0.015468
0.000000
0.001024
0.000000
0.021951
0.000000
0.000000
0.000000
0.008603
0.000000
0.000000
0.000000
Morgunova, E.
Popov, A.
Taipale, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
93.790
90.000
64.650
45.555
116.499
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
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
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
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
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
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
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
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
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
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
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
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
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
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
N
259
N
C
N
260
N
C
N
261
N
O
N
262
N
N
N
263
N
O
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
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
O
N
283
N
O
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
N
N
294
N
C
N
295
N
C
N
296
N
O
N
297
N
O
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
Y
308
N
C
Y
309
N
N
Y
310
N
C
Y
311
N
C
Y
312
N
N
N
313
N
O
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
H
N
324
N
O
N
325
N
H
N
326
N
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
S
C
N
332
N
C
N
333
N
C
N
334
N
C
N
335
N
O
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
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
C
N
357
N
O
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
N
N
380
N
O
N
381
N
H
N
382
N
H
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
H
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
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
N
407
N
O
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
H
N
419
N
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
N
424
N
O
N
425
N
O
N
426
N
H
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
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
R
C
N
438
N
O
N
439
N
C
N
440
N
O
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
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
N
Y
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
N
464
N
O
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
N
N
478
S
C
N
479
N
C
N
480
N
O
N
481
N
C
Y
482
N
C
Y
483
N
C
Y
484
N
C
Y
485
N
C
Y
486
N
C
Y
487
N
C
N
488
N
O
N
489
N
O
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
H
N
499
N
H
N
500
N
H
N
501
N
N
N
502
S
C
N
503
N
C
N
504
N
O
N
505
N
C
N
506
N
C
N
507
N
C
N
508
N
O
N
509
N
H
N
510
N
H
N
511
N
H
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
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
sing
N
44
N
sing
N
45
N
doub
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
sing
N
57
N
doub
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
doub
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
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
doub
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
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
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
doub
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
sing
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
Y
131
N
sing
Y
132
N
sing
Y
133
N
doub
N
134
N
sing
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
doub
N
140
N
sing
N
141
N
sing
Y
142
N
sing
Y
143
N
doub
N
144
N
sing
Y
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
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
sing
N
170
N
sing
N
171
N
doub
N
172
N
sing
N
173
N
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
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
N
202
N
sing
N
203
N
sing
Y
204
N
sing
Y
205
N
sing
Y
206
N
doub
N
207
N
sing
Y
208
N
sing
N
209
N
sing
Y
210
N
doub
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
doub
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
doub
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
sing
N
244
N
sing
N
245
N
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
doub
N
250
N
sing
N
251
N
sing
N
252
N
doub
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
doub
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
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
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
doub
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
doub
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
doub
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
Y
314
N
sing
Y
315
N
doub
Y
316
N
doub
N
317
N
sing
Y
318
N
sing
N
319
N
sing
Y
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
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
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
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
doub
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
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
doub
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
Y
403
N
doub
Y
404
N
sing
Y
405
N
sing
N
406
N
sing
Y
407
N
doub
N
408
N
sing
Y
409
N
doub
N
410
N
sing
Y
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
doub
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
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
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
doub
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
Y
455
N
doub
Y
456
N
sing
Y
457
N
sing
N
458
N
sing
Y
459
N
doub
Y
460
N
sing
Y
461
N
sing
N
462
N
sing
Y
463
N
sing
Y
464
N
doub
N
465
N
sing
Y
466
N
doub
N
467
N
sing
Y
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
doub
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
Y
483
N
doub
Y
484
N
sing
Y
485
N
sing
N
486
N
sing
Y
487
N
doub
N
488
N
sing
Y
489
N
doub
N
490
N
sing
Y
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
doub
N
503
N
sing
N
504
N
sing
N
505
N
sing
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
US
Science
SCIEAS
0038
1095-9203
356
10.1126/science.aaj2239
28473536
Impact of cytosine methylation on DNA binding specificities of human transcription factors.
