0.027989
0.000000
0.006752
-0.000000
0.025158
0.000000
0.000000
-0.000000
0.018292
0.000000
0.000000
0.000000
Tempel, W.
Xu, C.
Liu, K.
Li, Y.
Bountra, C.
Arrowsmith, C.H.
Edwards, A.M.
Min, J.
Structural Genomics Consortium (SGC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.000
103.560
90.000
35.728
39.748
56.238
C11 H16 N5 O7 P
361.248
n
N6-METHYLADENOSINE-5'-MONOPHOSPHATE
RNA 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
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA 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
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
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UNKNOWN ATOM OR ION
non-polymer
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Y
1
N
C
Y
2
N
C
Y
3
N
C
N
4
N
O
N
5
N
O
Y
6
N
N
Y
7
N
N
Y
8
N
N
Y
9
N
C
N
10
N
N
N
11
N
C
Y
12
N
N
Y
13
N
C
N
14
N
O
N
15
N
C
N
16
R
C
N
17
N
O
N
18
R
C
N
19
R
C
N
20
N
O
N
21
S
C
N
22
N
O
N
23
N
P
N
24
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
O
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
N
N
55
S
C
N
56
N
C
N
57
N
O
N
58
N
C
N
59
N
C
N
60
N
C
N
61
N
N
N
62
N
C
N
63
N
N
N
64
N
N
N
65
N
O
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
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
N
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
H
N
98
N
N
N
99
S
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
C
N
104
N
O
N
105
N
O
N
106
N
O
N
107
N
H
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
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
N
O
N
124
R
C
N
125
N
O
N
126
R
C
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
C
N
132
N
N
N
133
N
C
N
134
N
C
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
H
N
148
N
H
N
149
N
N
N
150
R
C
N
151
N
C
N
152
N
O
N
153
N
C
N
154
N
S
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
O
N
164
N
P
N
165
N
O
N
166
N
O
N
167
N
O
N
168
N
C
N
169
R
C
N
170
N
O
N
171
S
C
N
172
N
O
N
173
R
C
N
174
N
O
N
175
R
C
Y
176
N
N
Y
177
N
C
Y
178
N
N
Y
179
N
C
N
180
N
C
N
181
N
O
N
182
N
N
N
183
N
C
N
184
N
N
N
185
N
N
Y
186
N
C
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
O
N
209
N
N
N
210
N
O
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
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
S
C
N
223
N
C
N
224
N
O
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
O
N
229
N
O
N
230
N
O
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
N
N
241
N
C
N
242
N
C
N
243
N
O
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
N
Y
257
N
C
Y
258
N
C
Y
259
N
N
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
O
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
S
C
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
H
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
H
N
294
N
