0.010994
0.000000
0.001250
0.000000
0.018615
0.000000
0.000000
0.000000
0.012339
0.00000
0.00000
0.00000
Hashimoto, H.
Hong, S.
Bhagwat, A.S.
Zhang, X.
Cheng, X.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
96.49
90.00
90.96
53.72
81.56
C5 H11 O7 P
214.110
2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE
ABASIC DEOXYRIBOSE
DNA linking
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
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
C5 H6 N2 O3
142.113
5-HYDROXYMETHYL URACIL
5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE
non-polymer
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
P
N
2
N
O
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
R
C
N
10
N
O
N
11
N
C
N
12
S
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
N
N
26
S
C
N
27
N
C
N
28
N
O
N
29
N
C
N
30
N
O
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
C
N
44
N
C
N
45
N
N
N
46
N
C
N
47
N
N
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
O
N
72
N
N
N
73
N
O
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
H
N
82
N
N
N
83
S
C
N
84
N
C
N
85
N
O
N
86
N
C
N
87
N
C
N
88
N
O
N
89
N
O
N
90
N
O
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
R
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
S
N
104
N
O
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
H
N
112
N
O
N
113
N
P
N
114
N
O
N
115
N
O
N
116
N
O
N
117
N
C
N
118
R
C
N
119
N
O
N
120
S
C
N
121
N
O
N
122
N
C
N
123
R
C
Y
124
N
N
Y
125
N
C
Y
126
N
N
Y
127
N
C
Y
128
N
C
N
129
N
N
Y
130
N
N
Y
131
N
C
Y
132
N
N
Y
133
N
C
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
H
N
148
N
O
N
149
N
P
N
150
N
O
N
151
N
O
N
152
N
O
N
153
N
C
N
154
R
C
N
155
N
O
N
156
S
C
N
157
N
O
N
158
N
C
N
159
R
C
N
160
N
N
N
161
N
C
N
162
N
O
N
163
N
N
N
164
N
C
N
165
N
N
N
166
N
C
N
167
N
C
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
H
N
182
N
O
N
183
N
P
N
184
N
O
N
185
N
O
N
186
N
O
N
187
N
C
N
188
R
C
N
189
N
O
N
190
S
C
N
191
N
O
N
192
N
C
N
193
R
C
Y
194
N
N
Y
195
N
C
Y
196
N
N
Y
197
N
C
N
198
N
C
N
199
N
O
N
200
N
N
N
201
N
C
N
202
N
N
N
203
N
N
Y
204
N
C
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
H
N
219
N
O
N
220
N
P
N
221
N
O
N
222
N
O
N
223
N
O
N
224
N
C
N
225
R
C
N
226
N
O
N
227
S
C
N
228
N
O
N
229
N
C
N
230
R
C
N
231
N
N
N
232
N
C
N
233
N
O
N
234
N
N
N
235
N
C
N
236
N
O
N
237
N
C
N
238
N
C
N
239
N
C
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
H
N
255
N
N
N
256
S
C
N
257
N
C
N
258
N
O
N
259
N
C
N
260
N
C
N
261
N
C
N
262
N
O
N
263
N
N
N
264
N
O
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
H
N
275
N
N
N
276
S
C
N
277
N
C
N
278
N
O
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
O
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
N
N
295
N
C
N
296
N
C
N
297
N
O
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
Y
309
N
C
Y
310
N
N
Y
311
N
C
Y
312
N
C
Y
313
N
N
N
314
N
O
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
H
N
325
N
N
N
326
N
C
N
327
N
O
N
328
N
N
N
329
N
C
N
330
N
O
N
331
N
O
N
332
N
C
N
333
N
C
N
334
N
C
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
O
N
342
N
H
N
343
N
H
N
344
N
N
N
345
S
C
N
346
N
C
N
347
N
O
N
348
S
C
N
349
N
C
N
350
N
C
N
351
N
C
N
352
N
O
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
H
N
364
N
H
N
365
N
H
N
366
N
N
N
367
S
C
N
368
N
C
N
369
N
O
N
370
N
C
N
371
N
C
N
372
N
C
N
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
H
N
387
N
H
N
388
N
N
N
389
S
C
N
390
N
C
N
391
N
O
N
392
N
C
N
393
N
C
N
394
N
C
N
395
N
C
N
396
N
N
N
397
N
O
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
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
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
N
418
N
C
N
419
N
S
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
H
N
432
N
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
C
N
444
N
O
N
445
N
H
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
N
N
457
S
C
N
458
N
C
N
459
N
O
N
460
N
C
N
461
N
C
N
462
N
C
N
463
N
O
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
N
N
474
S
C
N
475
N
C
N
476
N
O
N
477
N
C
N
478
N
O
N
479
N
O
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
N
N
488
S
C
N
489
N
C
N
490
N
O
N
491
R
C
N
492
N
O
N
493
N
C
N
494
N
O
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
H
N
502
N
H
N
503
N
H
N
504
N
N
N
505
S
C
N
506
N
C
N
507
N
O
N
508
N
C
Y
509
N
C
Y
510
N
C
Y
511
N
C
Y
512
N
N
Y
513
N
C
Y
514
N
C
Y
515
N
C
Y
516
N
C
Y
517
N
C
N
518
N
O
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
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
N
N
532
S
C
N
533
N
C
N
534
N
O
N
535
N
C
Y
536
N
C
Y
537
N
C
Y
538
N
C
Y
539
N
C
Y
540
N
C
Y
541
N
C
N
542
N
O
N
543
N
O
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
H
N
555
N
N
N
556
S
C
N
557
N
C
N
558
N
O
N
559
N
C
N
560
N
C
N
561
N
C
N
562
N
O
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
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
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
doub
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
doub
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
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
doub
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
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
sing
N
85
N
doub
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
doub
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
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
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
Y
130
N
sing
Y
131
N
sing
Y
132
N
doub
N
133
N
sing
Y
134
N
sing
Y
135
N
sing
Y
136
N
doub
N
137
N
sing
Y
138
N
doub
N
139
N
sing
N
140
N
sing
Y
141
N
sing
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
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
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
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
N
202
N
sing
Y
203
N
sing
Y
204
N
sing
Y
205
N
doub
N
206
N
sing
Y
207
N
sing
N
208
N
sing
Y
209
N
doub
N
210
N
doub
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
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
doub
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
doub
N
249
N
sing
N
250
N
sing
N
251
N
doub
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
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
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
Y
313
N
sing
Y
314
N
doub
Y
315
N
doub
N
316
N
sing
Y
317
N
sing
N
318
N
sing
Y
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
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
doub
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
doub
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
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
doub
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
sing
N
388
N
sing
N
389
N
doub
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
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
doub
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
Y
437
N
doub
Y
438
N
sing
Y
439
N
sing
N
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
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
N
474
N
sing
N
475
N
sing
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
doub
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
doub
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
Y
506
N
doub
Y
507
N
sing
Y
508
N
sing
N
509
N
sing
Y
510
N
doub
Y
511
N
sing
Y
512
N
sing
N
513
N
sing
Y
514
N
sing
Y
515
N
doub
N
516
N
sing
Y
517
N
doub
N
518
N
sing
Y
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
N
529
N
doub
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
Y
534
N
doub
Y
535
N
sing
Y
536
N
sing
N
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
sing
N
553
N
doub
N
554
N
sing
N
555
N
sing
N
556
N
sing
N
557
N
sing
N
558
N
sing
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
N
563
N
sing
N
564
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
40
10203
10214
10.1093/nar/gks845
22962365
Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.