2017
10.2210/pdb5lux/pdb
pdb_00005lux
100
1
PIXEL
2016-07-03
DECTRIS PILATUS 6M-F
SINGLE WAVELENGTH
M
x-ray
1
0.9724
1.0
ID23-1
ESRF
0.9724
SYNCHROTRON
ESRF BEAMLINE ID23-1
5173.370
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3')
1
syn
polymer
7887.118
Homeobox protein CDX-1
2
man
polymer
5462.551
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')
1
syn
polymer
5267.478
DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
1
syn
polymer
5596.684
DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
1
syn
polymer
18.015
water
10
nat
water
Caudal-type homeobox protein 1
no
yes
(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DT)(DA)(5CM)(DG)(DA)(DC)(DC)(DT)(DC)
TTGTGTTTTACGACCTC
A
polydeoxyribonucleotide
no
no
TKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKK
TKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKK
K,L
polypeptide(L)
no
yes
(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DT)(DA)(5CM)(DG)(DA)(DC)(DC)(DT)(DC)(DC)
TTGTGTTTTACGACCTCC
B
polydeoxyribonucleotide
no
yes
(DG)(DA)(DG)(DG)(DT)(5CM)(DG)(DT)(DA)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DA)
GAGGTCGTAAAACACAA
F
polydeoxyribonucleotide
no
yes
(DG)(DG)(DA)(DG)(DG)(DT)(5CM)(DG)(DT)(DA)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DA)
GGAGGTCGTAAAACACAA
E
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
Human
sample
1
63
CDX1
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
Rosetta
plasmid
Biological sequence
pETG20A
1
2.30
46.43
VAPOR DIFFUSION, SITTING DROP
8.0
PEG MME (5000),KCl, MgCl2, 2-Methyl propanol, Tris buffer
293
-11.439
1
20
A
1
F
36
1.613
A_DT1:DA36_F
1
-27.677
0.540
0.743
-0.101
1.304
1
20
A
2
F
35
3.869
A_DT2:DA35_F
2
-31.677
-0.499
-0.696
0.298
-23.572
1
19
A
3
F
34
-1.435
A_DG3:DC34_F
3
-1.868
-0.415
-0.231
0.052
-11.434
1
20
A
4
F
33
1.645
A_DT4:DA33_F
4
-2.788
-0.405
0.823
-0.259
1.759
1
19
A
5
F
32
0.844
A_DG5:DC32_F
5
-15.850
-0.987
0.338
-0.150
-9.515
1
20
A
6
F
31
0.805
A_DT6:DA31_F
6
-13.005
0.389
0.454
0.020
-6.860
1
20
A
7
F
30
1.990
A_DT7:DA30_F
7
-13.963
0.513
0.228
-0.140
-11.227
1
20
A
8
F
29
3.436
A_DT8:DA29_F
8
-11.967
0.330
0.407
-0.300
-7.605
1
20
A
9
F
28
0.510
A_DT9:DA28_F
9
0.070
0.151
0.687
-0.388
1.260
1
20
A
10
F
27
2.156
A_DA10:DT27_F
10
-3.416
-0.026
0.155
-0.127
7.988
1
19
A
11
F
26
-6.338
A_5CM11:DG26_F
11
-20.452
0.395
-0.430
-0.320
5.053
1
19
A
12
F
25
-5.926
A_DG12:5CM25_F
12
-5.529
0.141
0.003
-0.048
11.779
1
20
A
13
F
24
-9.639
A_DA13:DT24_F
13
-3.766
1.059
0.220
-0.275
20.335
1
19
A
14
F
23
-2.054
A_DC14:DG23_F
14
-18.909
0.290
-0.135
-0.373
-1.994
1
A
15
F
22
6.473
A_DC15:DG22_F
15
-18.319
-0.704
0.651
0.295
6.878
1
20
A
16
F
21
-6.860
A_DT16:DA21_F
16
-14.880
-0.534
0.532
0.182
-0.875
1
19
A
17
F
20
-0.463
A_DC17:DG20_F
17
-8.113
0.265
-0.450
0.136
-7.000
1
20
B
1
E
36
1.717
B_DT1:DA36_E
18
-25.813
0.521
0.937
-0.128
-25.043
1
19
B
3
E
34
-1.942
B_DG3:DC34_E
19
-2.508
-0.136
-0.198
0.085
-12.743
1
20
B
4
E
33
0.513
B_DT4:DA33_E
20
-2.935
-0.170
0.896
-0.250
0.682
1
19
B
5
E
32
-0.077
B_DG5:DC32_E
21
-15.924
-0.875
0.375
-0.180
-10.037
1
20
B
6
E
31
0.281
B_DT6:DA31_E
22
-12.521
0.429
0.514
-0.034
-7.194
1
20
B
7
E
30
2.464
B_DT7:DA30_E
23
-13.716
0.545
0.266
-0.157
-11.531
1
20
B
8
E
29
4.794
B_DT8:DA29_E
24
-11.670
0.406
0.427
-0.255
-7.622
1
20
B
9
E
28
1.445
B_DT9:DA28_E
25
-0.376
0.164
0.661
-0.343
2.131
