C
2
n
2
DC
2
D
T
3
n
3
DT
3
D
G
4
n
4
DG
4
D
C
5
n
5
DC
5
D
G
6
n
6
DG
6
D
C
7
n
7
DC
7
D
G
8
n
8
DG
8
D
C
9
n
9
DC
9
D
T
10
n
10
DT
10
D
G
11
n
11
DG
11
D
G
12
n
12
DG
12
D
author_and_software_defined_assembly
PISA
3
trimeric
3820
-11
10240
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
MET
426
A
MET
1
1
Y
1
A
LEU
427
A
LEU
2
1
Y
1
A
SER
428
A
SER
3
1
Y
1
A
PRO
429
A
PRO
4
1
Y
1
A
PRO
430
A
PRO
5
1
Y
1
A
ARG
431
A
ARG
6
1
Y
1
A
ARG
432
A
ARG
7
1
Y
1
A
LYS
433
A
LYS
8
1
Y
1
A
ALA
434
A
ALA
9
1
Y
1
A
PHE
435
A
PHE
10
1
Y
1
A
LYS
436
A
LYS
11
1
Y
1
A
GLU
575
A
GLU
150
1
Y
1
A
LYS
576
A
LYS
151
1
Y
1
A
LEU
577
A
LEU
152
1
Y
1
A
SER
578
A
SER
153
1
Y
1
A
LEU
579
A
LEU
154
1
Y
1
A
SER
580
A
SER
155
1
Y
1
A
HIS
581
A
HIS
156
1
Y
1
A
HIS
582
A
HIS
157
1
Y
1
A
HIS
583
A
HIS
158
1
Y
1
A
HIS
584
A
HIS
159
1
Y
1
A
HIS
585
A
HIS
160
1
Y
1
A
HIS
586
A
HIS
161
1
Y
1
4.64
0.30
108.30
112.94
C
C
C
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.88
0.60
118.90
123.78
C
C
C
N1
C2
O2
DC
DC
DC
1
1
1
N
1
-4.38
0.70
121.90
117.52
C
C
C
N3
C2
O2
DC
DC
DC
1
1
1
N
1
7.52
1.10
118.80
126.32
C
C
C
C2
N1
C1'
DC
DC
DC
1
1
1
N
1
7.75
1.20
119.70
127.45
C
C
C
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
2.67
0.30
108.30
110.97
C
C
C
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
7.20
1.20
119.70
126.90
C
C
C
C3'
O3'
P
DG
DG
3DR
6
6
7
Y
1
2.53
0.30
108.30
110.83
C
C
C
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
9.35
1.20
119.70
129.05
C
C
C
C3'
O3'
P
DG
DG
DC
11
11
12
Y
1
2.02
0.30
108.30
110.32
C
C
C
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
11.55
1.20
119.70
131.25
D
D
D
C3'
O3'
P
DG
DG
DC
1
1
2
Y
1
9.86
1.20
119.70
129.56
D
D
D
C3'
O3'
P
DC
DC
DT
2
2
3
Y
1
3.55
0.30
108.30
111.85
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.42
0.30
108.30
110.72
D
D
D
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
8.06
1.20
119.70
127.76
D
D
D
C3'
O3'
P
DG
DG
DG
11
11
12
Y
1
2.99
0.30
108.30
111.29
D
D
D
O4'
C1'
N9
DG
DG
DG
12
12
12
N
0.9431
0.9289
0.2485
0.2141
0.2158
1.79
37.80
1101
21600
21487
5.12
99.27
0.132
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 4ENE
Engh & Huber
0.238
1.79
37.80
86
1747
4
478
1179
0.010
1760
HARMONIC
2.00
1.07
2479
HARMONIC
2.00
678
SINUSOIDAL
2.00
26
HARMONIC
2.00
193
HARMONIC
5.00
1760
HARMONIC
20.00
3.21
18.29
216
SEMIHARMONIC
5.00
1915
SEMIHARMONIC
4.00
0.1973
0.2340
0.2319
1.88
140
2564
2704
11
5.18
99.27
1.79
38
4E9F
21600
21525
2
2
0.063
1
13.3
99.6
1.79
1.9
1
98.5
data collection
DNA
phasing
PHASER
refinement
BUSTER
2.10.0
data reduction
XDS
data scaling
XDS
Structure of the glycosylase domain of MBD4 bound to AP site containing DNA
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
VAL
448
A
VAL
23
HELX_P
A
PHE
453
A
PHE
28
1
1
6
A
ASP
455
A
ASP
30
HELX_P
A
LEU
466
A
LEU
41
1
2
12
A
SER
470
A
SER
45
HELX_P
A
TYR
485
A
TYR
60
1
3
16
A
SER
487
A
SER
62
HELX_P
A
ARG
492
A
ARG
67
1
4
6
A
ASP
495
A
ASP
70
HELX_P
A
LYS
504
A
LYS
79
1
5
10
A
PRO
505
A
PRO
80
HELX_P
A
GLY
507
A
GLY
82
5
6
3
A
LEU
508
A
LEU
83
HELX_P
A
LYS
526
A
LYS
101
1
7
19
A
TYR
530
A
TYR
105
HELX_P
A
LEU
534
A
LEU
109
5
8
5
A