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
C
N
302
N
C
N
303
N
C
N
304
N
O
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
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
N
323
N
C
N
324
N
C
N
325
N
C
N
326
N
N
N
327
N
O
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
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
S
N
350
N
C
N
351
N
O
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
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
N
374
N
O
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
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
O
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
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
N
408
N
O
N
409
N
O
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
N
N
418
S
C
N
419
N
C
N
420
N
O
N
421
R
C
N
422
N
O
N
423
N
C
N
424
N
O
N
425
N
H
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
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
N
Y
443
N
C
Y
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
N
448
N
O
N
449
N
H
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
N
N
462
S
C
N
463
N
C
N
464
N
O
N
465
N
C
Y
466
N
C
Y
467
N
C
Y
468
N
C
Y
469
N
C
Y
470
N
C
Y
471
N
C
N
472
N
O
N
473
N
O
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
O
N
486
N
P
N
487
N
O
N
488
N
O
N
489
N
O
N
490
N
C
N
491
R
C
N
492
N
O
N
493
S
C
N
494
N
O
N
495
R
C
N
496
N
O
N
497
R
C
N
498
N
N
N
499
N
C
N
500
N
O
N
501
N
N
N
502
N
C
N
503
N
O
N
504
N
C
N
505
N
C
N
506
N
H
N
507
N
H
N
508
N
H
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
N
N
520
S
C
N
521
N
C
N
522
N
O
N
523
N
C
N
524
N
C
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
H
N
537
N
H
Y
1
N
sing
Y
2
N
sing
Y
3
N
sing
Y
4
N
doub
Y
5
N
doub
Y
6
N
doub
Y
7
N
sing
N
8
N
sing
N
9
N
sing
Y
10
N
sing
Y
11
N
sing
Y
12
N
doub
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
sing
N
35
N
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
doub
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
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
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
doub
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
doub
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
doub
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
sing
N
103
N
doub
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
doub
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
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
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
doub
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
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
Y
185
N
sing
Y
186
N
sing
Y
187
N
doub
N
188
N
sing
Y
189
N
sing
N
190
N
sing
Y
191
N
doub
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
