0.013371
0.007720
0.000000
0.000000
0.015439
0.000000
0.000000
0.000000
0.011579
0.00000
0.00000
0.00000
Ren, X.
Pyle, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
74.790
74.790
86.360
C21 H22 N3 O9 P
491.388
n
2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate)
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
C10 H15 N2 O8 P
322.208
n
THYMIDINE-3'-PHOSPHATE
DNA 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
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
Na 1
22.990
SODIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
O4 P -3
94.971
PHOSPHATE ION
non-polymer
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
C
N
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
N
6
N
C
N
7
N
C
N
8
N
C
Y
9
N
C
Y
10
N
C
N
11
N
O
N
12
N
N
N
13
N
O
N
14
N
C
N
15
N
N
N
16
R
C
N
17
N
O
N
18
N
C
N
19
S
C
N
20
N
O
N
21
R
C
N
22
N
C
N
23
N
O
N
24
N
P
N
25
N
O
N
26
N
O
N
27
N
O
N
28
N
N
Y
29
N
C
Y
30
N
C
Y
31
N
C
Y
32
N
C
Y
33
N
C
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
H
N
42
N
H
N
43
N
H
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
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
O
N
57
N
N
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
C
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
N
N
71
S
C
N
72
N
C
N
73
N
O
N
74
N
C
N
75
N
C
N
76
N
C
N
77
N
N
N
78
N
C
N
79
N
N
N
80
N
N
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
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
H
N
96
N
H
N
97
N
N
N
98
S
C
N
99
N
C
N
100
N
O
N
101
N
C
N
102
N
C
N
103
N
O
N
104
N
N
N
105
N
O
N
106
N
H
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
N
N
115
S
C
N
116
N
C
N
117
N
O
N
118
N
C
N
119
N
C
N
120
N
O
N
121
N
O
N
122
N
O
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
P
N
131
N
O
N
132
N
O
N
133
N
O
N
134
N
O
N
135
N
C
N
136
R
C
N
137
N
O
N
138
S
C
N
139
N
O
N
140
N
C
N
141
S
C
N
142
N
N
N
143
N
C
N
144
N
O
N
145
N
N
N
146
N
C
N
147
N
O
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
H
N
152
N
H
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
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
R
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
S
N
172
N
O
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
O
N
181
N
P
N
182
N
O
N
183
N
O
N
184
N
O
N
185
N
C
N
186
R
C
N
187
N
O
N
188
S
C
N
189
N
O
N
190
N
C
N
191
R
C
Y
192
N
N
Y
193
N
C
Y
194
N
N
Y
195
N
C
Y
196
N
C
N
197
N
N
Y
198
N
N
Y
199
N
C
Y
200
N
N
Y
201
N
C
N
202
N
H
N
203
N
H
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
O
N
217
N
P
N
218
N
O
N
219
N
O
N
220
N
O
N
221
N
C
N
222
R
C
N
223
N
O
N
224
S
C
N
225
N
O
N
226
N
C
N
227
R
C
N
228
N
N
N
229
N
C
N
230
N
O
N
231
N
N
N
232
N
C
N
233
N
N
N
234
N
C
N
235
N
C
N
236
N
H
N
237
N
H
N
238
N
H
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
O
N
251
N
P
N
252
N
O
N
253
N
O
N
254
N
O
N
255
N
C
N
256
R
C
N
257
N
O
N
258
S
C
N
259
N
O
N
260
N
C
N
261
R
C
Y
262
N
N
Y
263
N
C
Y
264
N
N
Y
265
N
C
N
266
N
C
N
267
N
O
N
268
N
N
N
269
N
C
N
270
N
N
N
271
N
N
Y
272
N
C
N
273
N
H
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
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
O
N
295
N
N
N
296
N
O
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
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
C
N
313
N
C
N
314
N
O
N
315
N
O
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
N
C
N
328
N
C
N
329
N
O
N
330
N
O
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
Y
341
N
C
Y
342
N
N
Y
343
N
C
Y
344
N
C
Y
345
N
N
N
346
N
O
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
O
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
S
C
N
365
N
C
N
366
N
C
N
367
N
C
N
368
N
O
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
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
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