1
20
B
10
E
27
4.310
B_DA10:DT27_E
26
-3.580
0.013
0.167
-0.103
8.837
1
19
B
11
E
26
-3.652
B_5CM11:DG26_E
27
-21.392
0.392
-0.428
-0.391
4.678
1
19
B
12
E
25
-4.788
B_DG12:5CM25_E
28
-5.285
0.054
-0.089
-0.113
11.278
1
20
B
13
E
24
-8.335
B_DA13:DT24_E
29
-3.239
0.990
0.118
-0.281
20.180
1
19
B
14
E
23
-1.026
B_DC14:DG23_E
30
-17.940
0.246
-0.254
-0.330
-1.424
1
B
15
E
22
7.126
B_DC15:DG22_E
31
-17.978
-0.619
0.470
0.337
7.059
1
20
B
16
E
21
-6.013
B_DT16:DA21_E
32
-16.840
-0.467
0.332
0.146
-4.768
1
19
B
17
E
20
3.455
B_DC17:DG20_E
33
-14.813
0.044
-0.426
0.287
11.856
1
B
18
E
19
40.944
B_DC18:DG19_E
34
-32.883
0.141
-1.039
0.296
2.342
34.395
A
A
1
2
2.415
F
F
36
35
2.531
1.402
-0.204
0.308
AA_DT1DT2:DA35DA36_FF
1
11.353
-19.549
32.491
0.353
1.704
4.007
47.738
A
A
2
3
9.127
F
F
35
34
3.943
7.310
0.217
1.589
AA_DT2DG3:DC34DA35_FF
2
-10.104
12.615
46.173
1.242
-1.266
2.811
22.787
A
A
3
4
15.599
F
F
34
33
3.190
5.932
-0.310
-0.544
AA_DG3DT4:DA33DC34_FF
3
-8.756
23.023
20.213
-3.449
-2.275
2.831
33.757
A
A
4
5
2.482
F
F
33
32
2.829
1.438
0.142
0.145
AA_DT4DG5:DC32DA33_FF
4
3.798
-6.555
33.519
0.047
0.290
3.466
41.289
A
A
5
6
4.563
F
F
32
31
3.535
3.214
-0.213
-0.852
AA_DG5DT6:DA31DC32_FF
5
-1.295
1.839
41.149
-1.578
0.152
3.047
36.448
A
A
6
7
-5.675
F
F
31
30
3.004
-3.544
-0.099
-0.663
AA_DT6DT7:DA30DA31_FF
6
1.399
-2.240
36.255
-0.604
0.339
3.269
38.029
A
A
7
8
-8.424
F
F
30
29
3.288
-5.465
0.323
0.015
AA_DT7DT8:DA29DA30_FF
7
3.354
-5.170
37.504
0.725
-0.064
3.175
33.600
A
A
8
9
14.806
F
F
29
28
3.257
8.471
-0.227
0.102
AA_DT8DT9:DA28DA29_FF
8
0.850
-1.486
32.534
-1.210
0.532
2.991
34.081
A
A
9
10
8.883
F
F
28
27
2.978
5.154
0.862
-0.436
AA_DT9DA10:DT27DA28_FF
9
6.824
-11.761
33.022
-1.505
-0.464
3.018
33.027
A
A
10
11
-0.673
F
F
27
26
3.127
-0.381
-0.520
-0.871
AA_DA105CM11:DG26DT27_FF
10
5.269
-9.306
32.613
-1.472
1.758
3.374
36.421
A
A
11
12
24.978
F
F
26
25
3.454
15.165
0.288
0.518
AA_5CM11DG12:5CM25DG26_FF
11
0.839
-1.381
33.201
-1.480
-0.333
3.002
38.866
A
A
12
13
9.770
F
F
25
24
2.999
6.459
-0.905
-0.260
AA_DG12DA13:DT245CM25_FF
12
-4.578
6.925
38.082
-1.119
0.844
3.003
27.859
A
A
13
14
10.958
F
F
24
23
3.120
5.244
0.536
-0.456
AA_DA13DC14:DG23DT24_FF
13
1.218
-2.544
27.344
-2.131
-0.837
3.140
37.134
A
A
14
15
13.346
F
F
23
22
3.536
8.399
0.223
-1.093
AA_DC14DC15:DG22DG23_FF
14
-5.584
8.873
35.785
-2.883
-1.126
3.314
31.752
A
A
15
16
-3.350
F
F
22
21
3.104
-1.823
-1.310
-0.761
AA_DC15DT16:DA21DG22_FF
15
-5.342
9.814
31.259
-1.059
1.424
3.309
45.889
A
A
16
17
-6.013
F
F
21
20
3.287
-4.667
0.909
0.566
AA_DT16DC17:DG20DA21_FF
16
6.511
-8.389
45.222
1.136
-0.593
6.782
80.485
B
B
1
3
-0.492
E
E
36
34
6.790
-0.635
-0.678
1.125
BB_DT1DG3:DC34DA36_EE
17
0.075
-0.058
80.483
0.905
0.529
2.809
22.631
B
B
3
4
15.904
E
E
34
33
3.185
6.000
-0.344
-0.540
BB_DG3DT4:DA33DC34_EE
18
-8.807
23.344
19.994
-3.502
-2.246
2.820
32.878
B
B
4
5
3.883
E
E
33
32
2.818
2.191
0.159
0.139
BB_DT4DG5:DC32DA33_EE
19
4.115
-7.294
32.555
-0.079
0.328
3.454
40.854
B
B
5
6
4.684
E
E
32
31
3.526
3.266
-0.198
-0.856
BB_DG5DT6:DA31DC32_EE
20
-1.301
1.866
40.709
-1.609
0.130
3.040
36.273
B
B
6
7
-5.223
E
E
31
30
3.002
-3.246
-0.068
-0.653
BB_DT6DT7:DA30DA31_EE
21
1.822
-2.932
36.088
-0.628
0.345
3.273
38.309
B
B
7
8
-8.783
E
E
30
29
3.294
-5.736
0.356
0.035
BB_DT7DT8:DA29DA30_EE
22
3.581
-5.484
37.729
0.781
-0.089