doub
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
doub
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
doub
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
doub
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
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
Y
258
N
sing
Y
259
N
doub
Y
260
N
doub
N
261
N
sing
Y
262
N
sing
N
263
N
sing
Y
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
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
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
sing
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
sing
N
317
N
sing
N
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
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
sing
N
340
N
sing
N
341
N
sing
N
342
N
doub
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
sing
N
361
N
doub
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
Y
366
N
doub
Y
367
N
sing
Y
368
N
sing
N
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
372
N
doub
N
373
N
sing
Y
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
doub
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
doub
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
doub
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
doub
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
Y
435
N
doub
Y
436
N
sing
Y
437
N
sing
N
438
N
sing
Y
439
N
doub
Y
440
N
sing
Y
441
N
sing
N
442
N
sing
Y
443
N
sing
Y
444
N
doub
N
445
N
sing
Y
446
N
doub
N
447
N
sing
Y
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
doub
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
Y
463
N
doub
Y
464
N
sing
Y
465
N
sing
N
466
N
sing
Y
467
N
doub
N
468
N
sing
Y
469
N
doub
N
470
N
sing
Y
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
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
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
doub
N
507
N
sing
N
508
N
doub
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
doub
N
518
N
sing
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
US
Nat.Chem.Biol.
1552-4450
10
927
929
10.1038/nchembio.1654
25242552
Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain.
2014
10.2210/pdb4r3i/pdb
pdb_00004r3i
100
1
IMAGE PLATE
2014-01-21
RIGAKU RAXIS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
18823.826
YTH domain-containing protein 1
1
man
polymer
1600.035
RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
1
syn
polymer
UNKNOWN ATOM OR ION
7
syn
non-polymer
18.015
water
89
nat
water
Putative splicing factor YT521, YT521-B
no
no
GTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGG
SPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQV
IHKMRH
GTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGG
SPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQV
IHKMRH
A
polypeptide(L)