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
N
N
405
S
C
N
406
N
C
N
407
N
O
N
408
N
C
N
409
N
C
N
410
N
C
N
411
N
C
N
412
N
N
N
413
N
O
N
414
N
H
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
H
N
427
N
H
N
428
N
H
N
429
N
N
N
430
S
C
N
431
N
C
N
432
N
O
N
433
N
C
N
434
N
C
N
435
N
S
N
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
MG
N
450
N
NA
N
451
N
N
N
452
S
C
N
453
N
C
N
454
N
O
N
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
N
462
N
O
N
463
N
H
N
464
N
H
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
P
N
475
N
O
N
476
N
O
N
477
N
O
N
478
N
O
N
479
N
N
N
480
S
C
N
481
N
C
N
482
N
O
N
483
N
C
N
484
N
C
N
485
N
C
N
486
N
O
N
487
N
H
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
N
N
497
S
C
N
498
N
C
N
499
N
O
N
500
N
C
N
501
N
O
N
502
N
O
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
N
N
511
S
C
N
512
N
C
N
513
N
O
N
514
R
C
N
515
N
O
N
516
N
C
N
517
N
O
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
H
N
525
N
H
N
526
N
H
N
527
N
N
N
528
S
C
N
529
N
C
N
530
N
O
N
531
N
C
Y
532
N
C
Y
533
N
C
Y
534
N
C
Y
535
N
N
Y
536
N
C
Y
537
N
C
Y
538
N
C
Y
539
N
C
Y
540
N
C
N
541
N
O
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
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
N
N
555
S
C
N
556
N
C
N
557
N
O
N
558
N
C
Y
559
N
C
Y
560
N
C
Y
561
N
C
Y
562
N
C
Y
563
N
C
Y
564
N
C
N
565
N
O
N
566
N
O
N
567
N
H
N
568
N
H
N
569
N
H
N
570
N
H
N
571
N
H
N
572
N
H
N
573
N
H
N
574
N
H
N
575
N
H
N
576
N
H
N
577
N
H
N
578
N
N
N
579
S
C
N
580
N
C
N
581
N
O
N
582
N
C
N
583
N
C
N
584
N
C
N
585
N
O
N
586
N
H
N
587
N
H
N
588
N
H
N
589
N
H
N
590
N
H
N
591
N
H
N
592
N
H
N
593
N
H
N
594
N
H
N
595
N
H
N
596
N
H
Y
1
N
doub
Y
2
N
sing
Y
3
N
sing
Y
4
N
doub
Y
5
N
doub
Y
6
N
sing
Y
7
N
sing
Y
8
N
sing
Y
9
N
doub
Y
10
N
doub
Y
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
doub
N
16
N
sing
N
17
N
doub
N
18
N
sing
N
19
N
sing
N
20
N
doub
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
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
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
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
sing
N
57
N
sing
N
58
N
sing
N
59
N
doub
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
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
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
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
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
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
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
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
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
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
doub
N
159
N
sing
N
160
N
sing
N
161
N
doub
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
doub
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
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
Y
207
N
sing
Y
208
N
doub
N
209
N
sing
Y
210
N
doub
N
211
N
sing
N
212
N
sing
Y
213
N
sing
Y
214
N
doub
N
215
N
sing
Y
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
doub
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
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
doub
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
doub
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
doub
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
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
Y
275
N
sing
Y
276
N
sing
Y
277
N
doub
N
278
N
sing
Y
279
N
sing
N
280
N
sing
Y
281
N
doub
N
282
N
doub
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
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
doub
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
doub
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
doub
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
doub