3.163
32.945
B
B
8
9
14.100
E
E
29
28
3.239
7.921
-0.262
0.104
BB_DT8DT9:DA28DA29_EE
23
1.092
-1.944
31.987
-1.156
0.647
2.985
33.776
B
B
9
10
7.846
E
E
28
27
2.950
4.519
0.900
-0.423
BB_DT9DA10:DT27DA28_EE
24
6.373
-11.064
32.886
-1.400
-0.600
3.008
32.812
B
B
10
11
-0.324
E
E
27
26
3.122
-0.182
-0.496
-0.859
BB_DA105CM11:DG26DT27_EE
25
5.348
-9.509
32.384
-1.491
1.745
3.366
36.645
B
B
11
12
26.042
E
E
26
25
3.470
15.864
0.198
0.509
BB_5CM11DG12:5CM25DG26_EE
26
1.054
-1.730
33.123
-1.590
-0.155
3.006
38.888
B
B
12
13
9.878
E
E
25
24
3.005
6.533
-0.906
-0.257
BB_DG12DA13:DT245CM25_EE
27
-4.546
6.873
38.095
-1.124
0.847
2.996
27.558
B
B
13
14
11.336
E
E
24
23
3.118
5.365
0.524
-0.447
BB_DA13DC14:DG23DT24_EE
28
1.336
-2.823
27.008
-2.178
-0.791
3.196
36.757
B
B
14
15
12.160
E
E
23
22
3.544
7.593
0.220
-1.079
BB_DC14DC15:DG22DG23_EE
29
-5.027
8.050
35.649
-2.794
-1.066
3.336
31.716
B
B
15
16
-5.393
E
E
22
21
3.112
-2.930
-1.296
-0.765
BB_DC15DT16:DA21DG22_EE
30
-5.253
9.667
31.155
-0.863
1.410
3.322
47.325
B
B
16
17
-9.443
E
E
21
20
3.361
-7.531
0.923
0.597
BB_DT16DC17:DG20DA21_EE
31
6.255
-7.843
46.359
1.376
-0.625
3.665
44.487
B
B
17
18
0.199
E
E
20
19
3.079
0.148
2.435
2.306
BB_DC17DC18:DG19DG20_EE
32
13.674
-18.330
42.435
3.031
-1.881
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ncs_dom_lim
repository
Initial release
Data collection
Database references
Refinement description
1
0
2017-05-17
1
1
2024-01-17
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ncs_dom_lim.beg_auth_comp_id
_struct_ncs_dom_lim.beg_label_asym_id
_struct_ncs_dom_lim.beg_label_comp_id
_struct_ncs_dom_lim.beg_label_seq_id
_struct_ncs_dom_lim.end_auth_comp_id
_struct_ncs_dom_lim.end_label_asym_id
_struct_ncs_dom_lim.end_label_comp_id
_struct_ncs_dom_lim.end_label_seq_id
N
PDBE
Y
PDBE
2016-09-12
REL
REL
HOH
water
9606
Homo sapiens
sample
1
17
9606
Homo sapiens
sample
1
18
9606
Homo sapiens
sample
1
17
9606
Homo sapiens
sample
1
18
5LTX
PDB
experimental model
HOH
9
6
HOH
HOH
101
A
HOH
1
6
HOH
HOH
102
A
HOH
6
6
HOH
HOH
301
K
HOH
4
6
HOH
HOH
101
B
HOH
3
6
HOH
HOH
102
B
HOH
8
6
HOH
HOH
301
L
HOH
10
6
HOH
HOH
302
L
HOH
2
6
HOH
HOH
101
F
HOH
7
6
HOH
HOH
101
E
HOH
5
6
HOH
HOH
102
E
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DG
3
n
3
DG
3
A
DT
4
n
4
DT
4
A
DG
5
n
5
DG
5
A
DT
6
n
6
DT
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
DT
9
n
9
DT
9
A
DA
10
n
10
DA
10
A
5CM
11
n
11
5CM
11
A
DG
12
n
12
DG
12
A
DA
13
n
13
DA
13
A
DC
14
n
14
DC
14
A
DC
15
n
15
DC
15
A
DT
16
n
16
DT
16
A
DC
17
n
17
DC
17
A
THR
153
n
1
THR
153
K
LYS
154
n
2
LYS
154
K
ASP
155
n
3
ASP
155
K
LYS
156
n
4
LYS
156
K
TYR
157
n
5
TYR
157
K
ARG
158
n
6
ARG
158
K
VAL
159
n
7
VAL
159
K
VAL
160
n
8
VAL
160
K
TYR
161
n
9
TYR
161
K
THR
162
n
10
THR
162
K
ASP
163
n
11
ASP
163
K
HIS
164
n
12
HIS
164
K
GLN
165
n
13
GLN
165
K
ARG
166
n
14
ARG
166
K
LEU
167
n
15
LEU
167
K
GLU
168
n
16
GLU
168
K
LEU
169
n
17
LEU
169
K
GLU
170
n
18
GLU
170
K
LYS
171
n
19
LYS
171
K
GLU
172
n
20
GLU
172
K
PHE
173
n
21
PHE
173
K
HIS
174
n
22
HIS
174
K
TYR
175
n
23
TYR
175
K
SER
176
n
24
SER
176
K
ARG
177
n
25
ARG
177
K
TYR
178
n
26
TYR
178
K
ILE
179
n
27
ILE
179
K
THR
180
n
28
THR
180
K
ILE
181
n
29
ILE
181
K
ARG
182
n
30
ARG
182
K
ARG
183
n
31
ARG
183
K
LYS
184
n
32
LYS
184
K
SER
185
n
33
SER
185
K
GLU
186
n
34
GLU
186
K
LEU
187
n
35
LEU
187
K
ALA
188
n
36
ALA