2012
10.2210/pdb4fnc/pdb
pdb_00004fnc
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror
CCD
2011-10-24
MARMOSAIC 300 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
22-ID
APS
1.0
SYNCHROTRON
APS BEAMLINE 22-ID
23070.670
G/T mismatch-specific thymine DNA glycosylase
3.2.2.29
human TDG glycosylase domain, UNP residues 111-308
1
man
polymer
8646.565
DNA (28-MER)
1
syn
polymer
8777.623
DNA (29-MER)
1
syn
polymer
142.113
5-HYDROXYMETHYL URACIL
1
syn
non-polymer
18.015
water
38
nat
water
Thymine-DNA glycosylase
no
no
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGK
YGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTET
LCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGK
YGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTET
LCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
A
polypeptide(L)
no
no
(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DA)(DG)(DC)(DA)(DG)(DT)
(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DT)
CAGCTCTGTACGTGAGCAGTGGACAGCT
C
polydeoxyribonucleotide
no
yes
(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DA)(AAB)(DG)(DT)
(DA)(DC)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)
AGCTGTCCACTGCTCAXGTACAGAGCTGT
D
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
TDG
9606
Homo sapiens
562
Escherichia coli
pXC1056
1
2.44
49.69
VAPOR DIFFUSION, SITTING DROP
4.6
30% polyethylene glycol (PEG) 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
289
4.448
1
19
C
1
D
28
-2.866
C_DC1:DG28_D
1
-6.836
-0.276
0.098
-0.213
11.446
1
20
C
2
D
27
-1.699
C_DA2:DT27_D
2
-8.884
-0.104
0.590
-0.227
7.519
1
19
C
3
D
26
-0.027
C_DG3:DC26_D
3
-12.626
-0.589
0.399
-0.637
-6.808
1
19
C
4
D
25
2.710
C_DC4:DG25_D
4
-15.042
0.207
0.354
-0.306
-8.909
1
20
C
5
D
24
-2.084
C_DT5:DA24_D
5
-10.910
-0.094
0.376
-0.444
-8.402
1
19
C
6
D
23
-4.875
C_DC6:DG23_D
6
-11.021
0.136
0.231
-0.381
0.390
1
20
C
7
D
22
2.739
C_DT7:DA22_D
7
-13.673
-0.086
0.001
-0.077
-7.701
1
19
C
8
D
21
-1.223
C_DG8:DC21_D
8
-1.363
-0.233
-0.185
-0.406
-8.236
1
20
C
9
D
20
-5.206
C_DT9:DA20_D
9
-11.723
-0.728
0.384
-0.443
2.623
1
20
C
10
D
19
3.710
C_DA10:DT19_D
10
-12.030
-0.040
0.112
-0.397
10.961
1
19
C
11
D
18
-1.154
C_DC11:DG18_D
11
-15.393
0.245
-0.231
-0.179
-13.105
1
20
C
13
D
16
-3.676
C_DT13:DA16_D
12
-12.635
-0.555
0.448
-0.119
-5.460
1
19
C
14
D
15
-0.436
C_DG14:DC15_D
13
-6.598
0.163
-0.128
-0.149
-4.323
1
20
C
15
D
14
0.284
C_DA15:DT14_D
14
-8.513
-0.411
0.234
-0.019
7.734
1
19
C
16
D
13
5.591
C_DG16:DC13_D
15
-14.554
0.121
0.786
0.141
-2.746
1
19
C
17
D
12
2.362
C_DC17:DG12_D
16
-18.766
0.680
0.487
-0.204
10.206
1
20
C
18
D
11
-3.341
C_DA18:DT11_D
17
-19.236
0.174
0.626
-0.359
-5.576
1
19
C
19
D
10
6.981
C_DG19:DC10_D
18
-15.549
-0.130
0.325
0.000
-3.313
1
20
C
20
D
9
0.044
C_DT20:DA9_D
19
-19.469
-0.110
0.329
-0.194
-9.305
1
19
C
21
D
8
0.684
C_DG21:DC8_D
20
-8.217
-0.677
-0.343
-0.589
-7.200
1
19
C
22
D
7
3.984
C_DG22:DC7_D
21
-15.809
-0.765
-0.062
-0.029
-6.597
1
20
C
23
D
6
-1.295
C_DA23:DT6_D
22
-15.534
0.148
-0.177
0.070
7.242
1
19
C
24
D
5
-3.108
C_DC24:DG5_D
23
-2.384
0.943
0.021
-0.436
4.682
1
20
C
25
D
4
0.024
C_DA25:DT4_D
24
-11.459
-0.805
-0.028
-0.302
10.176
1
C
26
D
3
9.022
C_DG26:DC3_D
25
-14.255
-0.615
0.579
0.032
-5.657
1
19
C
27
D
2
-0.963
C_DC27:DG2_D
26
-24.995
0.766
0.863
-0.093
-9.295
1
20
C
28
D
1
-10.022
C_DT28:DA1_D
27
-24.484
0.884
0.319
-0.296
3.141