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
doub
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
Y
348
N
sing
Y
349
N
doub
Y
350
N
doub
N
351
N
sing
Y
352
N
sing
N
353
N
sing
Y
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
doub
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
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
doub
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
sing
N
406
N
sing
N
407
N
sing
N
408
N
doub
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
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
doub
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
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
sing
N
451
N
doub
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
Y
456
N
doub
Y
457
N
sing
Y
458
N
sing
N
459
N
sing
Y
460
N
doub
N
461
N
sing
Y
462
N
doub
N
463
N
sing
Y
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
doub
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
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
doub
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
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
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
doub
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
Y
529
N
doub
Y
530
N
sing
Y
531
N
sing
N
532
N
sing
Y
533
N
doub
Y
534
N
sing
Y
535
N
sing
N
536
N
sing
Y
537
N
sing
Y
538
N
doub
N
539
N
sing
Y
540
N
doub
N
541
N
sing
Y
542
N
sing
N
543
N
sing
N
544
N
sing
N
545
N
sing
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
doub
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
sing
Y
557
N
doub
Y
558
N
sing
Y
559
N
sing
N
560
N
sing
Y
561
N
doub
N
562
N
sing
Y
563
N
doub
N
564
N
sing
Y
565
N
sing
N
566
N
sing
N
567
N
sing
N
568
N
sing
N
569
N
sing
N
570
N
sing
N
571
N
sing
N
572
N
sing
N
573
N
sing
N
574
N
sing
N
575
N
sing
N
576
N
doub
N
577
N
sing
N
578
N
sing
N
579
N
sing
N
580
N
sing
N
581
N
sing
N
582
N
sing
N
583
N
sing
N
584
N
sing
N
585
N
sing
N
586
N
sing
N
587
N
sing
UK
Nat Commun
2041-1723
8
810
810
10.1038/s41467-017-00864-2
28993621
Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling.
2017
10.2210/pdb5uc6/pdb
pdb_00005uc6
100
1
PIXEL
2014-03-20
DECTRIS PILATUS 6M-F
SINGLE WAVELENGTH
M
x-ray
1
0.9999
1.0
24-ID-C
APS
0.9999
SYNCHROTRON
APS BEAMLINE 24-ID-C
18064.486
Interleukin-1 alpha
residues 113-271
1
man
polymer
8366.890
DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3')
1
syn
polymer
24.305
MAGNESIUM ION
4
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
18.015
water
145
nat
water
IL-1 alpha,Hematopoietin-1
no
no
SAPFSFLSNVKYNFMRIIKYEFILNDALNQSIIRANDQYLTAAALHNLDEAVKFDMGAYKSSKDDAKITVILRISKTQLY
VTAQDEDQPVLLKEMPEIPKTITGSETNLLFFWETHGTKNYFTSVAHPNLFIATKQDYWVCLAGGPPSITDFQILENQA
SAPFSFLSNVKYNFMRIIKYEFILNDALNQSIIRANDQYLTAAALHNLDEAVKFDMGAYKSSKDDAKITVILRISKTQLY
VTAQDEDQPVLLKEMPEIPKTITGSETNLLFFWETHGTKNYFTSVAHPNLFIATKQDYWVCLAGGPPSITDFQILENQA
A
polypeptide(L)
no
yes
(DC)(DG)(85Y)(DG)(DA)(DG)(85Y)(85Y)(DA)(85Y)(DG)(DG)(DG)(85Y)(85Y)(DA)(DG)(DA)
(DG)(85Y)(DC)(DG)(ATD)
CGXGAGXXAXGGGXXAGAGXCGT
B
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
Human
sample
1
159
IL1A, IL1F1
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.64
53.37
EVAPORATION
0.2 M NaCl, 0.1 M Na acetate, and 22% polyethylene glycol 8,000
291
3.097
1
19
B
1
B
22
-1.135
B_DC1:DG22_B
1
-3.220
-0.179
0.508
-0.183
2.991
1
19
B
2
B
21
-2.490
B_DG2:DC21_B
2
0.423
0.639
0.333
-0.215
26.127
4
7
B
4
B
19
-113.973
B_DG4:DG19_B
3
13.108
5.504
0.530
-0.110
-2.318
8
2
B
5
B
18
-176.296
B_DA5:DA18_B
4
-23.807
-5.691
0.312
-5.009
13.950
2
3
B
6
B
17
-172.278
B_DG6:DG17_B
5
18.538
1.143
0.196
-1.117
-1.494
1
20
B
8
B
16
-1.991
B_85Y8:DA16_B
6
-4.957
-0.198
0.294
-0.090
-11.219
1
20
B
9
B
15
-10.897
B_DA9:85Y15_B
7
-17.672
0.145
0.046
-0.099
2.015
-5.097
B
B
1
2
-15.019
B
B
22
21
3.739
1.283
-0.008
5.111