no
yes
GG(6MZ)CU
GGACU
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
YTHDC1, KIAA1966, YT521
9606
Homo sapiens
562
Escherichia coli
BL21-V2R-pRARE2
plasmid
pET28-MHL
1
1.9
35.8
VAPOR DIFFUSION
6.5
25% PEG3350, 0.2 M amonium sulfate, 0.1 M bis-tris, pH 6.5, vapor diffusion, temperature 291K
291
Structural Genomics Consortium
SGC
chem_comp_atom
chem_comp_bond
database_2
entity_poly
struct_conn
struct_ref_seq_dif
pdbx_initial_refinement_model
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
Polymer sequence
Refinement description
1
0
2014-09-17
1
1
2014-10-01
1
2
2014-11-19
2
0
2024-02-28
2
1
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity_poly.pdbx_seq_one_letter_code_can
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2014-08-15
REL
REL
UNX
UNKNOWN ATOM OR ION
HOH
water
32630
synthetic construct
sample
a different crystal form of same protein
Other
experimental model
UNX
1
3
UNX
UNX
601
A
UNX
2
3
UNX
UNX
602
A
UNX
3
3
UNX
UNX
603
A
UNX
4
3
UNX
UNX
604
A
UNX
5
3
UNX
UNX
605
A
UNX
6
3
UNX
UNX
606
A
UNX
7
3
UNX
UNX
607
A
HOH
1
4
HOH
HOH
701
A
HOH
3
4
HOH
HOH
702
A
HOH
6
4
HOH
HOH
703
A
HOH
9
4
HOH
HOH
704
A
HOH
10
4
HOH
HOH
705
A
HOH
11
4
HOH
HOH
706
A
HOH
12
4
HOH
HOH
707
A
HOH
13
4
HOH
HOH
708
A
HOH
14
4
HOH
HOH
709
A
HOH
18
4
HOH
HOH
710
A
HOH
19
4
HOH
HOH
711
A
HOH
20
4
HOH
HOH
712
A
HOH
21
4
HOH
HOH
713
A
HOH
22
4
HOH
HOH
714
A
HOH
23
4
HOH
HOH
715
A
HOH
24
4
HOH
HOH
716
A
HOH
25
4
HOH
HOH
717
A
HOH
26
4
HOH
HOH
718
A
HOH
27
4
HOH
HOH
719
A
HOH
28
4
HOH
HOH
720
A
HOH
29
4
HOH
HOH
721
A
HOH
30
4
HOH
HOH
722
A
HOH
34
4
HOH
HOH
723
A
HOH
36
4
HOH
HOH
724
A
HOH
37
4
HOH
HOH
725
A
HOH
39
4
HOH
HOH
726
A
HOH
40
4
HOH
HOH
727
A
HOH
44
4
HOH
HOH
728
A
HOH
45
4
HOH
HOH
729
A
HOH
46
4
HOH
HOH
730
A
HOH
47
4
HOH
HOH
731
A
HOH
48
4
HOH
HOH
732
A
HOH
51
4
HOH
HOH
733
A
HOH
52
4
HOH
HOH
734
A
HOH
54
4
HOH
HOH
735
A
HOH
56
4
HOH
HOH
736
A
HOH
58
4
HOH
HOH
737
A
HOH
59
4
HOH
HOH
738
A
HOH
60
4
HOH
HOH
739
A
HOH
62
4
HOH
HOH
740
A
HOH
63
4
HOH
HOH
741
A
HOH
64
4
HOH
HOH
742
A
HOH
65
4
HOH
HOH
743
A
HOH
66
4
HOH
HOH
744
A
HOH
67
4
HOH
HOH
745
A
HOH
68
4
HOH
HOH
746
A
HOH
69
4
HOH
HOH
747
A
HOH
70
4
HOH
HOH
748
A
HOH
71
4
HOH
HOH
749
A
HOH
72
4
HOH
HOH
750
A
HOH
73
4
HOH
HOH
751
A
HOH
74
4
HOH
HOH
752
A
HOH
75
4
HOH
HOH
753
A
HOH
76
4
HOH
HOH
754
A
HOH
77
4
HOH
HOH
755
A
HOH
79
4
HOH
HOH
756
A
HOH
80
4
HOH
HOH
757
A
HOH
81
4
HOH
HOH
758
A
HOH
82
4
HOH
HOH
759
A
HOH
83
4
HOH
HOH
760
A
HOH
86
4
HOH
HOH
761
A
HOH
87
4
HOH
HOH
762
A
HOH
88
4
HOH
HOH
763
A
HOH
89
4
HOH
HOH
764
A
HOH
90
4
HOH
HOH
765
A
HOH
91
4
HOH
HOH
766
A
HOH
92
4
HOH
HOH
767
A
HOH
94
4
HOH
HOH
768
A
HOH
95
4
HOH
HOH
769
A
HOH
96
4
HOH
HOH
770
A
HOH
97
4
HOH
HOH
771
A
HOH
98
4
HOH
HOH
772
A
HOH
99
4
HOH
HOH
773
A
HOH
100
4
HOH
HOH
774
A
HOH
5
4
HOH
