0.015497
0.000000
0.000000
0.000000
0.015497
0.000000
0.000000
0.000000
0.006368
0.00000
0.00000
0.00000
Franco-Echevarria, E.
Perez-Canadillas, J.M.
Gonzalez, B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
64.529
64.529
157.033
C10 H14 N5 O7 P
347.221
y
ADENOSINE-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
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
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
N
N
147
R
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
S
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
O
N
161
N
P
N
162
N
O
N
163
N
O
N
164
N
O
N
165
N
C
N
166
R
C
N
167
N
O
N
168
S
C
N
169
N
O
N
170
R
C
N
171
N
O
N
172
R
C
Y
173
N
N
Y
174
N
C
Y
175
N
N
Y
176
N
C
N
177
N
C
N
178
N
O
N
179
N
N
N
180
N
C
N
181
N
N
N
182
N
N
Y
183
N
C
N
184
N
H
N
185
N
H
N
186
N
H
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
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
O
N
206
N
N
N
207
N
O
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
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
O
N
226
N
O
N
227
N
O
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
N
N
238
N
C
N
239
N
C
N
240
N
O
N
241
N
O
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
Y
252
N
C
Y
253
N
N
Y
254
N
C
Y
255
N
C
Y
256
N
N
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
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
O
N
269
N
H
N
270
N
H
N
271
N
N
N
272
S
C
N
273
N
C
N
274
N
O
N
275
S
C
N
276
N
C
N
277
N
C
N
278
N
C
N
279
N
O
N
280
N
H
N
281
N
H
N
282
N
H
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
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
C
N
299
N
C
N
300
N
C
N
301
N
O
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
N
N
316
S
C
N
317
N
C
N
318
N
O
N
319
N
C
N
320
N
C
N
321
N
C
N
322
N
C
N
323
N
N
N
324
N
O
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
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
N
N
341
S
C
N
342
N
C
N
343
N
O
N
344
N
C
N
345
N
C
N
346
N
S
N
347
N
C
N
348
N
O
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
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
N
371
N
O
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
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
N
388
N
C
N
389
N
C
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
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
N
405
N
O
N
406
N
O
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
N
N
415
S
C
N
416
N
C
N
417
N
O
N
418
R
C
N
419
N
O
N
420
N
C
N
421
N
O
N
422
N
H
N
423
N
H
N
424
N
H
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
N
N
432
S
C
N
433
N
C
N
434
N
O
N
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
N
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
C
Y
444
N
C
N
445
N
O
N
446
N
H
N
447
N
H
N
448
N
H
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
N
N
459
S
C
N
460
N
C
N
461
N
O
N
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
Y
466
N
C
Y
467
N
C
Y
468
N
C
N
469
N
O
N
470
N
O
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
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
O
N
483
N
P
N
484
N
O
N
485
N
O
N
486
N
O
N
487
N
C
N
488
R
C
N
489
N
O
N
490
S
C
N
491
N
O
N
492
R
C
N
493
N
O
N
494
R
C
N
495
N
N
N
496
N
C
N
497
N
O
N
498
N
N
N
499
N
C
N
500
N
O
N
501
N
C
N
502
N
C
N
503
N
H
N
504
N
H
N
505
N
H
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
N
N
517
S
C
N
518
N
C
N
519
N
O
N
520
N
C
N
521
N
C
N
522
N
C
N
523
N
O
N
524
N
H
N
525
N
H
N
526
N
H
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
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
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
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
doub
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
sing
N
58
N
doub
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
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
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
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
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
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
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
doub
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
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
Y
182
N
sing
Y
183
N
sing
Y
184
N
doub
N
185
N
sing
Y
186
N
sing
N
187
N
sing
Y
188
N
doub
N
189
N
doub
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
doub
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
N
204
N
doub
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
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
doub
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
doub
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
Y
255
N
sing
Y
256
N
doub
Y
257
N
doub
N
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
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
sing
N
271
N
sing
N
272
N
sing
N
273
N
doub
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
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
doub
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
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
doub
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
Y
363
N
doub
Y
364
N
sing
Y
365
N
sing
N
366
N
sing
Y
367
N
doub
N
368
N
sing
Y
369
N
doub
N
370
N
sing
Y
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
doub
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
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
doub
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
doub
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
Y
432
N
doub
Y
433
N
sing
Y
434
N
sing
N
435
N
sing
Y
436
N
doub
Y
437
N
sing
Y
438
N
sing
N
439
N
sing
Y
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
443
N
doub
N
444
N
sing
Y
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
doub
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
Y
460
N
doub
Y
461
N
sing
Y
462
N
sing
N
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
doub
N
476
N
sing
N
477
N
sing
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
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
doub
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
doub
N
504
N
sing
N
505
N
doub
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
N
514
N
doub
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
1362-4962
45
10293
10305
10.1093/nar/gkx685
28973465
The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition.