BB_DC1DG2:DC21DG22_BB
1
2.034
23.813
-4.495
-66.112
13.615
5.264
7.372
B
B
5
6
-38.004
B
B
18
17
4.821
-3.748
2.158
-3.804
BB_DA5DG6:DG17DA18_BB
2
5.848
-59.290
2.473
0.261
29.779
2.967
-142.328
B
B
6
8
0.817
B
B
17
16
2.977
-1.547
-0.237
-0.694
BB_DG685Y8:DA16DG17_BB
3
-7.600
-4.015
-142.238
0.374
-0.161
6.268
-12.823
B
B
8
9
55.006
B
B
16
15
3.693
-10.495
-0.077
5.067
BB_85Y8DA9:85Y15DA16_BB
4
0.450
2.357
-7.366
0.453
0.646
citation
citation_author
atom_site
entity
struct_conn
struct_site
atom_site
pdbx_validate_rmsd_angle
struct_conn
pdbx_audit_support
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
repository
Initial release
Database references
Atomic model
Derived calculations
Non-polymer description
Structure summary
Atomic model
Data collection
Derived calculations
Author supporting evidence
Data collection
Database references
Derived calculations
Refinement description
1
0
2017-10-11
1
1
2017-10-18
2
0
2017-11-15
3
0
2018-08-22
3
1
2019-11-20
3
2
2023-10-04
_citation.country
_citation.journal_abbrev
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.type_symbol
_chem_comp.formula
_chem_comp.id
_chem_comp.name
_entity.formula_weight
_entity.pdbx_description
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_label_comp_id
_struct_site.details
_struct_site.pdbx_auth_comp_id
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_struct_conn.pdbx_leaving_atom_flag
_pdbx_audit_support.funding_organization
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
United States
Howard Hughes Medical Institute (HHMI)
N
RCSB
Y
RCSB
2016-12-21
REL
REL
MG
MAGNESIUM ION
NA
SODIUM ION
PO4
PHOSPHATE ION
HOH
water
32630
synthetic construct
sample
1
23
2ILA
PDB
experimental model
MG
1
3
MG
MG
201
A
NA
2
4
NA
NA
202
A
MG
3
3
MG
MG
203
A
MG
4
3
MG
MG
204
A
MG
5
3
MG
MG
205
A
PO3
23
5
PO4
PO4
101
B
HOH
131
6
HOH
HOH
301
A
HOH
76
6
HOH
HOH
302
A
HOH
89
6
HOH
HOH
303
A
HOH
69
6
HOH
HOH
304
A
HOH
102
6
HOH
HOH
305
A
HOH
35
6
HOH
HOH
306
A
HOH
130
6
HOH
HOH
307
A
HOH
121
6
HOH
HOH
308
A
HOH
28
6
HOH
HOH
309
A
HOH
10
6
HOH
HOH
310
A
HOH
21
6
HOH
HOH
311
A
HOH
137
6
HOH
HOH
312
A
HOH
100
6
HOH
HOH
313
A
HOH
68
6
HOH
HOH
314
A
HOH
4
6
HOH
HOH
315
A
HOH
140
6
HOH
HOH
316
A
HOH
111
6
HOH
HOH
317
A
HOH
27
6
HOH
HOH
318
A
HOH
55
6
HOH
HOH
319
A
HOH
17
6
HOH
HOH
320
A
HOH
30
6
HOH
HOH
321
A
HOH
53
6
HOH
HOH
322
A
HOH
94
6
HOH
HOH
323
A
HOH
3
6
HOH
HOH
324
A
HOH
80
6
HOH
HOH
325
A
HOH
1
6
HOH
HOH
326
A
HOH
96
6
HOH
HOH
327
A
HOH
105
6
HOH
HOH
328
A
HOH
75
6
HOH
HOH
329
A
HOH
32
6
HOH
HOH
330
A
HOH
85
6
HOH
HOH
331
A
HOH
45
6
HOH
HOH
332
A
HOH
19
6
HOH
HOH
333
A
HOH
59
6
HOH
HOH
334
A
HOH
38
6
HOH
HOH
335
A
HOH
41
6
HOH
HOH
336
A
HOH
44
6
HOH
HOH
337
A
HOH
40
6
HOH
HOH
338
A
HOH
79
6
HOH
HOH
339
A
HOH
7
6
HOH
HOH
340
A
HOH
115
6
HOH
HOH
341
A
HOH
34
6
HOH
HOH
342
A
HOH
22
6
HOH
HOH
343
A
HOH
120
6
HOH
HOH
344
A
HOH
8
6
HOH
HOH
345
A
HOH
119
6
HOH
HOH
346
A
HOH
57
6
HOH
HOH
347
A
HOH
128
6
HOH
HOH
348
A
HOH
127
6
HOH
HOH
349
A
HOH
87
6
HOH
HOH
350
A
HOH
11
6
HOH
HOH
351
A
HOH
47
6
HOH
HOH
352
A
HOH
18
6
HOH
HOH
353
A
HOH
109
6
HOH
HOH
354
A
HOH
39
6
HOH
HOH
355
A
HOH
97
6
HOH
HOH
356
A
HOH
5
6
HOH
HOH
357
A
HOH
33
6
HOH
HOH
358
A
HOH
113
6
HOH
HOH
359
A
HOH
125
6
HOH
HOH
360
A
HOH
46
6
HOH
HOH
361
A
HOH
61
6
HOH
HOH
362
A
HOH
37
6
HOH
HOH
363
A
HOH
13
6
HOH
HOH
364
A
HOH
123
6
HOH
HOH
365
A
HOH
26
6
HOH
HOH
366
A
HOH
29
6
HOH
HOH
367
A
HOH
103
6
HOH
HOH
368
A
HOH
138
6
HOH
HOH
369
A
HOH
6
6
HOH
HOH
370
A
HOH
122
6
HOH
HOH
371
A
HOH
133
6
HOH
HOH
372
A
HOH
135
6
HOH
HOH
373
A
HOH
116
6
HOH
HOH
374
A
HOH
134
6
HOH
HOH
375
A
HOH
64
6
HOH
HOH
376
A
HOH
126
6
HOH
HOH
377
A
HOH
110
6
HOH
HOH
378
A
HOH
74
6
HOH
HOH
379
A
HOH
101
6
HOH
HOH
380
A
HOH
118
6
HOH
HOH
381
A
HOH
65
6
HOH
HOH
382
A
HOH
95
6
HOH
HOH
383
A
HOH
73
6
HOH
HOH
384
A
HOH
141
6
HOH
HOH
385
A
HOH
142
6
HOH
HOH
386
A
HOH
132
6
HOH