HOH
101
B
HOH
7
4
HOH
HOH
102
B
HOH
8
4
HOH
HOH
103
B
HOH
31
4
HOH
HOH
104
B
HOH
32
4
HOH
HOH
105
B
HOH
33
4
HOH
HOH
106
B
HOH
35
4
HOH
HOH
107
B
HOH
41
4
HOH
HOH
108
B
HOH
49
4
HOH
HOH
109
B
HOH
50
4
HOH
HOH
110
B
HOH
53
4
HOH
HOH
111
B
HOH
55
4
HOH
HOH
112
B
HOH
57
4
HOH
HOH
113
B
HOH
61
4
HOH
HOH
114
B
HOH
85
4
HOH
HOH
115
B
GLY
344
n
1
GLY
344
A
THR
345
n
2
THR
345
A
SER
346
n
3
SER
346
A
LYS
347
n
4
LYS
347
A
LEU
348
n
5
LEU
348
A
LYS
349
n
6
LYS
349
A
TYR
350
n
7
TYR
350
A
VAL
351
n
8
VAL
351
A
LEU
352
n
9
LEU
352
A
GLN
353
n
10
GLN
353
A
ASP
354
n
11
ASP
354
A
ALA
355
n
12
ALA
355
A
ARG
356
n
13
ARG
356
A
PHE
357
n
14
PHE
357
A
PHE
358
n
15
PHE
358
A
LEU
359
n
16
LEU
359
A
ILE
360
n
17
ILE
360
A
LYS
361
n
18
LYS
361
A
SER
362
n
19
SER
362
A
ASN
363
n
20
ASN
363
A
ASN
364
n
21
ASN
364
A
HIS
365
n
22
HIS
365
A
GLU
366
n
23
GLU
366
A
ASN
367
n
24
ASN
367
A
VAL
368
n
25
VAL
368
A
SER
369
n
26
SER
369
A
LEU
370
n
27
LEU
370
A
ALA
371
n
28
ALA
371
A
LYS
372
n
29
LYS
372
A
ALA
373
n
30
ALA
373
A
LYS
374
n
31
LYS
374
A
GLY
375
n
32
GLY
375
A
VAL
376
n
33
VAL
376
A
TRP
377
n
34
TRP
377
A
SER
378
n
35
SER
378
A
THR
379
n
36
THR
379
A
LEU
380
n
37
LEU
380
A
PRO
381
n
38
PRO
381
A
VAL
382
n
39
VAL
382
A
ASN
383
n
40
ASN
383
A
GLU
384
n
41
GLU
384
A
LYS
385
n
42
LYS
385
A
LYS
386
n
43
LYS
386
A
LEU
387
n
44
LEU
387
A
ASN
388
n
45
ASN
388
A
LEU
389
n
46
LEU
389
A
ALA
390
n
47
ALA
390
A
PHE
391
n
48
PHE
391
A
ARG
392
n
49
ARG
392
A
SER
393
n
50
SER
393
A
ALA
394
n
51
ALA
394
A
ARG
395
n
52
ARG
395
A
SER
396
n
53
SER
396
A
VAL
397
n
54
VAL
397
A
ILE
398
n
55
ILE
398
A
LEU
399
n
56
LEU
399
A
ILE
400
n
57
ILE
400
A
PHE
401
n
58
PHE
401
A
SER
402
n
59
SER
402
A
VAL
403
n
60
VAL
403
A
ARG
404
n
61
ARG
404
A
GLU
405
n
62
GLU
405
A
SER
406
n
63
SER
406
A
GLY
407
n
64
GLY
407
A
LYS
408
n
65
LYS
408
A
PHE
409
n
66
PHE
409
A
GLN
410
n
67
GLN
410
A
GLY
411
n
68
GLY
411
A
PHE
412
n
69
PHE
412
A
ALA
413
n
70
ALA
413
A
ARG
414
n
71
ARG
414
A
LEU
415
n
72
LEU
415
A
SER
416
n
73
SER
416
A
SER
417
n
74
SER
417
A
GLU
418
n
75
GLU
418
A
SER
419
n
76
SER
419
A
HIS
420
n
77
HIS
420
A
HIS
421
n
78
HIS
421
A
GLY
422
n
79
GLY
422
A
GLY
423
n
80
GLY
423
A
SER
424
n
81
SER
424
A
PRO
425
n
82
PRO
425
A
ILE
426
n
83
ILE
426
A
HIS
427
n
84
HIS
427
A
TRP
428
n
85
TRP
428
A
VAL
429
n
86
VAL
429
A
LEU
430
n
87
LEU
430
A
PRO
431
n
88
PRO
431
A
ALA
432
n
89
ALA
432
A
GLY
433
n
90
GLY
433
A
MET
434
n
91
MET
434
A
SER
435
n
92
SER
435
A
ALA
436
n
93
ALA
436
A
LYS
437
n
94
LYS
437
A
MET
438
n
95
MET
438
A
LEU
439
n
96
LEU
439
A
GLY
440
n
97
GLY
440
A
GLY
441
n
98
GLY
441
A
VAL
442
n
99
VAL
442
A
PHE
443
n
100
PHE
443
A
LYS
444
n
101
LYS
444
A
ILE
445
n
102
ILE
445
A
ASP
446
n
103
ASP
446
A
TRP
447
n
104
TRP
447
A
ILE
448
n
105
ILE
448
A
CYS
449
n
106
CYS
449
A
ARG
450
n