2017
10.2210/pdb5o1z/pdb
pdb_00005o1z
100
1
PIXEL
2016-11-09
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.979290
1.0
XALOC
ALBA
0.979290
SYNCHROTRON
ALBA BEAMLINE XALOC
20108.586
Protein NRD1
UNP residues 290-468
1
man
polymer
1899.213
RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')
1
syn
polymer
18.015
water
1
nat
water
no
no
GSIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHIKVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSV
ILNNSRKHAFVKVYSRHEAENVLQNFNKDGALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSG
QPLVTGIVFEEPDIIVGEGV
GSIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHIKVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSV
ILNNSRKHAFVKVYSRHEAENVLQNFNKDGALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSG
QPLVTGIVFEEPDIIVGEGV
A
polypeptide(L)
no
no
CGUAAA
CGUAAA
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Baker's yeast
sample
1
180
NRD1, YNL251C, N0868
4932
Saccharomyces cerevisiae
562
Escherichia coli
Biological sequence
1
2.32
66.88
VAPOR DIFFUSION
1M Sodium Potassium Phosphate pH 7.4
291
struct
citation
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Structure summary
Database references
Data collection
Database references
Refinement description
1
0
2017-08-02
1
1
2017-09-13
1
2
2017-10-11
1
3
2024-01-17
_struct.title
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Spain
CSIC
BFU2014-53762-P, CTQ2014-52633
N
PDBE
Y
PDBE
2017-05-19
REL
REL
HOH
water
4932
Saccharomyces cerevisiae
sample
1
6
5O1W
PDB
experimental model
HOH
1
3
HOH
HOH
501
A
n
1
289
A
n
2
290
A
n
3
291
A
n
4
292
A
n
5
293
A
n
6
294
A
n
7
295
A
n
8
296
A
n
9
297
A
n
10
298
A
n
11
299
A
n
12
300
A
n
13
301
A
ASN
302
n
14
ASN
302
A
HIS
303
n
15
HIS
303
A
HIS
304
n
16
HIS
304
A
LEU
305
n
17
LEU
305
A
TYR
306
n
18
TYR
306
A
PRO
307
n
19
PRO
307
A
ASP
308
n
20
ASP
308
A
GLU
309
n
21
GLU
309
A
LEU
310
n
22
LEU
310
A
ASN
311
n
23
ASN
311
A
VAL
312
n
24
VAL
312
A
SER
313
n
25
SER
313
A
ASN
314
n
26
ASN
314
A
ASN
315
n
27
ASN
315
A
PRO
316
n
28
PRO
316
A
HIS
317
n
29
HIS
317
A
TYR
318
n
30
TYR
318
A
ARG
319
n
31
ARG
319
A
PRO
320
n
32
PRO
320
A
LYS
321
n
33
LYS
321
A
PRO
322
n
34
PRO
322
A
VAL
323
n
35
VAL
323
A
SER
324
n
36
SER
324
A
TYR
325
n
37
TYR
325
A
ASP
326
n
38
ASP
326
A
SER
327
n
39
SER
327
A
THR
328
n
40
THR
328
A
LEU
329
n
41
LEU
329
A
PRO
330
n
42
PRO
330
A
PRO
331
n
43
PRO
331
A
ASP
332
n
44
ASP
332
A
HIS
333
n
45
HIS
333
A
ILE
334
n
46
ILE
334
A
LYS
335
n
47
LYS
335
A
VAL
336
n
48
VAL
336
A
TYR
337
n
49
TYR
337
A
SER
338
n
50
SER
338
A
ARG
339
n
51
ARG
339
A
THR
340
n
52
THR
340
A
LEU
341
n
53
LEU
341
A
PHE
342
n
54
PHE
342
A
ILE
343
n
55
ILE
343
A
GLY
344
n
56
GLY
344
A
GLY
345
n
57
GLY
345
A
VAL
346
n
58
VAL
346
A
PRO
347
n
59
PRO
347
A
LEU
348
n
60
LEU
348
A
ASN
349
n
61
ASN
349
A
MET
350
n
62
MET
350
A
LYS
351
n
63
LYS
351
A
GLU
352
n
64
GLU
352
A
TRP
353