GLY
538
A
GLY
113
HELX_P
A
CYS
549
A
CYS
124
1
9
12
A
GLU
552
A
GLU
127
HELX_P
A
VAL
556
A
VAL
131
5
10
5
A
ASP
560
A
ASP
135
HELX_P
A
ASN
573
A
ASN
148
1
11
14
covale
1.656
both
C
DG
6
B
O3'
DG
6
1_555
C
3DR
7
B
P
3DR
7
1_555
covale
1.605
both
C
3DR
7
B
O3'
3DR
7
1_555
C
DG
8
B
P
DG
8
1_555
hydrog
DC-DG PAIR
C
DC
1
B
N4
DC
1
1_555
D
DG
12
C
O6
DG
12
1_555
hydrog
DC-DG PAIR
C
DC
2
B
O2
DC
2
1_555
D
DG
11
C
N1
DG
11
1_555
hydrog
WATSON-CRICK
C
DA
3
B
N1
DA
3
1_555
D
DT
10
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
C
DA
3
B
N6
DA
3
1_555
D
DT
10
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
C
DG
4
B
N1
DG
4
1_555
D
DC
9
C
N3
DC
9
1_555
hydrog
WATSON-CRICK
C
DG
4
B
N2
DG
4
1_555
D
DC
9
C
O2
DC
9
1_555
hydrog
WATSON-CRICK
C
DG
4
B
O6
DG
4
1_555
D
DC
9
C
N4
DC
9
1_555
hydrog
WATSON-CRICK
C
DC
5
B
N3
DC
5
1_555
D
DG
8
C
N1
DG
8
1_555
hydrog
WATSON-CRICK
C
DC
5
B
N4
DC
5
1_555
D
DG
8
C
O6
DG
8
1_555
hydrog
WATSON-CRICK
C
DC
5
B
O2
DC
5
1_555
D
DG
8
C
N2
DG
8
1_555
hydrog
WATSON-CRICK
C
DG
6
B
N1
DG
6
1_555
D
DC
7
C
N3
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
6
B
N2
DG
6
1_555
D
DC
7
C
O2
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
6
B
O6
DG
6
1_555
D
DC
7
C
N4
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
8
B
N1
DG
8
1_555
D
DC
5
C
N3
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
8
B
N2
DG
8
1_555
D
DC
5
C
O2
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
8
B
O6
DG
8
1_555
D
DC
5
C
N4
DC
5
1_555
hydrog
WATSON-CRICK
C
DC
9
B
N3
DC
9
1_555
D
DG
4
C
N1
DG
4
1_555
hydrog
WATSON-CRICK
C
DC
9
B
N4
DC
9
1_555
D
DG
4
C
O6
DG
4
1_555
hydrog
WATSON-CRICK
C
DC
9
B
O2
DC
9
1_555
D
DG
4
C
N2
DG
4
1_555
hydrog
WATSON-CRICK
C
DA
10
B
N1
DA
10
1_555
D
DT
3
C
N3
DT
3
1_555
hydrog
WATSON-CRICK
C
DA
10
B
N6
DA
10
1_555
D
DT
3
C
O4
DT
3
1_555
hydrog
WATSON-CRICK
C
DG
11
B
N1
DG
11
1_555
D
DC
2
C
N3
DC
2
1_555
hydrog
WATSON-CRICK
C
DG
11
B
N2
DG
11
1_555
D
DC
2
C
O2
DC
2
1_555
hydrog
WATSON-CRICK
C
DG
11
B
O6
DG
11
1_555
D
DC
2
C
N4
DC
2
1_555
hydrog
WATSON-CRICK
C
DC
12
B
N3
DC
12
1_555
D
DG
1
C
N1
DG
1
1_555
hydrog
WATSON-CRICK
C
DC
12
B
N4
DC
12
1_555
D
DG
1
C
O6
DG
1
1_555
hydrog
WATSON-CRICK
C
DC
12
B
O2
DC
12
1_555
D
DG
1
C
N2
DG
1
1_555
HYDROLASE/DNA
HhH DNA glycosylase family, HYDROLASE-DNA complex
A
LYS
437
A
LYS
12
1
A
TRP
438
A
TRP
13
-6.56
MBD4_HUMAN
UNP
1
427
O95243
LSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPL
GLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS
4E9F
PDB
2
1
4E9F
CCAGCGNGCAGC
4E9F
PDB
3
1
4E9F
GCTGCGCGCTGG
427
580
4E9F
427
580
O95243
A
1
2
155
1
12
4E9F
1
12
4E9F
C
2
1
12
1
12
4E9F
1
12
4E9F
D
3
1
12
1
expression tag
MET
426
4E9F
A
O95243
UNP
1
1
expression tag
HIS
581
4E9F
A
O95243
UNP
156
1
expression tag
HIS
582
4E9F
A
O95243
UNP
157
1
expression tag
HIS
583
4E9F
A
O95243
UNP
158
1
expression tag
HIS
584
4E9F
A
O95243
UNP
159
1
expression tag
HIS
585
4E9F
A
O95243
UNP
160
1
expression tag
HIS
586
4E9F
A
O95243
UNP
161
BINDING SITE FOR RESIDUE EDO C 101
C
EDO
101
Software
4
A
ARG
468
A
ARG
43
4
1_555
C
DC
5
B
DC
5
4
1_555
C
DG
6
B
DG
6
4
1_555
D
DG
6
C
DG
6
4
1_555
19
P 21 21 21