37.678
C
C
1
2
-2.726
D
D
28
27
3.136
-1.760
0.423
-0.373
CC_DC1DA2:DT27DG28_DD
1
-0.749
1.161
37.631
-0.359
-0.748
3.126
34.650
C
C
2
3
9.517
D
D
27
26
3.303
5.634
0.151
-0.645
CC_DA2DG3:DC26DT27_DD
2
-3.775
6.376
34.000
-1.942
-0.829
3.652
37.628
C
C
3
4
-5.360
D
D
26
25
3.602
-3.453
-0.420
-0.804
CC_DG3DC4:DG25DC26_DD
3
0.584
-0.906
37.471
-0.747
0.736
3.292
34.518
C
C
4
5
5.907
D
D
25
24
3.332
3.500
-0.347
-0.187
CC_DC4DT5:DA24DG25_DD
4
0.596
-1.007
34.341
-0.865
0.678
3.217
39.169
C
C
5
6
1.810
D
D
24
23
3.195
1.211
0.368
0.093
CC_DT5DC6:DG23DA24_DD
5
4.050
-6.052
38.950
-0.003
-0.073
3.024
31.892
C
C
6
7
10.418
D
D
23
22
3.097
5.686
-0.075
-0.023
CC_DC6DT7:DA22DG23_DD
6
3.133
-5.740
31.241
-1.019
0.676
3.553
38.333
C
C
7
8
10.418
D
D
22
21
3.515
6.805
0.143
0.585
CC_DT7DG8:DC21DA22_DD
7
-1.756
2.689
37.707
-0.037
-0.457
3.349
25.454
C
C
8
9
2.005
D
D
21
20
3.340
0.878
-0.480
-0.593
CC_DG8DT9:DA20DC21_DD
8
-4.733
10.804
25.003
-1.606
-0.312
3.150
40.858
C
C
9
10
5.583
D
D
20
19
3.079
3.888
0.412
0.679
CC_DT9DA10:DT19DA20_DD
9
3.294
-4.730
40.552
0.565
-0.244
3.019
33.932
C
C
10
11
-1.729
D
D
19
18
3.060
-1.007
-0.182
0.197
CC_DA10DC11:DG18DT19_DD
10
3.557
-6.107
33.736
0.488
0.843
3.472
39.515
C
C
13
14
7.879
D
D
16
15
3.242
5.286
0.882
1.196
CC_DT13DG14:DC15DA16_DD
11
7.023
-10.469
38.563
1.123
-0.445
3.433
34.936
C
C
14
15
6.610
D
D
15
14
3.263
3.928
-0.994
0.470
CC_DG14DA15:DT14DC15_DD
12
-7.872
13.246
33.843
0.165
0.417
2.921
37.260
C
C
15
16
5.617
D
D
14
13
3.058
3.571
0.459
-0.254
CC_DA15DG16:DC13DT14_DD
13
-5.635
8.864
36.679
-0.834
-1.407
3.487
38.414
C
C
16
17
-9.054
D
D
13
12
3.477
-5.935
-0.763
-0.291
CC_DG16DC17:DG12DC13_DD
14
-0.234
0.356
37.969
0.349
1.129
2.838
33.049
C
C
17
18
19.605
D
D
12
11
2.939
10.953
-0.495
0.184
CC_DC17DA18:DT11DG12_DD
15
0.205
-0.367
31.229
-1.362
0.901
3.635
37.125
C
C
18
19
-1.861
D
D
11
10
3.604
-1.184
0.462
-0.527
CC_DA18DG19:DC10DT11_DD
16
1.731
-2.720
37.068
-0.653
-0.469
3.173
30.418
C
C
19
20
-1.654
D
D
10
9
3.163
-0.868
-0.674
-0.637
CC_DG19DT20:DA9DC10_DD
17
0.304
-0.579
30.405
-1.046
1.344
3.626
35.017
C
C
20
21
11.288
D
D
9
8
3.502
6.734
0.793
0.607
CC_DT20DG21:DC8DA9_DD
18
4.582
-7.681
34.086
-0.112
-0.556
3.245
35.833
C
C
21
22
3.907
D
D
8
7
3.114
2.389
-0.839
0.559
CC_DG21DG22:DC7DC8_DD
19
-6.833
11.177
35.118
0.572
0.400
3.312
40.483
C
C
22
23
4.538
D
D
7
6
3.269
3.136
-0.823
0.149
CC_DG22DA23:DT6DC7_DD
20
-2.369
3.429
40.300
-0.139
0.923
2.903
33.677
C
C
23
24
2.024
D
D
6
5
2.979
1.170
0.487
-0.188
CC_DA23DC24:DG5DT6_DD
21
-3.661
6.331
33.464
-0.497
-1.378
3.418
31.897
C
C
24
25
-3.162
D
D
5
4
3.478
-1.736
-0.006
0.890
CC_DC24DA25:DT4DG5_DD
22
2.115
-3.853
31.782
1.953
0.418
3.026
35.149
C
C
25
26
12.240
D
D
4
3
3.118
7.317
-0.074
-0.041
CC_DA25DG26:DC3DT4_DD
23
-4.948
8.276
34.055
-1.111
-0.583
3.652
39.232
C
C
26
27
-5.451
D
D
3
2
3.607
-3.653
-0.303
-0.542
CC_DG26DC27:DG2DC3_DD
24
-2.392
3.569
38.998
-0.322
0.133
2.678
39.175
C
C
27
28
21.275
D
D
2
1
3.111
13.908
-0.661
-0.268
CC_DC27DT28:DA1DG2_DD
25
6.604
-10.102
36.132
-1.939
1.717
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_validate_polymer_linkage
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Database references
Non-polymer description
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-09-19
1
1
2012-10-17
1
2
2012-11-21
1
3
2014-07-09
1
4