n
65
TRP
353
A
ASP
354
n
66
ASP
354
A
LEU
355
n
67
LEU
355
A
ALA
356
n
68
ALA
356
A
ASN
357
n
69
ASN
357
A
VAL
358
n
70
VAL
358
A
LEU
359
n
71
LEU
359
A
LYS
360
n
72
LYS
360
A
PRO
361
n
73
PRO
361
A
PHE
362
n
74
PHE
362
A
ALA
363
n
75
ALA
363
A
GLU
364
n
76
GLU
364
A
VAL
365
n
77
VAL
365
A
GLN
366
n
78
GLN
366
A
SER
367
n
79
SER
367
A
VAL
368
n
80
VAL
368
A
ILE
369
n
81
ILE
369
A
LEU
370
n
82
LEU
370
A
ASN
371
n
83
ASN
371
A
ASN
372
n
84
ASN
372
A
SER
373
n
85
SER
373
A
ARG
374
n
86
ARG
374
A
LYS
375
n
87
LYS
375
A
HIS
376
n
88
HIS
376
A
ALA
377
n
89
ALA
377
A
PHE
378
n
90
PHE
378
A
VAL
379
n
91
VAL
379
A
LYS
380
n
92
LYS
380
A
VAL
381
n
93
VAL
381
A
TYR
382
n
94
TYR
382
A
SER
383
n
95
SER
383
A
ARG
384
n
96
ARG
384
A
HIS
385
n
97
HIS
385
A
GLU
386
n
98
GLU
386
A
ALA
387
n
99
ALA
387
A
GLU
388
n
100
GLU
388
A
ASN
389
n
101
ASN
389
A
VAL
390
n
102
VAL
390
A
LEU
391
n
103
LEU
391
A
GLN
392
n
104
GLN
392
A
ASN
393
n
105
ASN
393
A
PHE
394
n
106
PHE
394
A
ASN
395
n
107
ASN
395
A
LYS
396
n
108
LYS
396
A
ASP
397
n
109
ASP
397
A
GLY
398
n
110
GLY
398
A
ALA
399
n
111
ALA
399
A
LEU
400
n
112
LEU
400
A
PRO
401
n
113
PRO
401
A
LEU
402
n
114
LEU
402
A
ARG
403
n
115
ARG
403
A
THR
404
n
116
THR
404
A
ARG
405
n
117
ARG
405
A
TRP
406
n
118
TRP
406
A
GLY
407
n
119
GLY
407
A
VAL
408
n
120
VAL
408
A
GLY
409
n
121
GLY
409
A
PHE
410
n
122
PHE
410
A
GLY
411
n
123
GLY
411
A
PRO
412
n
124
PRO
412
A
ARG
413
n
125
ARG
413
A
ASP
414
n
126
ASP
414
A
CYS
415
n
127
CYS
415
A
CYS
416
n
128
CYS
416
A
ASP
417
n
129
ASP
417
A
TYR
418
n
130
TYR
418
A
GLN
419
n
131
GLN
419
A
HIS
420
n
132
HIS
420
A
GLY
421
n
133
GLY
421
A
TYR
422
n
134
TYR
422
A
SER
423
n
135
SER
423
A
ILE
424
n
136
ILE
424
A
ILE
425
n
137
ILE
425
A
PRO
426
n
138
PRO
426
A
MET
427
n
139
MET
427
A
HIS
428
n
140
HIS
428
A
ARG
429
n
141
ARG
429
A
LEU
430
n
142
LEU
430
A
THR
431
n
143
THR
431
A
ASP
432
n
144
ASP
432
A
ALA
433
n
145
ALA
433
A
ASP
434
n
146
ASP
434
A
LYS
435
n
147
LYS
435
A
LYS
436
n
148
LYS
436
A
TRP
437
n
149
TRP
437
A
SER
438
n
150
SER
438
A
VAL
439
n
151
VAL
439
A
SER
440
n
152
SER
440
A
ALA
441
n
153
ALA
441
A
GLN
442
n
154
GLN
442
A
TRP
443
n
155
TRP
443
A
GLY
444
n
156
GLY
444
A
GLY
445
n
157
GLY
445
A
THR
446
n
158
THR
446
A
SER
447
n
159
SER
447
A
GLY
448
n
160
GLY
448
A
GLN
449
n
161
GLN
449
A
PRO
450
n
162
PRO
450
A
LEU
451
n
163
LEU
451
A
VAL
452
n
164
VAL
452
A
THR
453
n
165
THR
453
A
GLY
454
n
166
GLY
454
A
ILE
455
n
167
ILE
455
A
VAL
456
n
168
VAL
456
A
PHE
457
n
169
PHE
457
A
GLU
458
n
170
GLU
458
A
GLU
459
n
171
GLU
459
A
PRO
460
n
172
PRO
460
A
ASP
461
n
173
ASP
461
A
ILE
462
n
174
ILE
462
A
ILE
463
n
175
ILE
463
A
VAL
464
n
176
VAL
464
A
n
177
465
A
n
178
466
A
n
179
467
A
n
180
468
A
C
1
n
1
C
1
B
G
2
n
2
G
2
B
U
3
n
3
U
3
B
A
4
n
4
A
4
B
A
5
n
5
A
5
B
A
6
n
6
A
6
B
author_and_software_defined_assembly
PISA
2
dimeric
gel filtration
1410
-3
9010