188
K
ALA
189
n
37
ALA
189
K
ASN
190
n
38
ASN
190
K
LEU
191
n
39
LEU
191
K
GLY
192
n
40
GLY
192
K
LEU
193
n
41
LEU
193
K
THR
194
n
42
THR
194
K
GLU
195
n
43
GLU
195
K
ARG
196
n
44
ARG
196
K
GLN
197
n
45
GLN
197
K
VAL
198
n
46
VAL
198
K
LYS
199
n
47
LYS
199
K
ILE
200
n
48
ILE
200
K
TRP
201
n
49
TRP
201
K
PHE
202
n
50
PHE
202
K
GLN
203
n
51
GLN
203
K
ASN
204
n
52
ASN
204
K
ARG
205
n
53
ARG
205
K
ARG
206
n
54
ARG
206
K
ALA
207
n
55
ALA
207
K
LYS
208
n
56
LYS
208
K
GLU
209
n
57
GLU
209
K
ARG
210
n
58
ARG
210
K
LYS
211
n
59
LYS
211
K
VAL
212
n
60
VAL
212
K
ASN
213
n
61
ASN
213
K
LYS
214
n
62
LYS
214
K
LYS
215
n
63
LYS
215
K
DT
1
n
1
DT
1
B
DT
2
n
2
DT
2
B
DG
3
n
3
DG
3
B
DT
4
n
4
DT
4
B
DG
5
n
5
DG
5
B
DT
6
n
6
DT
6
B
DT
7
n
7
DT
7
B
DT
8
n
8
DT
8
B
DT
9
n
9
DT
9
B
DA
10
n
10
DA
10
B
5CM
11
n
11
5CM
11
B
DG
12
n
12
DG
12
B
DA
13
n
13
DA
13
B
DC
14
n
14
DC
14
B
DC
15
n
15
DC
15
B
DT
16
n
16
DT
16
B
DC
17
n
17
DC
17
B
DC
18
n
18
DC
18
B
THR
153
n
1
THR
153
L
LYS
154
n
2
LYS
154
L
ASP
155
n
3
ASP
155
L
LYS
156
n
4
LYS
156
L
TYR
157
n
5
TYR
157
L
ARG
158
n
6
ARG
158
L
VAL
159
n
7
VAL
159
L
VAL
160
n
8
VAL
160
L
TYR
161
n
9
TYR
161
L
THR
162
n
10
THR
162
L
ASP
163
n
11
ASP
163
L
HIS
164
n
12
HIS
164
L
GLN
165
n
13
GLN
165
L
ARG
166
n
14
ARG
166
L
LEU
167
n
15
LEU
167
L
GLU
168
n
16
GLU
168
L
LEU
169
n
17
LEU
169
L
GLU
170
n
18
GLU
170
L
LYS
171
n
19
LYS
171
L
GLU
172
n
20
GLU
172
L
PHE
173
n
21
PHE
173
L
HIS
174
n
22
HIS
174
L
TYR
175
n
23
TYR
175
L
SER
176
n
24
SER
176
L
ARG
177
n
25
ARG
177
L
TYR
178
n
26
TYR
178
L
ILE
179
n
27
ILE
179
L
THR
180
n
28
THR
180
L
ILE
181
n
29
ILE
181
L
ARG
182
n
30
ARG
182
L
ARG
183
n
31
ARG
183
L
LYS
184
n
32
LYS
184
L
SER
185
n
33
SER
185
L
GLU
186
n
34
GLU
186
L
LEU
187
n
35
LEU
187
L
ALA
188
n
36
ALA
188
L
ALA
189
n
37
ALA
189
L
ASN
190
n
38
ASN
190
L
LEU
191
n
39
LEU
191
L
GLY
192
n
40
GLY
192
L
LEU
193
n
41
LEU
193
L
THR
194
n
42
THR
194
L
GLU
195
n
43
GLU
195
L
ARG
196
n
44
ARG
196
L
GLN
197
n
45
GLN
197
L
VAL
198
n
46
VAL
198
L
LYS
199
n
47
LYS
199
L
ILE
200
n
48
ILE
200
L
TRP
201
n
49
TRP
201
L
PHE
202
n
50
PHE
202
L
GLN
203
n
51
GLN
203
L
ASN
204
n
52
ASN
204
L
ARG
205
n
53
ARG
205
L
ARG
206
n
54
ARG
206
L
ALA
207
n
55
ALA
207
L
LYS
208
n
56
LYS
208
L
GLU
209
n
57
GLU
209
L
ARG
210
n
58
ARG
210
L
LYS
211
n
59
LYS
211
L
VAL
212
n
60
VAL
212
L
ASN
213
n
61
ASN
213
L
LYS
214
n
62
LYS
214
L
n
63
215
L
DG
20
n
1
DG
20
F
DA
21
n
2
DA
21
F
DG
22
n
3
DG
22
F
DG
23
n
4
DG
23
F
DT
24
n
5
DT
24
F
5CM
25
n
6
5CM
25
F
DG
26
n
7
DG
26
F
DT
27
n
8
DT
27
F
DA
28
n
9
DA
28
F
DA
29
n
10
DA
29
F
DA
30
n
11
DA
30
F
DA
31
n
12
DA
31
F
DC
32
n
13
DC
32
F
DA
33
n
14
DA
33
F
DC
34
n
15
DC
34
F
DA
35
n
16
DA
35
F
DA
36
n
17
DA
36
F
DG
19
n
1
DG
19
E
DG
20
n
2
DG
20
E
DA
21
n
3
DA
21
E
DG
22
n
4
DG
22
E
DG
23
n
5
DG
23
E
DT
24
n
6
DT
24
E
5CM
25
n
7
5CM
25
E
DG
26
n
8
DG
26
E
DT
27
n
9
DT
27
E
DA
28
n
10
DA
28
E
DA
29
n
11
DA
29
E
DA
30
n
12
DA
30
E
DA
31
n
13
DA
31
E
DC
32
n
14
DC
32
E
DA
33
n
15
DA
33
E
DC
34
n
16
DC
34
E
DA
35
n
17
DA
35
E
DA
36
n
18
DA
36
E
3.7738
-5.3455
1.1137
8.5789
-0.7686
1.0503
0.0883
0.0943
-0.0935
-0.2177
-0.1055
0.3280
-0.0066
-0.0123
0.0172
0.0627
-0.0169
-0.1382
0.0728
0.0922
1.2139
refined
-16.9594
-28.0758
-18.8237
X-RAY DIFFRACTION
3.0003
-0.4198
-0.7761
4.9472
-0.8368
8.2518
-0.0088
-0.1938
0.4035
0.1509
0.3714
0.1172
-0.1827
-0.3809
-0.3626