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-06-19
REL
REL
HMU
5-HYDROXYMETHYL URACIL
HOH
water
DNA oligonucleotide synthesis
sample
DNA oligonucleotide synthesis
sample
2RBA
PDB ENTRY 2RBA
PDB
experimental model
HMU
17
4
HMU
HMU
401
A
HOH
1
5
HOH
HOH
501
A
HOH
2
5
HOH
HOH
502
A
HOH
4
5
HOH
HOH
503
A
HOH
6
5
HOH
HOH
504
A
HOH
7
5
HOH
HOH
505
A
HOH
9
5
HOH
HOH
506
A
HOH
10
5
HOH
HOH
507
A
HOH
11
5
HOH
HOH
508
A
HOH
12
5
HOH
HOH
509
A
HOH
13
5
HOH
HOH
510
A
HOH
14
5
HOH
HOH
511
A
HOH
15
5
HOH
HOH
512
A
HOH
16
5
HOH
HOH
513
A
HOH
17
5
HOH
HOH
514
A
HOH
18
5
HOH
HOH
515
A
HOH
19
5
HOH
HOH
516
A
HOH
20
5
HOH
HOH
517
A
HOH
21
5
HOH
HOH
518
A
HOH
22
5
HOH
HOH
519
A
HOH
23
5
HOH
HOH
520
A
HOH
25
5
HOH
HOH
521
A
HOH
26
5
HOH
HOH
522
A
HOH
27
5
HOH
HOH
523
A
HOH
29
5
HOH
HOH
524
A
HOH
33
5
HOH
HOH
525
A
HOH
34
5
HOH
HOH
526
A
HOH
35
5
HOH
HOH
527
A
HOH
36
5
HOH
HOH
528
A
HOH
37
5
HOH
HOH
529
A
HOH
38
5
HOH
HOH
530
A
HOH
39
5
HOH
HOH
531
A
HOH
40
5
HOH
HOH
532
A
HOH
8
5
HOH
HOH
101
C
HOH
42
5
HOH
HOH
102
C
HOH
3
5
HOH
HOH
101
D
HOH
5
5
HOH
HOH
102
D
HOH
24
5
HOH
HOH
103
D
HOH
41
5
HOH
HOH
104
D
n
1
105
A
n
2
106
A
n
3
107
A
n
4
108
A
n
5
109
A
SER
110
n
6
SER
110
A
PHE
111
n
7
PHE
111
A
ASN
112
n
8
ASN
112
A
GLY
113
n
9
GLY
113
A
VAL
114
n
10
VAL
114
A
SER
115
n
11
SER
115
A
ALA
116
n
12
GLU
116
A
ALA
117
n
13
ALA
117
A
ALA
118
n
14
GLU
118
A
LEU
119
n
15
LEU
119
A
LEU
120
n
16
LEU
120
A
THR
121
n
17
THR
121
A
LYS
122
n
18
LYS
122
A
THR
123
n
19
THR
123
A
LEU
124
n
20
LEU
124
A
PRO
125
n
21
PRO
125
A
ASP
126
n
22
ASP
126
A
ILE
127
n
23
ILE
127
A
LEU
128
n
24
LEU
128
A
THR
129
n
25
THR
129
A
PHE
130
n
26
PHE
130
A
ASN
131
n
27
ASN
131
A
LEU
132
n
28
LEU
132
A
ASP
133
n
29
ASP
133
A
ILE
134
n
30
ILE
134
A
VAL
135
n
31
VAL
135
A
ILE
136
n
32
ILE
136
A
ILE
137
n
33
ILE
137
A
GLY
138
n
34
GLY
138
A
ILE
139
n
35
ILE
139
A
ASN
140
n
36
ASN
140
A
PRO
141
n
37
PRO
141
A
GLY
142
n
38
GLY
142
A
LEU
143
n
39
LEU
143
A
MET
144
n
40
MET
144
A
ALA
145
n
41
ALA
145
A
ALA
146
n
42
ALA
146
A
TYR
147
n
43
TYR
147
A
LYS
148
n
44
LYS
148
A
GLY
149
n
45
GLY
149
A
HIS
150
n
46
HIS
150
A
HIS
151
n
47
HIS
151
A
TYR
152
n
48
TYR
152
A
PRO
153
n
49
PRO
153
A
GLY
154
n
50
GLY
154
A
PRO
155
n
51
PRO
155
A
GLY
156
n
52
GLY
156
A
ASN
157
n
53
ASN
157
A
HIS
158
n
54
HIS
158
A
PHE
159
n
55
PHE
159
A
TRP
160
n
56
TRP
160
A
LYS
161
n
57
LYS
161
A
CYS
162
n
58
CYS
162
A
LEU
163
n
59
LEU
163
A
PHE
164
n
60
PHE
164
A
MET
165
n
61
MET
165
A
SER
166
n
62
SER
166
A
GLY
167
n
63
GLY
167
A
LEU
168
n
64
LEU
168
A
SER
169
n
65
SER
169
A
GLU
170
n
66
GLU
170
A
VAL
171
n
67
VAL
171
A
GLN
172
n
68
GLN
172
A
LEU
173
n
69
LEU
173
A
ASN
174
n
70
ASN
174
A
HIS
175
n
71
HIS
175
A
MET
176
n
72
MET
176
A
ASP
177
n
73
ASP
177
A
ASP
178
n
74
ASP
178
A
HIS
179
n
75
HIS
179
A
THR
180
n
76
THR
180
A
LEU
181
n
77
LEU
181
A
PRO
182
n
78
PRO
182
A
GLY
183
n
79
GLY
183
A
LYS
184
n
80
LYS
184
A
TYR
185
n
81
TYR
185
A
GLY
186
n
82
GLY
186
A
ILE
187
n
83
ILE
187
A
GLY
188
n
84
GLY
188
A
PHE
189
n
85
PHE
189
A
THR
190
n
86
THR
190
A
ASN
191
n
87
ASN
191
A
MET
192
n
88
MET
192
A
VAL
193
n
89
VAL
193
A
GLU
194
n
90
GLU
194
A
ARG
195
n
91
ARG
195
A
THR
196
n
92
THR
196
A
THR
197
n
93
THR
197
A
PRO
198
n
94
PRO
198
A
GLY
199
n
95
GLY
199
A
SER
200
n
96
SER
200
A
LYS
201
n
97
LYS
201
A
ASP
202
n
98
ASP
202
A
LEU
203
n
99
LEU
203
A
SER
204
n
100
SER
204
A
SER
205
n
101
SER
205
A
LYS
206
n
102
LYS
206
A
GLU