HOH
387
A
HOH
136
6
HOH
HOH
388
A
HOH
48
6
HOH
HOH
389
A
HOH
81
6
HOH
HOH
390
A
HOH
50
6
HOH
HOH
391
A
HOH
42
6
HOH
HOH
201
B
HOH
144
6
HOH
HOH
202
B
HOH
12
6
HOH
HOH
203
B
HOH
145
6
HOH
HOH
204
B
HOH
92
6
HOH
HOH
205
B
HOH
23
6
HOH
HOH
206
B
HOH
71
6
HOH
HOH
207
B
HOH
14
6
HOH
HOH
208
B
HOH
66
6
HOH
HOH
209
B
HOH
52
6
HOH
HOH
210
B
HOH
90
6
HOH
HOH
211
B
HOH
67
6
HOH
HOH
212
B
HOH
36
6
HOH
HOH
213
B
HOH
20
6
HOH
HOH
214
B
HOH
106
6
HOH
HOH
215
B
HOH
15
6
HOH
HOH
216
B
HOH
16
6
HOH
HOH
217
B
HOH
108
6
HOH
HOH
218
B
HOH
124
6
HOH
HOH
219
B
HOH
49
6
HOH
HOH
220
B
HOH
104
6
HOH
HOH
221
B
HOH
2
6
HOH
HOH
222
B
HOH
58
6
HOH
HOH
223
B
HOH
56
6
HOH
HOH
224
B
HOH
77
6
HOH
HOH
225
B
HOH
63
6
HOH
HOH
226
B
HOH
129
6
HOH
HOH
227
B
HOH
24
6
HOH
HOH
228
B
HOH
143
6
HOH
HOH
229
B
HOH
88
6
HOH
HOH
230
B
HOH
107
6
HOH
HOH
231
B
HOH
114
6
HOH
HOH
232
B
HOH
9
6
HOH
HOH
233
B
HOH
78
6
HOH
HOH
234
B
HOH
43
6
HOH
HOH
235
B
HOH
51
6
HOH
HOH
236
B
HOH
62
6
HOH
HOH
237
B
HOH
139
6
HOH
HOH
238
B
HOH
83
6
HOH
HOH
239
B
HOH
91
6
HOH
HOH
240
B
HOH
99
6
HOH
HOH
241
B
HOH
84
6
HOH
HOH
242
B
HOH
112
6
HOH
HOH
243
B
HOH
86
6
HOH
HOH
244
B
HOH
25
6
HOH
HOH
245
B
HOH
60
6
HOH
HOH
246
B
HOH
82
6
HOH
HOH
247
B
HOH
72
6
HOH
HOH
248
B
HOH
54
6
HOH
HOH
249
B
HOH
93
6
HOH
HOH
250
B
HOH
98
6
HOH
HOH
251
B
HOH
117
6
HOH
HOH
252
B
HOH
70
6
HOH
HOH
253
B
HOH
31
6
HOH
HOH
254
B
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
ASN
9
n
9
ASN
9
A
VAL
10
n
10
VAL
10
A
LYS
11
n
11
LYS
11
A
TYR
12
n
12
TYR
12
A
ASN
13
n
13
ASN
13
A
PHE
14
n
14
PHE
14
A
MET
15
n
15
MET
15
A
ARG
16
n
16
ARG
16
A
ILE
17
n
17
ILE
17
A
ILE
18
n
18
ILE
18
A
LYS
19
n
19
LYS
19
A
TYR
20
n
20
TYR
20
A
GLU
21
n
21
GLU
21
A
PHE
22
n
22
PHE
22
A
ILE
23
n
23
ILE
23
A
LEU
24
n
24
LEU
24
A
ASN
25
n
25
ASN
25
A
ASP
26
n
26
ASP
26
A
ALA
27
n
27
ALA
27
A
LEU
28
n
28
LEU
28
A
ASN
29
n
29
ASN
29
A
GLN
30
n
30
GLN
30
A
SER
31
n
31
SER
31
A
ILE
32
n
32
ILE
32
A
ILE
33
n
33
ILE
33
A
ARG
34
n
34
ARG
34
A
ALA
35
n
35
ALA
35
A
ASN
36
n
36
ASN
36
A
ASP
37
n
37
ASP
37
A
GLN
38
n
38
GLN
38
A
TYR
39
n
39
TYR
39
A
LEU
40
n
40
LEU
40
A
THR
41
n
41
THR
41
A
ALA
42
n
42
ALA
42
A
ALA
43
n
43
ALA
43
A
ALA
44
n
44
ALA
44
A
LEU
45
n
45
LEU
45
A
HIS
46
n
46
HIS
46
A
ASN
47
n
47
ASN
47
A
LEU
48
n
48
LEU
48
A
ASP
49
n
49
ASP
49
A
GLU
50
n
50
GLU
50
A
ALA
51
n
51
ALA
51
A
VAL
52
n
52
VAL
52
A
LYS
53
n
53
LYS
53
A
PHE
54
n
54
PHE
54
A
ASP
55
n
55
ASP
55
A
MET
56
n
56
MET
56
A
GLY
57
n
57
GLY
57
A
ALA
58
n
58
ALA
58
A
TYR
59
n
59
TYR
59
A
LYS
60
n
60
LYS
60
A
SER
61
n
61
SER
61
A
SER
62
n
62
SER
62
A
LYS
63
n
63
LYS
63
A
ASP
64
n
64
ASP
64
A
ASP
65
n
65
ASP
65
A
ALA
66
n
66
ALA
66
A
LYS
67
n
67
LYS
67
A
ILE
68
n
68
ILE
68
A
THR
69
n
69
THR
69
A
VAL
70
n
70
VAL
70
A
ILE
71
n
71
ILE
71
A
LEU
72
n
72
LEU
72
A
ARG
73
n
73
ARG
73
A
ILE
74
n
74
ILE
74
A
SER
75
n
75
SER
75
A
LYS
76
n
76
LYS
76
A
THR
77
n
77
THR
77
A
GLN
78
n
78
GLN
78
A
LEU
79
n
79
LEU
79
A
TYR
80
n
80
TYR
80
A
VAL
81
n
81
VAL
81
A
THR
82
n
82
THR
82
A
ALA
83
n
83
ALA
83
A
GLN
84
n
84
GLN
84
A
ASP
85
n
85
ASP
85
A
GLU
86
n
86
GLU
86
A
ASP
87
n
87
ASP
87
A
GLN
88
n
88
GLN
88
A
PRO
89
n
89
PRO
89
A
VAL
90
n
90
VAL
90
A
LEU
91
n
91
LEU
91
A
LEU
92
n
92
LEU
92
A
LYS
93
n
93
LYS
93
A
GLU
94
n
94
GLU
94
A
MET
95
n
95
MET
95
A
PRO
96
n
96
PRO
96
A
GLU
97
n
97
GLU
97
A
ILE
98
n
98
ILE
98
A
PRO
99
n
99
PRO
99
A
LYS
100
n
100
LYS
100
A
THR
101
n
101
THR
101
A
ILE
102
n
102
ILE
102
A
THR
103
n
103
THR
103
A
GLY
104
n
104
GLY
104
A
SER
105
n
105
SER
105
A
GLU
106
n
106
GLU
106
A
THR
107
n
107
THR
107
A
ASN
108
n
108
ASN
108
A
LEU
109
n
109
LEU
109
A
LEU
110
n
110
LEU
110
A
PHE
111
n
111
PHE
111
A
PHE
112
n
112
PHE
112
A
TRP
113
n
113
TRP
113
A
GLU
114
n
114
GLU
114
A
THR
115
n
115
THR
115
A
HIS
116
n
116
HIS
116
A
GLY
117
n
117
GLY
117
A
THR
118
n
118
THR
118
A
LYS
119
n
119
LYS
119
A
ASN
120
n
120
ASN
120
A
TYR
121
n