0.0884
0.0463
-0.1102
0.0683
0.0197
1.0710
refined
-16.3559
-19.2056
-8.3546
X-RAY DIFFRACTION
2.4681
4.1588
-0.0137
7.2239
0.2636
0.5077
-0.0367
-0.0832
0.4386
-0.0412
-0.0567
0.6200
0.0848
0.0868
0.0934
0.1097
-0.0271
-0.1752
0.0468
-0.0149
1.4353
refined
-17.2022
-26.1199
19.0727
X-RAY DIFFRACTION
3.8612
2.7022
-0.8118
2.9736
-0.6212
7.9813
-0.3573
0.6044
-0.1185
0.0009
0.2294
-0.1786
0.4174
-0.4584
0.1279
0.1140
-0.1174
-0.1012
0.1439
0.0210
1.1686
refined
-15.8970
-34.0289
8.4250
X-RAY DIFFRACTION
A
1
A
17
X-RAY DIFFRACTION
1
F
20
F
36
X-RAY DIFFRACTION
1
K
153
K
215
X-RAY DIFFRACTION
2
B
1
B
18
X-RAY DIFFRACTION
3
E
19
E
36
X-RAY DIFFRACTION
3
L
153
L
214
X-RAY DIFFRACTION
4
software_defined_assembly
PISA
3
trimeric
software_defined_assembly
PISA
3
trimeric
4990
-15
9110
5090
-15
9380
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
L
LYS
215
D
LYS
63
1
Y
1
A
K
OP2
OH
DA
TYR
10
161
2.13
1
K
K
LYS
TYR
156
157
-31.06
1
L
L
LYS
TYR
156
157
-33.01
1
16.68
2.70
111.00
127.68
K
K
K
N
CA
C
ASP
ASP
ASP
155
155
155
N
1
3.01
0.50
120.30
123.31
K
K
K
NE
CZ
NH1
ARG
ARG
ARG
158
158
158
N
1
16.32
2.70
111.00
127.32
L
L
L
N
CA
C
ASP
ASP
ASP
155
155
155
N
1
-8.99
0.90
105.70
96.71
E
E
E
O5'
P
OP1
DG
DG
DG
22
22
22
N
1
A
A
O3'
P
DT
DT
8
9
-0.087
0.012
1.607
1.520
Y
1
F
F
O3'
P
DA
DA
30
31
-0.072
0.012
1.607
1.535
Y
1
K
LYS
156
170.13
84.92
1
L
LYS
156
169.16
85.19
237.960
90.6030
35.870
4.6900
0.0000
0.3800
-2.6800
0.0000
-2.0400
0.9170
0.8640
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
0.2995
0.2411
0.2467
3.2300
58.1200
515
4909
9.5000
97.1200
100.7090
0.6970
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.7290
0.8000
0.8000
1.2000
5LTX
3.2300
58.1200
10
2552
92.56
0
1439
1103
195
0.013
0.015
2731
0.004
0.020
1929
1.852
1.521
3970
1.689
3.000
4473
8.182
5.000
123
37.059
21.562
64
21.348
15.000
238
15.538
15.000
18
0.124
0.200
365
0.009
0.020
2042
0.003
0.020
615
3.548
4.388
498
3.529
4.371
497
6.051
6.540
619
1
A
1
5198
X-RAY DIFFRACTION
interatomic distance
0.010
0.050
2
B
1
5198
X-RAY DIFFRACTION
interatomic distance
0.010
0.050
1
K
2
15516
X-RAY DIFFRACTION
interatomic distance
0.080
0.050
2
L
2
15516
X-RAY DIFFRACTION
interatomic distance
0.080
0.050
1
F
3
5388
X-RAY DIFFRACTION
interatomic distance
0.010
0.050
2
E
3
5388
X-RAY DIFFRACTION
interatomic distance
0.010
0.050
0.2900
0.3380
3.3170
27
262
289
20
73.3500
57
3.230
58.120
5LUX
5425
0.995
0.174
1
5.300
3.400
97.200
0.533
3.230
3.490
1.91
0.891
1
3.200
88.900
data scaling
Aimless
0.5.25
refinement
REFMAC
5.8.0135
data extraction
PDB_EXTRACT
3.20
data reduction
XDS
phasing
MOLREP
N
Homeobox transcription factor CDX1 bound to methylated DNA
1
N
N
2
N
N
3
N
N
2
N
N
4
N
N
5
N
N
6
N
N
6
N
N
6
N
N
6
N
N
6
N
N
6
N
N
K
THR
162
B
THR
10
HELX_P
K
SER
176
B
SER
24
1
AA1
15
K
THR
180
B
THR
28
HELX_P
K
GLY
192
B
GLY
40
1
AA2
13
K
THR
194
B
THR
42
HELX_P
K
LYS
215
B
LYS
63
1
AA3
22
L
THR
162
D
THR
10
HELX_P
L
SER
176
D
SER
24
1
AA4
15
L
THR
180
D
THR
28
HELX_P
L
GLY
192
D
GLY
40
1
AA5
13
L
THR
194
D
THR
42
HELX_P
L
LYS
214
D
LYS
62
1
AA6
21
covale
1.590
both
A
DA
10
A
O3'
DA
10
1_555
A
5CM
11
A
P
5CM
11
1_555
covale
1.606
both
A
5CM
11
A
O3'
5CM
11
1_555
A
DG
12
A
P
DG
12
1_555
covale
1.550
both
B
DA
10
C
O3'
DA
10
1_555
B
5CM
11
C
P
5CM
11
1_555
covale
1.593
both
B
5CM
11
C
O3'
5CM
11
1_555
B
DG
12
C
P
DG
12
1_555
covale
1.651