207
n
103
GLU
207
A
PHE
208
n
104
PHE
208
A
ARG
209
n
105
ARG
209
A
GLU
210
n
106
GLU
210
A
GLY
211
n
107
GLY
211
A
GLY
212
n
108
GLY
212
A
ARG
213
n
109
ARG
213
A
ILE
214
n
110
ILE
214
A
LEU
215
n
111
LEU
215
A
VAL
216
n
112
VAL
216
A
GLN
217
n
113
GLN
217
A
LYS
218
n
114
LYS
218
A
LEU
219
n
115
LEU
219
A
GLN
220
n
116
GLN
220
A
LYS
221
n
117
LYS
221
A
TYR
222
n
118
TYR
222
A
GLN
223
n
119
GLN
223
A
PRO
224
n
120
PRO
224
A
ARG
225
n
121
ARG
225
A
ILE
226
n
122
ILE
226
A
ALA
227
n
123
ALA
227
A
VAL
228
n
124
VAL
228
A
PHE
229
n
125
PHE
229
A
ASN
230
n
126
ASN
230
A
GLY
231
n
127
GLY
231
A
LYS
232
n
128
LYS
232
A
CYS
233
n
129
CYS
233
A
ILE
234
n
130
ILE
234
A
TYR
235
n
131
TYR
235
A
GLU
236
n
132
GLU
236
A
ILE
237
n
133
ILE
237
A
PHE
238
n
134
PHE
238
A
SER
239
n
135
SER
239
A
LYS
240
n
136
LYS
240
A
GLU
241
n
137
GLU
241
A
VAL
242
n
138
VAL
242
A
PHE
243
n
139
PHE
243
A
GLY
244
n
140
GLY
244
A
VAL
245
n
141
VAL
245
A
LYS
246
n
142
LYS
246
A
VAL
247
n
143
VAL
247
A
LYS
248
n
144
LYS
248
A
ASN
249
n
145
ASN
249
A
LEU
250
n
146
LEU
250
A
GLU
251
n
147
GLU
251
A
PHE
252
n
148
PHE
252
A
GLY
253
n
149
GLY
253
A
LEU
254
n
150
LEU
254
A
GLN
255
n
151
GLN
255
A
PRO
256
n
152
PRO
256
A
HIS
257
n
153
HIS
257
A
LYS
258
n
154
LYS
258
A
ILE
259
n
155
ILE
259
A
PRO
260
n
156
PRO
260
A
ASP
261
n
157
ASP
261
A
THR
262
n
158
THR
262
A
GLU
263
n
159
GLU
263
A
THR
264
n
160
THR
264
A
LEU
265
n
161
LEU
265
A
CYS
266
n
162
CYS
266
A
TYR
267
n
163
TYR
267
A
VAL
268
n
164
VAL
268
A
MET
269
n
165
MET
269
A
PRO
270
n
166
PRO
270
A
SER
271
n
167
SER
271
A
SER
272
n
168
SER
272
A
SER
273
n
169
SER
273
A
ALA
274
n
170
ALA
274
A
ARG
275
n
171
ARG
275
A
CYS
276
n
172
CYS
276
A
ALA
277
n
173
ALA
277
A
GLN
278
n
174
GLN
278
A
PHE
279
n
175
PHE
279
A
PRO
280
n
176
PRO
280
A
ARG
281
n
177
ARG
281
A
ALA
282
n
178
ALA
282
A
GLN
283
n
179
GLN
283
A
ASP
284
n
180
ASP
284
A
LYS
285
n
181
LYS
285
A
VAL
286
n
182
VAL
286
A
HIS
287
n
183
HIS
287
A
TYR
288
n
184
TYR
288
A
TYR
289
n
185
TYR
289
A
ILE
290
n
186
ILE
290
A
LYS
291
n
187
LYS
291
A
LEU
292
n
188
LEU
292
A
LYS
293
n
189
LYS
293
A
ASP
294
n
190
ASP
294
A
LEU
295
n
191
LEU
295
A
ARG
296
n
192
ARG
296
A
ASP
297
n
193
ASP
297
A
GLN
298
n
194
GLN
298
A
LEU
299
n
195
LEU
299
A
LYS
300
n
196
LYS
300
A
GLY
301
n
197
GLY
301
A
ALA
302
n
198
ILE
302
A
GLU
303
n
199
GLU
303
A
ARG
304
n
200
ARG
304
A
ALA
305
n
201
ASN
305
A
n
202
306
A
n
203
307
A
n
204
308
A
DC
1
n
1
DC
1
C
DA
2
n
2
DA
2
C
DG
3
n
3
DG
3
C
DC
4
n
4
DC
4
C
DT
5
n
5
DT
5
C
DC
6
n
6
DC
6
C
DT
7
n
7
DT
7
C
DG
8
n
8
DG
8
C
DT
9
n
9
DT
9
C
DA
10
n
10
DA
10
C
DC
11
n
11
DC
11
C
DG
12
n
12
DG
12
C
DT
13
n
13
DT
13
C
DG
14
n
14
DG
14
C
DA
15
n
15
DA
15
C
DG
16
n
16
DG
16
C
DC
17
n
17
DC
17
C
DA
18
n
18
DA
18
C
DG
19
n
19
DG
19
C
DT
20
n
20
DT
20
C
DG
21
n
21
DG
21
C
DG
22
n
22
DG
22
C
DA
23
n
23
DA
23
C
DC
24
n
24
DC
24
C
DA
25
n
25
DA
25
C
DG
26
n
26
DG
26
C
DC
27
n
27
DC
27
C
DT
28
n
28
DT
28
C
DA
1
n
1
DA
1
D
DG
2
n
2
DG
2
D
DC
3
n
3
DC
3
D
DT
4
n
4
DT
4
D
DG
5
n
5
DG
5
D
DT
6
n
6
DT
6
D
DC
7
n
7
DC
7
D
DC
8
n
8
DC
8
D
DA
9
n
9
DA
9
D
DC
10
n
10
DC
10
D
DT
11
n
11
DT
11
D
DG
12
n
12
DG
12
D
DC
13
n
13
DC
13
D
DT
14
n
14
DT
14
D
DC
15
n
15
DC
15
D
DA
16
n
16
DA
16
D
AAB
17
n
17
AAB
17
D
DG
18
n
18
DG
18
D
DT
19
n
19
DT
19
D
DA
20
n
20
DA
20
D
DC
21
n
21
DC
21
D
DA
22
n
22
DA
22
D
DG
23
n
23
DG
23
D
DA
24
n
24
DA
24
D
DG
25
n
25
DG
25
D
DC
26
n