107
ARG
450
A
ARG
451
n
108
ARG
451
A
GLU
452
n
109
GLU
452
A
LEU
453
n
110
LEU
453
A
PRO
454
n
111
PRO
454
A
PHE
455
n
112
PHE
455
A
THR
456
n
113
THR
456
A
LYS
457
n
114
LYS
457
A
SER
458
n
115
SER
458
A
ALA
459
n
116
ALA
459
A
HIS
460
n
117
HIS
460
A
LEU
461
n
118
LEU
461
A
THR
462
n
119
THR
462
A
ASN
463
n
120
ASN
463
A
PRO
464
n
121
PRO
464
A
TRP
465
n
122
TRP
465
A
ASN
466
n
123
ASN
466
A
GLU
467
n
124
GLU
467
A
HIS
468
n
125
HIS
468
A
LYS
469
n
126
LYS
469
A
PRO
470
n
127
PRO
470
A
VAL
471
n
128
VAL
471
A
LYS
472
n
129
LYS
472
A
ILE
473
n
130
ILE
473
A
GLY
474
n
131
GLY
474
A
ARG
475
n
132
ARG
475
A
ASP
476
n
133
ASP
476
A
GLY
477
n
134
GLY
477
A
GLN
478
n
135
GLN
478
A
GLU
479
n
136
GLU
479
A
ILE
480
n
137
ILE
480
A
GLU
481
n
138
GLU
481
A
LEU
482
n
139
LEU
482
A
GLU
483
n
140
GLU
483
A
CYS
484
n
141
CYS
484
A
GLY
485
n
142
GLY
485
A
THR
486
n
143
THR
486
A
GLN
487
n
144
GLN
487
A
LEU
488
n
145
LEU
488
A
CYS
489
n
146
CYS
489
A
LEU
490
n
147
LEU
490
A
LEU
491
n
148
LEU
491
A
PHE
492
n
149
PHE
492
A
PRO
493
n
150
PRO
493
A
PRO
494
n
151
PRO
494
A
ASP
495
n
152
ASP
495
A
GLU
496
n
153
GLU
496
A
SER
497
n
154
SER
497
A
ILE
498
n
155
ILE
498
A
ASP
499
n
156
ASP
499
A
LEU
500
n
157
LEU
500
A
TYR
501
n
158
TYR
501
A
GLN
502
n
159
GLN
502
A
VAL
503
n
160
VAL
503
A
ILE
504
n
161
ILE
504
A
HIS
505
n
162
HIS
505
A
LYS
506
n
163
LYS
506
A
MET
507
n
164
MET
507
A
n
165
508
A
n
166
509
A
G
1
n
1
G
1
B
G
2
n
2
G
2
B
6MZ
3
n
3
6MZ
3
B
C
4
n
4
C
4
B
U
5
n
5
U
5
B
software_defined_assembly
PISA
2
dimeric
1990
-9
8310
B
6MZ
3
N6-METHYLADENOSINE-5'-MONOPHOSPHATE
B
6MZ
3
A
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
TRP
377
A
N
TRP
34
A
O
PHE
443
A
O
PHE
100
A
O
ILE
448
A
O
ILE
105
A
N
PHE
412
A
N
PHE
69
A
O
ALA
413
A
O
ALA
70
A
N
LEU
399
A
N
LEU
56
A
O
ILE
398
A
O
ILE
55
A
N
ARG
356
A
N
ARG
13
A
N
PHE
357
A
N
PHE
14
A
O
ILE
480
A
O
ILE
137
A
N
PHE
409
A
N
PHE
66
A
O
LEU
453
A
O
LEU
110
1
A
OG1
THR
345
A
OG1
THR
2
1
Y
1
A
CG2
THR
345
A
CG2
THR
2
1
Y
1
A
OG
SER
346
A
OG
SER
3
1
Y
1
A
CE
LYS
349
A
CE
LYS
6
1
Y
1
A
NZ
LYS
349
A
NZ
LYS
6
1
Y
1
A
CD
LYS
374
A
CD
LYS
31
1
Y
1
A
CE
LYS
374
A
CE
LYS
31
1
Y
1
A
NZ
LYS
374
A
NZ
LYS
31
1
Y
1
A
CD
LYS
386
A
CD
LYS
43
1
Y
1
A
CE
LYS
386
A
CE
LYS
43
1
Y
1
A
NZ
LYS
386
A
NZ
LYS
43
1
Y
1
A
NE
ARG
392
A
NE
ARG
49
1
Y
1
A
CZ
ARG
392
A
CZ
ARG
49
1
Y
1
A
NH1
ARG
392
A
NH1
ARG
49
1
Y
1
A
NH2
ARG
392
A
NH2
ARG
49
1
Y
1
A
NZ
LYS
408
A
NZ
LYS
65
1
Y
1
A
CG
LYS
437
A
CG
LYS
94
1
Y
1
A
CD
LYS
437
A
CD
LYS
94
1
Y
1
A
CE
LYS
437
A
CE
LYS
94
1
Y
1
A
NZ
LYS
437
A
NZ
LYS
94
1
Y
1
A
CG
GLN
502
A
CG
GLN
159
1
Y
1
A
CD
GLN
502
A
CD
GLN
159
1
Y
1
A
OE1
GLN
502
A
OE1
GLN
159
1
Y
1
A
NE2
GLN
502
A
NE2
GLN
159
1
Y
1
A
CG
HIS
505
A
CG
HIS
162
1
Y
1
A
ND1
HIS
505
A
ND1
HIS
162
1
Y
1
A
CD2
HIS
505
A
CD2
HIS
162
1
Y
1
A