121
TYR
121
A
PHE
122
n
122
PHE
122
A
THR
123
n
123
THR
123
A
SER
124
n
124
SER
124
A
VAL
125
n
125
VAL
125
A
ALA
126
n
126
ALA
126
A
HIS
127
n
127
HIS
127
A
PRO
128
n
128
PRO
128
A
ASN
129
n
129
ASN
129
A
LEU
130
n
130
LEU
130
A
PHE
131
n
131
PHE
131
A
ILE
132
n
132
ILE
132
A
ALA
133
n
133
ALA
133
A
THR
134
n
134
THR
134
A
LYS
135
n
135
LYS
135
A
GLN
136
n
136
GLN
136
A
ASP
137
n
137
ASP
137
A
TYR
138
n
138
TYR
138
A
TRP
139
n
139
TRP
139
A
VAL
140
n
140
VAL
140
A
CYS
141
n
141
CYS
141
A
LEU
142
n
142
LEU
142
A
ALA
143
n
143
ALA
143
A
GLY
144
n
144
GLY
144
A
GLY
145
n
145
GLY
145
A
PRO
146
n
146
PRO
146
A
PRO
147
n
147
PRO
147
A
SER
148
n
148
SER
148
A
ILE
149
n
149
ILE
149
A
THR
150
n
150
THR
150
A
ASP
151
n
151
ASP
151
A
PHE
152
n
152
PHE
152
A
GLN
153
n
153
GLN
153
A
ILE
154
n
154
ILE
154
A
LEU
155
n
155
LEU
155
A
GLU
156
n
156
GLU
156
A
ASN
157
n
157
ASN
157
A
GLN
158
n
158
GLN
158
A
ALA
159
n
159
ALA
159
A
DC
1
n
1
DC
1
B
DG
2
n
2
DG
2
B
2VJ
3
n
3
85Y
3
B
DG
4
n
4
DG
4
B
DA
5
n
5
DA
5
B
DG
6
n
6
DG
6
B
2VJ
7
n
7
85Y
7
B
2VJ
8
n
8
85Y
8
B
DA
9
n
9
DA
9
B
2VJ
10
n
10
85Y
10
B
DG
11
n
11
DG
11
B
DG
12
n
12
DG
12
B
DG
13
n
13
DG
13
B
2VJ
14
n
14
85Y
14
B
2VJ
15
n
15
85Y
15
B
DA
16
n
16
DA
16
B
DG
17
n
17
DG
17
B
DA
18
n
18
DA
18
B
DG
19
n
19
DG
19
B
2VJ
20
n
20
85Y
20
B
DC
21
n
21
DC
21
B
DG
22
n
22
DG
22
B
n
23
23
B
author_and_software_defined_assembly
PISA
2
dimeric
1690
-31
10720
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
A
ASP
65
A
O
ASP
65
1_555
106.0
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
A
HOH
333
I
O
HOH
1_555
80.9
A
ASP
65
A
O
ASP
65
1_555
A
NA
202
D
NA
NA
1_555
A
HOH
333
I
O
HOH
1_555
79.1
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
B
85Y
7
B
O21
85Y
7
1_555
91.8
A
ASP
65
A
O
ASP
65
1_555
A
NA
202
D
NA
NA
1_555
B
85Y
7
B
O21
85Y
7
1_555
86.9
A
HOH
333
I
O
HOH
1_555
A
NA
202
D
NA
NA
1_555
B
85Y
7
B
O21
85Y
7
1_555
161.6
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
222
J
O
HOH
1_555
160.5
A
ASP
65
A
O
ASP
65
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
222
J
O
HOH
1_555
93.1
A
HOH
333
I
O
HOH
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
222
J
O
HOH
1_555
99.0
B
85Y
7
B
O21
85Y
7
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
222
J
O
HOH
1_555
93.5
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
89.3
A
ASP
65
A
O
ASP
65
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
163.3
A
HOH
333
I
O
HOH
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
97.0
B
85Y
7
B
O21
85Y
7
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
99.8
B
HOH
222
J
O
HOH
1_555
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
71.3
A
VAL
90
A
O
VAL
90
1_555
A
MG
204
F
MG
MG
1_555
A
VAL
140
A
O
VAL
140
1_555
103.3
A
ASN
108
A
O
ASN
108
1_555
A
MG
205
G
MG
MG
1_555
A
LEU
110
A
O
LEU
110
1_555
106.0
A
ASN
108
A
O
ASN
108
1_555
A
MG
205
G
MG
MG
1_555
A
SER
124
A
OG
SER
124
1_555
138.0
A
LEU
110
A
O
LEU
110
1_555
A
MG
205
G
MG
MG
1_555
A
SER
124
A
OG
SER
124
1_555
113.8
A
ILE
132
A
O
ILE
132
1_555
A
MG
203
E
MG
MG
1_555
A
THR
150
A
O
THR
150
1_555
92.4
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
O
ILE
102
A
O
ILE
102
A
N
TYR
12
A
N
TYR
12
A
N
ASN
25
A
N
ASN
25
A
O
GLN
153
A
O
GLN
153
A
O
PHE
152
A
O
PHE
152
A
N
ASN
120
A
N
ASN
120
A
O
THR
123
A
O
THR
123
A
N
PHE
112
A
N
PHE
112
A
O
PHE
111
A
O
PHE
111
A
N
VAL
70
A
N
VAL
70
A
O
ARG
73
A
O
ARG
73
A
N
ASP
55
A
N
ASP
55
A
O
ALA
58
A
O
ALA
58
A
N
MET
15
A
N
MET
15
A
N
SER
31
A
N
SER
31
A
O
ALA
43
A
O
ALA
43
A
N
TYR
80
A
N
TYR
80
A
O
LYS
93
A
O
LYS
93
A
N
PHE
131
A
N
PHE
131
A
O
ALA
143
A
O
ALA
143
1
A
HOH
375
I
HOH
1
A
SER
1
A
SER
1
1
Y
1
A
ALA
2
A
ALA
2
1
Y
1
A
PRO
3
A
PRO
3
1
Y
1
A
PHE
4
A
PHE
4
1
Y
1
A
SER
5
A
SER
5
1
Y
1
A
PHE
6
A
PHE
6
1
Y
1
A
LEU
7
A
LEU
7
1
Y
1
A
SER
8
A
SER
8
1
Y
1
B
ATD
23
B
ATD
23
1
Y
1
A
A
O
O
HOH
HOH
360
385
2.02
1
B