26
DC
26
D
DT
27
n
27
DT
27
D
DG
28
n
28
DG
28
D
DT
29
n
29
DT
29
D
author_and_software_defined_assembly
PISA
3
trimeric
5320
-23
17860
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
GLY
188
A
O
GLY
84
A
N
ILE
134
A
N
ILE
30
A
N
ILE
137
A
N
ILE
33
A
O
VAL
228
A
O
VAL
124
A
N
ALA
227
A
N
ALA
123
A
O
LEU
265
A
O
LEU
161
A
O
VAL
268
A
O
VAL
164
A
N
GLY
253
A
N
GLY
149
1
A
CG
GLU
116
A
CG
GLU
12
1
Y
1
A
CD
GLU
116
A
CD
GLU
12
1
Y
1
A
OE1
GLU
116
A
OE1
GLU
12
1
Y
1
A
OE2
GLU
116
A
OE2
GLU
12
1
Y
1
A
CG
GLU
118
A
CG
GLU
14
1
Y
1
A
CD
GLU
118
A
CD
GLU
14
1
Y
1
A
OE1
GLU
118
A
OE1
GLU
14
1
Y
1
A
OE2
GLU
118
A
OE2
GLU
14
1
Y
1
A
CG
LYS
161
A
CG
LYS
57
1
Y
1
A
CD
LYS
161
A
CD
LYS
57
1
Y
1
A
CE
LYS
161
A
CE
LYS
57
1
Y
1
A
NZ
LYS
161
A
NZ
LYS
57
1
Y
1
A
CG
GLU
194
A
CG
GLU
90
1
Y
1
A
CD
GLU
194
A
CD
GLU
90
1
Y
1
A
OE1
GLU
194
A
OE1
GLU
90
1
Y
1
A
OE2
GLU
194
A
OE2
GLU
90
1
Y
1
A
CG
LYS
206
A
CG
LYS
102
1
Y
1
A
CD
LYS
206
A
CD
LYS
102
1
Y
1
A
CE
LYS
206
A
CE
LYS
102
1
Y
1
A
NZ
LYS
206
A
NZ
LYS
102
1
Y
1
A
CG
LYS
246
A
CG
LYS
142
1
Y
1
A
CD
LYS
246
A
CD
LYS
142
1
Y
1
A
CE
LYS
246
A
CE
LYS
142
1
Y
1
A
NZ
LYS
246
A
NZ
LYS
142
1
Y
1
A
CG
LYS
248
A
CG
LYS
144
1
Y
1
A
CD
LYS
248
A
CD
LYS
144
1
Y
1
A
CE
LYS
248
A
CE
LYS
144
1
Y
1
A
NZ
LYS
248
A
NZ
LYS
144
1
Y
1
A
CG
GLN
298
A
CG
GLN
194
1
Y
1
A
CD
GLN
298
A
CD
GLN
194
1
Y
1
A
OE1
GLN
298
A
OE1
GLN
194
1
Y
1
A
NE2
GLN
298
A
NE2
GLN
194
1
Y
1
A
CG1
ILE
302
A
CG1
ILE
198
1
Y
1
A
CG2
ILE
302
A
CG2
ILE
198
1
Y
1
A
CD1
ILE
302
A
CD1
ILE
198
1
Y
1
A
CG
ASN
305
A
CG
ASN
201
1
Y
1
A
OD1
ASN
305
A
OD1
ASN
201
1
Y
1
A
ND2
ASN
305
A
ND2
ASN
201
1
Y
1
D
O2P
AAB
17
C
O2P
AAB
17
1
Y
1
D
C5'
DT
29
C
C5'
DT
29
1
Y
1
D
C4'
DT
29
C
C4'
DT
29
1
Y
1
D
O4'
DT
29
C
O4'
DT
29
1
Y
1
D
C3'
DT
29
C
C3'
DT
29
1
Y
1
D
O3'
DT
29
C
O3'
DT
29
1
Y
1
D
C2'
DT
29
C
C2'
DT
29
1
Y
1
D
C1'
DT
29
C
C1'
DT
29
1
Y
1
D
N1
DT
29
C
N1
DT
29
1
Y
1
D
C2
DT
29
C
C2
DT
29
1
Y
1
D
O2
DT
29
C
O2
DT
29
1
Y
1
D
N3
DT
29
C
N3
DT
29
1
Y
1
D
C4
DT
29
C
C4
DT
29
1
Y
1
D
O4
DT
29
C
O4
DT
29
1
Y
1
D
C5
DT
29
C
C5
DT
29
1
Y
1
D
C7
DT
29
C
C7
DT
29
1
Y
1
D
C6
DT
29
C
C6
DT
29
1
Y
1
A
GLY
105
A
GLY
1
1
Y
1
A
SER
106
A
SER
2
1
Y
1
A
HIS
107
A
HIS
3
1
Y
1
A
MET
108
A
MET
4
1
Y
1
A
ALA
109
A
ALA
5
1
Y
1
A
MET
306
A
MET
202
1
Y
1
A
ASP
307
A
ASP
203
1
Y
1
A
VAL
308
A
VAL
204
1
Y
1
D
D
O3'
C1'
DA
AAB
16
17
6.35
1
D
D
C1'
P
AAB
DG
17
18
4.19
1
3.11
0.30
108.30
111.41
C
C
C
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
2.62
0.30
108.30
110.92
D
D
D
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.66
0.30
108.30
110.96
D
D
D
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.33
0.30
108.30
110.63
D
D
D
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
A
GLU
170
48.83
-3.46
1
A
SER
200
57.03
-95.36
1
A
LYS
221
-97.21
-63.51
1
A
GLN
223
33.67
81.57
1
A
ASN
249
-106.40
77.59
25.2992
-0.0000
16.1207
-10.7805
0.0000
-14.5187
0.2665
0.2239
0.2259
2.493
39.161
680
13673
4.97
98.73
0.86
random
1
THROUGHOUT
1.34
MOLECULAR REPLACEMENT
32.14
0.90
1.11
PDB ENTRY 2RBA
ML
FLAT BULK SOLVENT MODEL
39.807
0.321
2.493
39.161
38
2712
10
1139
1525
0.003
2851
0.863
4097
23.614
1126
0.056
453
0.003
329
0.4923
0.3840
2.6854
119
2476
95.00
0.3920
0.3314
2.9556
153
2583
100.00
0.3172
0.2307
3.3831
143
2596
100.00
0.2367
0.2169
4.2615
123
2644
100.00
0.2158
0.1853
39.1656
142
2694
100.00
58.71
2.49
39.161
4FNC
13702
-3.0
0.081
1
25.3
10.2
99.1