CE1
HIS
505
A
CE1
HIS
162
1
Y
1
A
NE2
HIS
505
A
NE2
HIS
162
1
Y
1
A
ARG
508
A
ARG
165
1
Y
1
A
HIS
509
A
HIS
166
1
Y
1
A
GLU
405
53.71
16.26
73.530
21.3503
2.110
-1.3300
-0.0000
0.7400
-1.5700
-0.0000
2.2800
0.9450
0.8920
Diffraction data for molecular replacement and early refinement were reduced with HKL3000. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
0.2636
0.2034
0.2064
1.8000
30.0000
700
14013
5.0000
97.1700
0.2466
0.1859
1.000
0.500
0.7846
4.2370
0.1280
0.1687
0.1627
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.1690
0.1630
0.8000
0.8000
1.2000
a different crystal form of same protein
MAXIMUM LIKELIHOOD
MASK
1.8000
30.0000
89
1477
7
106
1275
0.012
0.019
1430
0.001
0.020
1308
1.371
1.923
1957
0.792
3.000
3013
6.206
5.000
163
31.952
23.636
55
11.705
15.000
225
15.135
15.000
7
0.077
0.200
215
0.007
0.021
1525
0.001
0.020
326
1.826
2.108
655
1.825
2.102
654
2.749
3.144
817
0.2910
0.2660
1.8470
48
932
980
20
94.4100
1.800
34.730
4R3I
14029
0.112
1
8.500
3.600
97.100
0.587
1.800
1.840
2.300
2551
773
0.369
1
3.300
90.700
0.041
8.990
34.730
23.600
366
114
0.027
1
3.200
92.000
data scaling
Phil Evans
07/01/14
http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html
Aimless
program
0.2.17
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
Dec. 10, 2013
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.14
data reduction
XDS
The crystal structure of an RNA complex
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
GLY
344
A
GLY
1
HELX_P
A
GLN
353
A
GLN
10
1
1
10
A
ASN
364
A
ASN
21
HELX_P
A
GLY
375
A
GLY
32
1
2
12
A
LEU
380
A
LEU
37
HELX_P
A
ARG
392
A
ARG
49
1
3
13
A
ALA
436
A
ALA
93
HELX_P
A
GLY
440
A
GLY
97
5
4
5
A
THR
456
A
THR
113
HELX_P
A
ALA
459
A
ALA
116
5
5
4
A
ASN
463
A
ASN
120
HELX_P
A
GLU
467
A
GLU
124
5
6
5
A
GLU
481
A
GLU
138
HELX_P
A
PHE
492
A
PHE
149
1
7
12
A
ASP
499
A
ASP
156
HELX_P
A
MET
507
A
MET
164
1
8
9
covale
1.610
both
B
G
2
B
O3'
G
2
1_555
B
6MZ
3
B
P
6MZ
3
1_555
covale
1.591
both
B
6MZ
3
B
O3'
6MZ
3
1_555
B
C
4
B
P
C
4
1_555
RNA BINDING PROTEIN/RNA
structural genomics, Structural Genomics Consortium, SGC, RNA BINDING PROTEIN-RNA complex
YTDC1_HUMAN
UNP
1
345
Q96MU7
TSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGS
PIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQVI
HKMRH
4R3I
PDB
2
4R3I
345
509
4R3I
345
509
Q96MU7
A
1
2
166
1
5
4R3I
1
5
4R3I
B
2
1
5
1
expression tag
GLY
344
4R3I
A
Q96MU7
UNP
1
6
2
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
VAL
376
A
VAL
33
A
TRP
377
A
TRP
34
A
PHE
443
A
PHE
100
A
CYS
449
A
CYS
106
A
GLY
411
A
GLY
68
A
LEU
415
A
LEU
72
A
SER
396
A
SER
53
A
VAL
403
A
VAL
60
A
ALA
355
A
ALA
12
A
SER
362
A
SER
19
A
GLU
479
A
GLU
136
A
ILE
480
A
ILE
137
A
LYS
408
A
LYS
65
A
PHE
409
A
PHE
66
A
LEU
453
A
LEU
110
A
PRO
454
A
PRO
111
4
P 1 21 1