B
O
O
HOH
HOH
226
248
2.03
1
A
B
O
O
HOH
HOH
328
218
2.03
1
A
A
OD1
O
ASP
HOH
49
301
2.07
1
B
B
O
O
HOH
HOH
236
247
2.09
1
A
A
O
O
HOH
HOH
348
377
2.19
1
9.42
1.20
119.70
129.12
B
B
B
C3'
O3'
P
DG
DG
85Y
2
2
3
Y
1
-21.51
1.90
104.00
82.49
B
B
B
O3'
P
O5'
DG
85Y
85Y
2
3
3
Y
1
6.79
1.10
110.50
117.29
B
B
B
O3'
P
OP1
DG
85Y
85Y
2
3
3
Y
1
-8.15
1.20
119.70
111.55
B
B
B
C3'
O3'
P
85Y
85Y
DG
3
3
4
Y
1
12.61
1.10
110.50
123.11
B
B
B
O3'
P
OP2
85Y
DG
DG
3
4
4
Y
1
6.78
1.10
110.50
117.28
B
B
B
O3'
P
OP2
DG
85Y
85Y
6
7
7
Y
1
9.46
1.20
119.70
129.16
B
B
B
C3'
O3'
P
85Y
85Y
85Y
7
7
8
Y
1
7.28
1.20
119.70
126.98
B
B
B
C3'
O3'
P
DA
DA
85Y
9
9
10
Y
1
6.67
1.10
110.50
117.17
B
B
B
O3'
P
OP2
DA
85Y
85Y
9
10
10
Y
1
2.08
0.30
108.30
110.38
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
1.89
0.30
108.30
110.19
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
19.61
1.20
119.70
139.31
B
B
B
C3'
O3'
P
DG
DG
85Y
13
13
14
Y
1
11.59
1.20
119.70
131.29
B
B
B
C3'
O3'
P
85Y
85Y
DA
15
15
16
Y
1
6.88
1.10
110.50
117.38
B
B
B
O3'
P
OP2
85Y
DA
DA
15
16
16
Y
1
17.94
1.90
104.00
121.94
B
B
B
O3'
P
O5'
DG
85Y
85Y
19
20
20
Y
1
7.17
1.10
110.50
117.67
B
B
B
O3'
P
OP2
DG
85Y
85Y
19
20
20
Y
1
-26.89
2.20
105.20
78.31
B
B
B
O3'
P
OP1
DG
85Y
85Y
19
20
20
Y
1
46.86
1.90
104.00
150.86
B
B
B
O3'
P
O5'
85Y
DC
DC
20
21
21
Y
1
-34.29
2.20
105.20
70.91
B
B
B
O3'
P
OP1
85Y
DC
DC
20
21
21
Y
1
B
B
O3'
C3'
DA
DA
5
5
-0.041
0.006
1.419
1.378
N
1
B
B
O3'
C3'
DG
DG
17
17
-0.038
0.006
1.419
1.381
N
1
A
B
O
O
HOH
HOH
346
243
2.18
1_555
3_884
1
A
MET
15
-96.55
-75.37
1
A
ASN
36
-132.46
-126.60
1
A
GLN
84
-109.96
-131.05
0.2193
0.1776
0.1794
2.100
64.770
787
16627
4.73
99.08
0.19
RANDOM
1
THROUGHOUT
1.34
MOLECULAR REPLACEMENT
22.45
0.90
1.11
2ILA
ML
FLAT BULK SOLVENT MODEL
2.100
64.770
145
1916
9
548
1214
0.007
1863
1.344
2581
20.686
966
0.097
279
0.006
244
0.2648
0.2144
2.2316
130
2626
100.00
0.2762
0.2278
2.4039
120
2625
100.00
0.2707
0.2170
2.6458
132
2598
100.00
0.2314
0.2106
3.0287
164
2601
99.00
0.1853
0.1648
3.8158
123
2658
99.00
0.2009
0.1497
64.8006
118
2732
97.00
2.1
64.77
5UC6
16642
0.092
1
11.2
9.7
99.5
0.56
2.1
2.21
3.4
1
9.9
100
refinement
PHENIX
(1.11.1_2575)
data reduction
iMOSFLM
data scaling
SCALA
phasing
PHASER
N
Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III
1
N
N
2
N
N
3
N
N
4
N
N
3
N
N
3
N
N
3
N
N
5
N
N
6
N
N
6
N
N
A
ASN
47
A
ASN
47
HELX_P
A
ALA
51
A
ALA
51
5
AA1
5
A
SER
105
A
SER
105
HELX_P
A
LEU
109
A
LEU
109
5
AA2
5
covale
1.558
both
B
DG
2
B
O3'
DG
2
1_555
B
85Y
3
B
P
85Y
3
1_555
covale
1.562
one
B
85Y
3
B
O3'
85Y
3
1_555
B
DG
4
B
P
DG
4
1_555
covale
1.562
both
B
DG
6
B
O3'
DG
6
1_555
B
85Y
7
B
P
85Y
7
1_555
covale
1.562
one
B
85Y
7
B
O3'
85Y
7
1_555
B
85Y
8
B
P
85Y
8
1_555
covale
1.558
one
B
85Y
8
B
O3'
85Y
8
1_555
B
DA
9
B
P
DA
9
1_555
covale
1.557
both
B
DA
9
B
O3'
DA
9
1_555
B
85Y
10
B
P
85Y
10
1_555
covale
1.564
one
B
85Y
10
B
O3'
85Y
10
1_555
B
DG
11
B
P
DG
11
1_555
covale
1.561
both
B
DG
13
B
O3'
DG
13
1_555
B
85Y
14
B
P
85Y
14
1_555
covale
1.562
one
B
85Y
14
B
O3'
85Y
14
1_555
B
85Y
15
B
P
85Y
15
1_555
covale
1.560
one
B
85Y
15
B
O3'
85Y
15
1_555
B
DA
16
B
P
DA
16
1_555
covale
1.559
both
B
DG
19
B
O3'
DG
19
1_555
B
85Y
20
B
P
85Y
20
1_555
covale
1.557
one
B
85Y
20
B
O3'
85Y
20
1_555
B
DC
21
B
P
DC
21
1_555
covale
1.559
one
B
DG
22
B
O3'
DG
22
1_555
B
PO4
101
H
P
PO4
1_555
metalc
2.857
A
LYS
11
A
O
LYS
11
1_555
A
MG
201
C
MG
MG
1_555
metalc
2.399
A
ASP
64
A
OD1
ASP
64
1_555
A
NA
202
D
NA
NA
1_555
metalc
2.344
A
ASP
65
A
O
ASP
65
1_555
A
NA
202
D
NA
NA
1_555
metalc
2.795
A
VAL
90
A
O
VAL
90
1_555
A
MG
204
F
MG
MG
1_555
metalc
2.894
A
ASN
108
A
O
ASN
108
1_555
A
MG
205
G
MG
MG
1_555
metalc
2.777
A
LEU
110
A
O
LEU
110
1_555
A
MG
205
G
MG
MG
1_555
metalc
2.620
A
SER
124
A
OG
SER
124
1_555
A
MG
205
G
MG
MG
1_555
metalc
2.963
A
ILE
132
A
O
ILE
132
1_555
A
MG
203
E
MG
MG