0.630
2.49
2.58
2.9
1282
1
8.5
93.6
data collection
HKL-2000
model building
PHENIX
refinement
PHENIX
(phenix.refine: 1.7.2_869)
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
SER
115
A
SER
11
HELX_P
A
LYS
122
A
LYS
18
1
1
8
A
GLY
142
A
GLY
38
HELX_P
A
GLY
149
A
GLY
45
1
2
8
A
HIS
158
A
HIS
54
HELX_P
A
SER
166
A
SER
62
1
3
9
A
ASN
174
A
ASN
70
HELX_P
A
HIS
179
A
HIS
75
5
4
6
A
THR
180
A
THR
76
HELX_P
A
TYR
185
A
TYR
81
1
5
6
A
GLY
199
A
GLY
95
HELX_P
A
LEU
203
A
LEU
99
5
6
5
A
SER
204
A
SER
100
HELX_P
A
GLN
223
A
GLN
119
1
7
20
A
GLY
231
A
GLY
127
HELX_P
A
PHE
243
A
PHE
139
1
8
13
A
ARG
281
A
ARG
177
HELX_P
A
ASN
305
A
ASN
201
1
9
25
hydrog
WATSON-CRICK
C
DC
1
B
N3
DC
1
1_555
D
DG
28
C
N1
DG
28
1_555
hydrog
WATSON-CRICK
C
DC
1
B
N4
DC
1
1_555
D
DG
28
C
O6
DG
28
1_555
hydrog
WATSON-CRICK
C
DC
1
B
O2
DC
1
1_555
D
DG
28
C
N2
DG
28
1_555
hydrog
WATSON-CRICK
C
DA
2
B
N1
DA
2
1_555
D
DT
27
C
N3
DT
27
1_555
hydrog
WATSON-CRICK
C
DA
2
B
N6
DA
2
1_555
D
DT
27
C
O4
DT
27
1_555
hydrog
WATSON-CRICK
C
DG
3
B
N1
DG
3
1_555
D
DC
26
C
N3
DC
26
1_555
hydrog
WATSON-CRICK
C
DG
3
B
N2
DG
3
1_555
D
DC
26
C
O2
DC
26
1_555
hydrog
WATSON-CRICK
C
DG
3
B
O6
DG
3
1_555
D
DC
26
C
N4
DC
26
1_555
hydrog
WATSON-CRICK
C
DC
4
B
N3
DC
4
1_555
D
DG
25
C
N1
DG
25
1_555
hydrog
WATSON-CRICK
C
DC
4
B
N4
DC
4
1_555
D
DG
25
C
O6
DG
25
1_555
hydrog
WATSON-CRICK
C
DC
4
B
O2
DC
4
1_555
D
DG
25
C
N2
DG
25
1_555
hydrog
WATSON-CRICK
C
DT
5
B
N3
DT
5
1_555
D
DA
24
C
N1
DA
24
1_555
hydrog
WATSON-CRICK
C
DT
5
B
O4
DT
5
1_555
D
DA
24
C
N6
DA
24
1_555
hydrog
WATSON-CRICK
C
DC
6
B
N3
DC
6
1_555
D
DG
23
C
N1
DG
23
1_555
hydrog
WATSON-CRICK
C
DC
6
B
N4
DC
6
1_555
D
DG
23
C
O6
DG
23
1_555
hydrog
WATSON-CRICK
C
DC
6
B
O2
DC
6
1_555
D
DG
23
C
N2
DG
23
1_555
hydrog
WATSON-CRICK
C
DT
7
B
N3
DT
7
1_555
D
DA
22
C
N1
DA
22
1_555
hydrog
WATSON-CRICK
C
DT
7
B
O4
DT
7
1_555
D
DA
22
C
N6
DA
22
1_555
hydrog
WATSON-CRICK
C
DG
8
B
N1
DG
8
1_555
D
DC
21
C
N3
DC
21
1_555
hydrog
WATSON-CRICK
C
DG
8
B
N2
DG
8
1_555
D
DC
21
C
O2
DC
21
1_555
hydrog
WATSON-CRICK
C
DG
8
B
O6
DG
8
1_555
D
DC
21
C
N4
DC
21
1_555
hydrog
WATSON-CRICK
C
DT
9
B
N3
DT
9
1_555
D
DA
20
C
N1
DA
20
1_555
hydrog
WATSON-CRICK
C
DT
9
B
O4
DT
9
1_555
D
DA
20
C
N6
DA
20
1_555
hydrog
WATSON-CRICK
C
DA
10
B
N1
DA
10
1_555
D
DT
19
C
N3
DT
19
1_555
hydrog
WATSON-CRICK
C
DA
10
B
N6
DA
10
1_555
D
DT
19
C
O4
DT
19
1_555
hydrog
WATSON-CRICK
C
DC
11
B
N3
DC
11
1_555
D
DG
18
C
N1
DG
18
1_555
hydrog
WATSON-CRICK
C
DC
11
B
N4
DC
11
1_555
D
DG
18
C
O6
DG
18
1_555
hydrog
WATSON-CRICK
C
DC
11
B
O2
DC
11
1_555
D
DG
18
C
N2
DG
18
1_555
hydrog
WATSON-CRICK
C
DT
13
B
N3
DT
13
1_555
D
DA
16
C
N1
DA
16
1_555
hydrog
WATSON-CRICK
C
DT
13
B
O4
DT
13
1_555
D
DA
16
C
N6
DA
16
1_555
hydrog
WATSON-CRICK
C
DG
14
B
N1
DG
14
1_555
D
DC
15
C
N3
DC
15
1_555
hydrog
WATSON-CRICK
C
DG
14
B
N2
DG
14
1_555
D
DC
15
C
O2
DC
15
1_555
hydrog
WATSON-CRICK
C
DG
14
B
O6
DG
14
1_555
D
DC
15
C
N4
DC
15
1_555
hydrog
WATSON-CRICK
C
DA
15
B
N1
DA
15
1_555
D
DT
14
C
N3
DT
14
1_555
hydrog
WATSON-CRICK
C
DA
15
B
N6
DA
15
1_555
D
DT
14
C
O4
DT
14
1_555
hydrog
WATSON-CRICK
C
DG
16
B
N1
DG
16
1_555
D
DC
13
C
N3
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
16
B
N2
DG
16
1_555
D
DC
13
C
O2
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
16
B
O6
DG
16
1_555
D
DC
13
C
N4
DC
13
1_555
hydrog
DC-DT MISPAIR
C
DC
17
B
N4
DC
17
1_555
D
DT
11
C
O4
DT
11
1_555