both
F
DT
24
E
O3'
DT
5
1_555
F
5CM
25
E
P
5CM
6
1_555
covale
1.575
both
F
5CM
25
E
O3'
5CM
6
1_555
F
DG
26
E
P
DG
7
1_555
covale
1.608
both
E
DT
24
F
O3'
DT
6
1_555
E
5CM
25
F
P
5CM
7
1_555
covale
1.584
both
E
5CM
25
F
O3'
5CM
7
1_555
E
DG
26
F
P
DG
8
1_555
hydrog
DT-DA PAIR
A
DT
1
A
O4
DT
1
1_555
F
DA
35
E
N6
DA
16
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
F
DA
36
E
N1
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
F
DA
36
E
N6
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
F
DA
35
E
N1
DA
16
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
F
DA
35
E
N6
DA
16
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
F
DC
34
E
N3
DC
15
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
F
DC
34
E
O2
DC
15
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
F
DC
34
E
N4
DC
15
1_555
hydrog
DT-DC MISPAIR
A
DT
4
A
O4
DT
4
1_555
F
DC
32
E
N4
DC
13
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
F
DA
33
E
N1
DA
14
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
F
DA
33
E
N6
DA
14
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
F
DC
32
E
N3
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
F
DC
32
E
O2
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
F
DC
32
E
N4
DC
13
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
F
DA
31
E
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
F
DA
31
E
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
F
DA
30
E
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
F
DA
30
E
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
F
DA
29
E
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
F
DA
29
E
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
F
DA
28
E
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
F
DA
28
E
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
F
DT
27
E
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
F
DT
27
E
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
5CM
11
A
N3
5CM
11
1_555
F
DG
26
E
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
5CM
11
A
N4
5CM
11
1_555
F
DG
26
E
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
5CM
11
A
O2
5CM
11
1_555
F
DG
26
E
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
F
5CM
25
E
N3
5CM
6
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
F
5CM
25
E
O2
5CM
6
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
F
5CM
25
E
N4
5CM
6
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
13
1_555
F
DT
24
E
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
13
1_555
F
DT
24
E
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N3
DC
14
1_555
F
DG
23
E
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N4
DC
14
1_555
F
DG
23
E
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
14
A
O2
DC
14
1_555
F
DG
23
E
N2
DG
4
1_555
hydrog
DC-DG PAIR
A
DC
15
A
O2
DC
15
1_555
F
DG
22
E
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DT
16
A
N3
DT
16
1_555
F
DA
21
E
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
16
A
O4
DT
16
1_555
F
DA
21
E
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DC
17
A
N3
DC
17
1_555
F
DG
20
E
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
17
A
N4
DC
17
1_555
F
DG
20
E
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
17
A
O2
DC
17
1_555
F
DG
20
E
N2
DG
1
1_555
hydrog
WATSON-CRICK
B
DT
1
C
N3
DT
1
1_555
E
DA
36
F
N1
DA
18
1_555
hydrog