1_555
metalc
2.942
A
VAL
140
A
O
VAL
140
1_555
A
MG
204
F
MG
MG
1_555
metalc
2.552
A
THR
150
A
O
THR
150
1_555
A
MG
203
E
MG
MG
1_555
metalc
2.422
A
NA
202
D
NA
NA
1_555
A
HOH
333
I
O
HOH
1_555
metalc
2.526
A
NA
202
D
NA
NA
1_555
B
85Y
7
B
O21
85Y
7
1_555
metalc
2.198
A
NA
202
D
NA
NA
1_555
B
HOH
222
J
O
HOH
1_555
metalc
2.627
A
NA
202
D
NA
NA
1_555
B
HOH
245
J
O
HOH
1_555
hydrog
WATSON-CRICK
B
DC
1
B
N3
DC
1
1_555
B
DG
22
B
N1
DG
22
1_555
hydrog
WATSON-CRICK
B
DC
1
B
N4
DC
1
1_555
B
DG
22
B
O6
DG
22
1_555
hydrog
WATSON-CRICK
B
DC
1
B
O2
DC
1
1_555
B
DG
22
B
N2
DG
22
1_555
hydrog
WATSON-CRICK
B
DG
2
B
N1
DG
2
1_555
B
DC
21
B
N3
DC
21
1_555
hydrog
WATSON-CRICK
B
DG
2
B
N2
DG
2
1_555
B
DC
21
B
O2
DC
21
1_555
hydrog
WATSON-CRICK
B
DG
2
B
O6
DG
2
1_555
B
DC
21
B
N4
DC
21
1_555
hydrog
REVERSED HOOGSTEEN
B
85Y
3
B
N3
85Y
3
1_555
B
DA
16
B
N7
DA
16
1_555
hydrog
REVERSED HOOGSTEEN
B
85Y
3
B
O2
85Y
3
1_555
B
DA
16
B
N6
DA
16
1_555
hydrog
TYPE_4_PAIR
B
DG
4
B
N2
DG
4
1_555
B
DG
17
B
N3
DG
17
1_555
hydrog
TYPE_4_PAIR
B
DG
4
B
N3
DG
4
1_555
B
DG
17
B
N2
DG
17
1_555
hydrog
TYPE_7_PAIR
B
DG
4
B
N1
DG
4
1_555
B
DG
19
B
N7
DG
19
1_555
hydrog
TYPE_7_PAIR
B
DG
4
B
N2
DG
4
1_555
B
DG
19
B
O6
DG
19
1_555
hydrog
TYPE_2_PAIR
B
DA
5
B
N6
DA
5
1_555
B
DA
18
B
N7
DA
18
1_555
hydrog
TYPE_2_PAIR
B
DA
5
B
N7
DA
5
1_555
B
DA
18
B
N6
DA
18
1_555
hydrog
TYPE_3_PAIR
B
DG
6
B
N1
DG
6
1_555
B
DG
17
B
O6
DG
17
1_555
hydrog
TYPE_3_PAIR
B
DG
6
B
O6
DG
6
1_555
B
DG
17
B
N1
DG
17
1_555
hydrog
WATSON-CRICK
B
85Y
8
B
N3
85Y
8
1_555
B
DA
16
B
N1
DA
16
1_555
hydrog
WATSON-CRICK
B
85Y
8
B
O4
85Y
8
1_555
B
DA
16
B
N6
DA
16
1_555
hydrog
WATSON-CRICK
B
DA
9
B
N1
DA
9
1_555
B
85Y
15
B
N3
85Y
15
1_555
hydrog
WATSON-CRICK
B
DA
9
B
N6
DA
9
1_555
B
85Y
15
B
O4
85Y
15
1_555
IMMUNE SYSTEM/DNA
SOMAmer, IMMUNE SYSTEM-DNA complex
A
PRO
146
A
PRO
146
1
A
PRO
147
A
PRO
147
3.92
IL1A_HUMAN
UNP
1
113
P01583
SAPFSFLSNVKYNFMRIIKYEFILNDALNQSIIRANDQYLTAAALHNLDEAVKFDMGAYKSSKDDAKITVILRISKTQLY
VTAQDEDQPVLLKEMPEIPKTITGSETNLLFFWETHGTKNYFTSVAHPNLFIATKQDYWVCLAGGPPSITDFQILENQA
5UC6
PDB
2
1
5UC6
113
271
5UC6
1
159
P01583
A
1
1
159
1
23
5UC6
1
23
5UC6
B
2
1
23
8
2
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
101
A
THR
101
A
THR
103
A
THR
103
A
LYS
11
A
LYS
11
A
ASP
26
A
ASP
26
A
PHE
152
A
PHE
152
A
LEU
155
A
LEU
155
A
LYS
119
A
LYS
119
A
SER
124
A
SER
124
A
PHE
111
A
PHE
111
A
HIS
116
A
HIS
116
A
THR
69
A
THR
69
A
ILE
74
A
ILE
74
A
PHE
54
A
PHE
54
A
SER
61
A
SER
61
A
LYS
11
A
LYS
11
A
ASP
26
A
ASP
26
A
SER
31
A
SER
31
A
ARG
34
A
ARG
34
A
LEU
40
A
LEU
40
A
ALA
43
A
ALA
43
A
LEU
79
A
LEU
79
A
THR
82
A
THR
82
A
LEU
91
A
LEU
91
A
GLU
94
A
GLU
94
A
PHE
131
A
PHE
131
A
ALA
133
A
ALA
133
A
CYS
141
A
CYS
141
A
ALA
143
A
ALA
143
binding site for residue MG A 201
A
MG
201
Software
5
binding site for residue NA A 202
A
NA
202
Software
6
binding site for residue MG A 203
A
MG
203
Software
5
binding site for residue MG A 204
A
MG
204
Software
6
binding site for residue MG A 205
A
MG
205
Software
6
binding site for residue PO4 B 101
B
PO4
101
Software
2
A
LYS
11
A
LYS
11
5
1_555
A
ASN
13
A
ASN
13
5
1_555
A
LYS
60
A
LYS
60
5
1_555
A
SER
61
A
SER
61
5
1_555
A
SER
62
A
SER
62
5
1_555
A
ASP
64
A
ASP
64
6
1_555
A
ASP
65
A
ASP
65
6
1_555
A
HOH
333
I
HOH
6
1_555
B
85Y
7
B
85Y
7
6
1_555
B
HOH
222
J
HOH
6
1_555
B
HOH
245
J
HOH
6
1_555
A
TYR
121
A
TYR
121
5
1_555
A
PHE
122
A
PHE
122
5
1_555
A
ILE
132
A
ILE
132
5
1_555
A
THR
150
A
THR
150
5
1_555
A
PHE
152
A
PHE
152
5
1_555
A
TYR
39
A
TYR
39
6
1_555
A
LEU
40
A
LEU
40
6
1_555
A
PRO
89
A
PRO
89
6
1_555
A
VAL
90
A
VAL
90
6
1_555
A
TRP
139
A
TRP
139
6
1_555
A
VAL
140
A
VAL
140
6
1_555
A
ALA
83
A
ALA
83
6
1_555
A
THR
107
A
THR
107
6
1_555
A
ASN
108
A
ASN
108
6
1_555
A
LEU
110
A
LEU
110
6
1_555
A
SER
124
A
SER
124
6
1_555
A
VAL
125
A
VAL
125
6
1_555
B
DG
22
B
DG
22
2
1_555
B
HOH
229
J
HOH
2
1_555
152
P 31 2 1