hydrog
WATSON-CRICK
C
DC
17
B
N3
DC
17
1_555
D
DG
12
C
N1
DG
12
1_555
hydrog
WATSON-CRICK
C
DC
17
B
N4
DC
17
1_555
D
DG
12
C
O6
DG
12
1_555
hydrog
WATSON-CRICK
C
DC
17
B
O2
DC
17
1_555
D
DG
12
C
N2
DG
12
1_555
hydrog
WATSON-CRICK
C
DA
18
B
N1
DA
18
1_555
D
DT
11
C
N3
DT
11
1_555
hydrog
WATSON-CRICK
C
DA
18
B
N6
DA
18
1_555
D
DT
11
C
O4
DT
11
1_555
hydrog
WATSON-CRICK
C
DG
19
B
N1
DG
19
1_555
D
DC
10
C
N3
DC
10
1_555
hydrog
WATSON-CRICK
C
DG
19
B
N2
DG
19
1_555
D
DC
10
C
O2
DC
10
1_555
hydrog
WATSON-CRICK
C
DG
19
B
O6
DG
19
1_555
D
DC
10
C
N4
DC
10
1_555
hydrog
WATSON-CRICK
C
DT
20
B
N3
DT
20
1_555
D
DA
9
C
N1
DA
9
1_555
hydrog
WATSON-CRICK
C
DT
20
B
O4
DT
20
1_555
D
DA
9
C
N6
DA
9
1_555
hydrog
WATSON-CRICK
C
DG
21
B
N1
DG
21
1_555
D
DC
8
C
N3
DC
8
1_555
hydrog
WATSON-CRICK
C
DG
21
B
N2
DG
21
1_555
D
DC
8
C
O2
DC
8
1_555
hydrog
WATSON-CRICK
C
DG
21
B
O6
DG
21
1_555
D
DC
8
C
N4
DC
8
1_555
hydrog
WATSON-CRICK
C
DG
22
B
N1
DG
22
1_555
D
DC
7
C
N3
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
22
B
N2
DG
22
1_555
D
DC
7
C
O2
DC
7
1_555
hydrog
WATSON-CRICK
C
DG
22
B
O6
DG
22
1_555
D
DC
7
C
N4
DC
7
1_555
hydrog
WATSON-CRICK
C
DA
23
B
N1
DA
23
1_555
D
DT
6
C
N3
DT
6
1_555
hydrog
WATSON-CRICK
C
DA
23
B
N6
DA
23
1_555
D
DT
6
C
O4
DT
6
1_555
hydrog
WATSON-CRICK
C
DC
24
B
N3
DC
24
1_555
D
DG
5
C
N1
DG
5
1_555
hydrog
WATSON-CRICK
C
DC
24
B
N4
DC
24
1_555
D
DG
5
C
O6
DG
5
1_555
hydrog
WATSON-CRICK
C
DC
24
B
O2
DC
24
1_555
D
DG
5
C
N2
DG
5
1_555
hydrog
WATSON-CRICK
C
DA
25
B
N1
DA
25
1_555
D
DT
4
C
N3
DT
4
1_555
hydrog
WATSON-CRICK
C
DA
25
B
N6
DA
25
1_555
D
DT
4
C
O4
DT
4
1_555
hydrog
DG-DC PAIR
C
DG
26
B
N1
DG
26
1_555
D
DC
3
C
O2
DC
3
1_555
hydrog
DC-DA MISPAIR
C
DC
27
B
N3
DC
27
1_555
D
DA
1
C
N6
DA
1
1_555
hydrog
WATSON-CRICK
C
DC
27
B
N3
DC
27
1_555
D
DG
2
C
N1
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
27
B
N4
DC
27
1_555
D
DG
2
C
O6
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
27
B
O2
DC
27
1_555
D
DG
2
C
N2
DG
2
1_555
hydrog
WATSON-CRICK
C
DT
28
B
N3
DT
28
1_555
D
DA
1
C
N1
DA
1
1_555
hydrog
WATSON-CRICK
C
DT
28
B
O4
DT
28
1_555
D
DA
1
C
N6
DA
1
1_555
HYDROLASE/DNA
base excision repair, HYDROLASE-DNA complex
TDG_HUMAN
UNP
1
111
Q13569
FNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFT
NMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMP
SSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
4FNC
PDB
2
4FNC
CAGCTCTGTACGTGAGCAGTGGACAGCT
4FNC
PDB
3
4FNC
AGCTGTCCACTGCTCAXGTACAGAGCTGT
111
308
4FNC
111
308
Q13569
A
1
7
204
1
28
4FNC
1
28
4FNC
C
2
1
28
1
29
4FNC
1
29
4FNC
D
3
1
29
1
expression tag
GLY
105
4FNC
A
Q13569
UNP
1
1
expression tag
SER
106
4FNC
A
Q13569
UNP
2
1
expression tag
HIS
107
4FNC
A
Q13569
UNP
3
1
expression tag
MET
108
4FNC
A
Q13569
UNP
4
1
expression tag
ALA
109
4FNC
A
Q13569
UNP
5
1
expression tag
SER
110
4FNC
A
Q13569
UNP
6
5
parallel
parallel
parallel
anti-parallel
A
ILE
187
A
ILE
83
A
ASN
191
A
ASN
87
A
ILE
134
A
ILE
30
A
GLY
138
A
GLY
34
A
ILE
226
A
ILE
122
A
ASN
230
A
ASN
126
A
LEU
265
A
LEU
161
A
MET
269
A
MET
165
A
GLY
253
A
GLY
149
A
LEU
254
A
LEU
150
BINDING SITE FOR RESIDUE HMU A 401
A
HMU
401
Software
9
A
GLY
138
A
GLY
34
9
1_555
A
ILE
139
A
ILE
35
9
1_555
A
ASN
140
A
ASN
36
9
1_555
A
TYR
152
A
TYR
48
9
1_555
A
ASN
157
A
ASN
53
9
1_555
A
ASN
230
A
ASN
126
9
1_555
A
SER
271
A
SER
167
9
1_555
A
HOH
529
E
HOH
9
1_555
D
AAB
17
C
AAB
17
9
1_555
5
C 1 2 1