WATSON-CRICK
B
DT
1
C
O4
DT
1
1_555
E
DA
36
F
N6
DA
18
1_555
hydrog
WATSON-CRICK
B
DG
3
C
N1
DG
3
1_555
E
DC
34
F
N3
DC
16
1_555
hydrog
WATSON-CRICK
B
DG
3
C
N2
DG
3
1_555
E
DC
34
F
O2
DC
16
1_555
hydrog
WATSON-CRICK
B
DG
3
C
O6
DG
3
1_555
E
DC
34
F
N4
DC
16
1_555
hydrog
DT-DC MISPAIR
B
DT
4
C
O4
DT
4
1_555
E
DC
32
F
N4
DC
14
1_555
hydrog
WATSON-CRICK
B
DT
4
C
N3
DT
4
1_555
E
DA
33
F
N1
DA
15
1_555
hydrog
WATSON-CRICK
B
DT
4
C
O4
DT
4
1_555
E
DA
33
F
N6
DA
15
1_555
hydrog
WATSON-CRICK
B
DG
5
C
N1
DG
5
1_555
E
DC
32
F
N3
DC
14
1_555
hydrog
WATSON-CRICK
B
DG
5
C
N2
DG
5
1_555
E
DC
32
F
O2
DC
14
1_555
hydrog
WATSON-CRICK
B
DG
5
C
O6
DG
5
1_555
E
DC
32
F
N4
DC
14
1_555
hydrog
WATSON-CRICK
B
DT
6
C
N3
DT
6
1_555
E
DA
31
F
N1
DA
13
1_555
hydrog
WATSON-CRICK
B
DT
6
C
O4
DT
6
1_555
E
DA
31
F
N6
DA
13
1_555
hydrog
WATSON-CRICK
B
DT
7
C
N3
DT
7
1_555
E
DA
30
F
N1
DA
12
1_555
hydrog
WATSON-CRICK
B
DT
7
C
O4
DT
7
1_555
E
DA
30
F
N6
DA
12
1_555
hydrog
WATSON-CRICK
B
DT
8
C
N3
DT
8
1_555
E
DA
29
F
N1
DA
11
1_555
hydrog
WATSON-CRICK
B
DT
8
C
O4
DT
8
1_555
E
DA
29
F
N6
DA
11
1_555
hydrog
WATSON-CRICK
B
DT
9
C
N3
DT
9
1_555
E
DA
28
F
N1
DA
10
1_555
hydrog
WATSON-CRICK
B
DT
9
C
O4
DT
9
1_555
E
DA
28
F
N6
DA
10
1_555
hydrog
WATSON-CRICK
B
DA
10
C
N1
DA
10
1_555
E
DT
27
F
N3
DT
9
1_555
hydrog
WATSON-CRICK
B
DA
10
C
N6
DA
10
1_555
E
DT
27
F
O4
DT
9
1_555
hydrog
WATSON-CRICK
B
5CM
11
C
N3
5CM
11
1_555
E
DG
26
F
N1
DG
8
1_555
hydrog
WATSON-CRICK
B
5CM
11
C
N4
5CM
11
1_555
E
DG
26
F
O6
DG
8
1_555
hydrog
WATSON-CRICK
B
5CM
11
C
O2
5CM
11
1_555
E
DG
26
F
N2
DG
8
1_555
hydrog
WATSON-CRICK
B
DG
12
C
N1
DG
12
1_555
E
5CM
25
F
N3
5CM
7
1_555
hydrog
WATSON-CRICK
B
DG
12
C
N2
DG
12
1_555
E
5CM
25
F
O2
5CM
7
1_555
hydrog
WATSON-CRICK
B
DG
12
C
O6
DG
12
1_555
E
5CM
25
F
N4
5CM
7
1_555
hydrog
WATSON-CRICK
B
DA
13
C
N1
DA
13
1_555
E
DT
24
F
N3
DT
6
1_555
hydrog
WATSON-CRICK
B
DA
13
C
N6
DA
13
1_555
E
DT
24
F
O4
DT
6
1_555
hydrog
WATSON-CRICK
B
DC
14
C
N3
DC
14
1_555
E
DG
23
F
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
14
C
N4
DC
14
1_555
E
DG
23
F
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
14
C
O2
DC
14
1_555
E
DG
23
F
N2
DG
5
1_555
hydrog
DC-DG PAIR
B
DC
15
C
O2
DC
15
1_555
E
DG
22
F
N2
DG
4
1_555
hydrog
WATSON-CRICK
B
DT
16
C
N3
DT
16
1_555
E
DA
21
F
N1
DA
3
1_555
hydrog
WATSON-CRICK
B
DT
16
C
O4
DT
16
1_555
E
DA
21
F
N6
DA
3
1_555
hydrog
WATSON-CRICK
B
DC
17
C
N3
DC
17
1_555
E
DG
20
F
N1
DG
2
1_555
hydrog
WATSON-CRICK
B
DC
17
C
N4
DC
17
1_555
E
DG
20
F
O6
DG
2
1_555
hydrog
WATSON-CRICK
B
DC
17
C
O2
DC
17
1_555
E
DG
20
F
N2
DG
2
1_555
hydrog
DC-DG PAIR
B
DC
18
C
O2
DC
18
1_555
E
DG
19
F
N2
DG
1
1_555
hydrog
DC-DG PAIR
B
DC
18
C
O2
DC
18
1_555
E
DG
20
F
N2
DG
2
1_555
TRANSCRIPTION
transcription, transcription factor, methylated DNA
A
B
K
L
F
E
A
DT
1
A
DT
1
A
DT
16
A
DT
16
0
B
DT
1
C
DT
1
B
DT
16
C
DT
16
0
K
THR
153
B
THR
1
K
ASN
213
B
ASN
61
0
L
THR
153
D
THR
1
L
ASN
213
D
ASN
61
0
F
DG
20
E
DG
1
F
DA
35
E
DA
16
0
E
DG
20
F
DG
2
E
DA
35
F
DA
17
0
5LUX
PDB
1
1
5LUX
CDX1_HUMAN
UNP
2
153
P47902
TKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKK
5LUX
PDB
3
1
5LUX
5LUX
PDB
4
1
5LUX
5LUX
PDB
5
1
5LUX
1
17
5LUX
1
17
5LUX
A
1
1
17
153
215
5LUX
153
215
P47902
K
2
1
63
1
18
5LUX
1
18
5LUX
B
3
1
18
153
215
5LUX
153
215
P47902
L
2
1
63
20
36
5LUX
20
36
5LUX
F
4
1
17
19
36
5LUX
19
36
5LUX
E
5
1
18
5
I 1 2 1