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
SER
324
A
N
SER
36
A
O
VAL
456
A
O
VAL
168
A
O
PHE
457
A
O
PHE
169
A
N
LYS
335
A
N
LYS
47
A
N
ILE
334
A
N
ILE
46
A
O
ILE
425
A
O
ILE
137
A
O
TYR
422
A
O
TYR
134
A
N
ASP
417
A
N
ASP
129
A
N
ILE
369
A
N
ILE
81
A
O
PHE
378
A
O
PHE
90
A
O
VAL
379
A
O
VAL
91
A
N
LEU
341
A
N
LEU
53
A
N
PHE
342
A
N
PHE
54
A
O
ARG
405
A
O
ARG
117
1
A
GLY
289
A
GLY
1
1
Y
1
A
SER
290
A
SER
2
1
Y
1
A
ILE
291
A
ILE
3
1
Y
1
A
GLY
292
A
GLY
4
1
Y
1
A
ALA
293
A
ALA
5
1
Y
1
A
PRO
294
A
PRO
6
1
Y
1
A
ASN
295
A
ASN
7
1
Y
1
A
THR
296
A
THR
8
1
Y
1
A
THR
297
A
THR
9
1
Y
1
A
PHE
298
A
PHE
10
1
Y
1
A
GLY
299
A
GLY
11
1
Y
1
A
THR
300
A
THR
12
1
Y
1
A
ASN
301
A
ASN
13
1
Y
1
A
GLY
465
A
GLY
177
1
Y
1
A
GLU
466
A
GLU
178
1
Y
1
A
GLY
467
A
GLY
179
1
Y
1
A
VAL
468
A
VAL
180
1
Y
86.054
6.58
0.00
0.00
6.58
0.00
-13.17
0.934
0.908
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.21585
0.18113
0.18301
3.40
59.69
246
4739
4.9
99.94
20.849
0.307
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.411
0.80
0.80
1.20
5O1W
3.40
59.69
1
1437
0
126
1310
0.007
0.018
1492
0.002
0.020
1268
1.223
1.866
2060
0.944
3.000
2956
6.003
5.000
162
34.924
23.788
66
14.241
15.000
212
23.406
15.000
8
0.068
0.200
218
0.005
0.021
1576
0.001
0.020
310
2.973
8.288
651
2.973
8.284
650
4.965
12.424
812
4.963
12.429
813
3.599
9.464
841
3.597
9.471
842
6.029
14.118
1249
8.085
97.938
1630
8.083
97.943
1631
0.388
0.254
3.488
9
331
20
100.00
3.4
59.69
5O1Z
5025
0.157
0.033
1
22.2
23.9
100
0.578
3.4
3.67
8.5
989
0.116
1
25.2
100
refinement
REFMAC
5.8.0158
data reduction
XDS
model building
Coot
data scaling
Aimless
N
Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA)
1
N
N
2
N
N
3
N
N
A
LYS
351
A
LYS
63
HELX_P
A
LYS
360
A
LYS
72
1
AA1
10
A
SER
383
A
SER
95
HELX_P
A
PHE
394
A
PHE
106
1
AA2
12
A
PRO
412
A
PRO
124
HELX_P
A
ASP
414
A
ASP
126
5
AA3
3
A
HIS
428
A
HIS
140
HELX_P
A
LEU
430
A
LEU
142
5
AA4
3
A
THR
431
A
THR
143
HELX_P
A
ALA
441
A
ALA
153
1
AA5
11
TRANSCRIPTION
Nrd1, RRM, RNA-binding, transcription non-coding RNAs, Nrd1 complex, transcription
NRD1_YEAST
UNP
1
290
P53617
SIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHIKVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSVI
LNNSRKHAFVKVYSRHEAENVLQNFNKDGALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSGQ
PLVTGIVFEEPDIIVGEGV
5O1Z
PDB
2
1
5O1Z
290
468
5O1Z
290
468
P53617
A
1
2
180
1
6
5O1Z
1
6
5O1Z
B
2
1
6
1
expression tag
GLY
289
5O1Z
A
P53617
UNP
1
5
4
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
323
A
VAL
35
A
TYR
325
A
TYR
37
A
ILE
455
A
ILE
167
A
GLU
458
A
GLU
170
A
HIS
333
A
HIS
45
A
TYR
337
A
TYR
49
A
TYR
422
A
TYR
134
A
PRO
426
A
PRO
138
A
CYS
416
A
CYS
128
A
ASP
417
A
ASP
129
A
VAL
365
A
VAL
77
A
ASN
371
A
ASN
83
A
HIS
376
A
HIS
88
A
VAL
381
A
VAL
93
A
THR
340
A
THR
52
A
GLY
344
A
GLY
56
A
ARG
403
A
ARG
115
A
TRP
406
A
TRP
118
96
P 43 21 2