0.011542
0.006664
0.000000
0.000000
0.013328
0.000000
0.000000
0.000000
0.016069
0.00000
0.00000
0.00000
Larsson, G.
Svensson, L.A.
Nyman, P.O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
9
90.00
90.00
120.00
86.640
86.640
62.230
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
C9 H14 N2 O11 P2
388.162
DEOXYURIDINE-5'-DIPHOSPHATE
non-polymer
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
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
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
N
N
89
N
C
N
90
N
N
N
91
N
C
N
92
N
C
N
93
N
C
N
94
N
O
N
95
N
O
N
96
R
C
N
97
N
C
N
98
S
C
N
99
R
C
N
100
N
O
N
101
N
O
N
102
N
C
N
103
N
O
N
104
S
P
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
P
N
109
N
O
N
110
N
O
N
111
N
O
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
N
N
127
S
C
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
O
N
134
N
N
N
135
N
O
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
S
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
O
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
N
N
166
N
C
N
167
N
C
N
168
N
O
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
N
N
176
S
C
N
177
N
C
N
178
N
O
N
179
N
C
Y
180
N
C
Y
181
N
N
Y
182
N
C
Y
183
N
C
Y
184
N
N
N
185
N
O
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
O
N
197
N
H
N
198
N
H
N
199
N
N
N
200
S
C
N
201
N
C
N
202
N
O
N
203
S
C
N
204
N
C
N
205
N
C
N
206
N
C
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
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
S
C
N
223
N
C
N
224
N
O
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
C
N
229
N
O
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
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
N
N
244
S
C
N
245
N
C
N
246
N
O
N
247
N
C
N
248
N
C
N
249
N
C
N
250
N
C
N
251
N
N
N
252
N
O
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
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
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
C
N
273
N
C
N
274
N
S
N
275
N
C
N
276
N
O
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
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
N
299
N
O
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
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
N
C
N
316
N
C
N
317
N
C
N
318
N
O
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
H
N
327
N
H
N
328
N
N
N
329
S
C
N
330
N
C
N
331
N
O
N
332
N
C
N
333
N
O
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
R
C
N
347
N
O
N
348
N
C
N
349
N
O
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
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
N
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
N
373
N
O
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
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
C
N
397
N
O
N
398
N
O
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
N
N
411
S
C
N
412
N
C
N
413
N
O
N
414
N
C
N
415
N
C
N
416
N
C
N
417
N
O
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
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
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
doub
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
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
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
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
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
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
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
doub
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
doub
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
doub
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
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
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
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
doub
N
240
N
sing
N
241
N
sing
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
sing
N
251
N
sing
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
sing
N
263
N
doub
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
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
sing
N
282
N
doub
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
Y
287
N
doub
Y
288
N
sing
Y
289
N
sing
N
290
N
sing
Y
291
N
doub
N
292
N
sing
Y
293
N
doub
N
294
N
sing
Y
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
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
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
doub
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
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
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
Y
356
N
doub
Y
357
N
sing
Y
358
N
sing
N
359
N
sing
Y
360
N
doub
Y
361
N
sing
Y
362
N
sing
N
363
N
sing
Y
364
N
sing
Y
365
N
doub
N
366
N
sing
Y
367
N
doub
N
368
N
sing
Y
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
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
Y
384
N
doub
Y
385
N
sing
Y
386
N
sing
N
387
N
sing
Y
388
N
doub
N
389
N
sing
Y
390
N
doub
N
391
N
sing
Y
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
doub
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
3
532
538
10.1038/nsb0696-532
8646539
Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP).
1996
10.2210/pdb1dud/pdb
pdb_00001dud
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
AREA DETECTOR
SIEMENS
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RUH2R
16302.615
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
3.6.1.23
1
nat
polymer
388.162
DEOXYURIDINE-5'-DIPHOSPHATE
1
syn
non-polymer
18.015
water
94
nat
water
no
no
MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGI
VLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ
MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGI
VLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
sample
562
Escherichia coli
2.76
55.36
pdbx_database_status
struct_conf
struct_conf_type
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Derived calculations
Other
Data collection
Database references
Derived calculations
1
0
1996-11-08
1
1
2008-03-24
1
2
2011-07-13
1
3
2017-11-29
1
4
2024-02-07
_pdbx_database_status.process_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1996-04-30
REL
REL
DUD
DEOXYURIDINE-5'-DIPHOSPHATE
HOH
water
SECONDARY STRUCTURE BOUNDARIES AS DETERMINED FOR THE MODEL
OF UNCOMPLEXED D-UTPASE (1DUP).
DUD
150
2
DUD
DUD
153
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
215
3
HOH
HOH
215
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
245
3
HOH
HOH
245
A
HOH
246
3
HOH
HOH
246
A
HOH
247
3
HOH
HOH
247
A
HOH
248
3
HOH
HOH
248
A
HOH
250
3
HOH
HOH
250
A
HOH
253
3
HOH
HOH
253
A
HOH
262
3
HOH
HOH
262
A
HOH
263
3
HOH
HOH
263
A
HOH
266
3
HOH
HOH
266
A
HOH
268
3
HOH
HOH
268
A
HOH
270
3
HOH
HOH
270
A
HOH
271
3
HOH
HOH
271
A
HOH
272
3
HOH
HOH
272
A
HOH
273
3
HOH
HOH
273
A
HOH
279
3
HOH
HOH
279
A
HOH
280
3
HOH
HOH
280
A
HOH
281
3
HOH
HOH
281
A
HOH
282
3
HOH
HOH
282
A
HOH
283
3
HOH
HOH
283
A
HOH
287
3
HOH
HOH
287
A
HOH
288
3
HOH
HOH
288
A
HOH
289
3
HOH
HOH
289
A
HOH
290
3
HOH
HOH
290
A
HOH
291
3
HOH
HOH
291
A
HOH
292
3
HOH
HOH
292
A
HOH
293
3
HOH
HOH
293
A
HOH
294
3
HOH
HOH
294
A
HOH
295
3
HOH
HOH
295
A
HOH
296
3
HOH
HOH
296
A
HOH
297
3
HOH
HOH
297
A
HOH
299
3
HOH
HOH
299
A
HOH
306
3
HOH
HOH
306
A
HOH
307
3
HOH
HOH
307
A
HOH
309
3
HOH
HOH
309
A
HOH
311
3
HOH
HOH
311
A
HOH
313
3
HOH
HOH
313
A
HOH
314
3
HOH
HOH
314
A
HOH
317
3
HOH
HOH
317
A
HOH
321
3
HOH
HOH
321
A
HOH
324
3
HOH
HOH
324
A
HOH
326
3
HOH
HOH
326
A
HOH
329
3
HOH
HOH
329
A
HOH
330
3
HOH
HOH
330
A
HOH
331
3
HOH
HOH
331
A
HOH
333
3
HOH
HOH
333
A
HOH
334
3
HOH
HOH
334
A
HOH
339
3
HOH
HOH
339
A
HOH
341
3
HOH
HOH
341
A
HOH
346
3
HOH
HOH
346
A
HOH
348
3
HOH
HOH
348
A
HOH
359
3
HOH
HOH
359
A
HOH
361
3
HOH
HOH
361
A
HOH
365
3
HOH
HOH
365
A
HOH
369
3
HOH
HOH
369
A
HOH
371
3
HOH
HOH
371
A
HOH
373
3
HOH
HOH
373
A
HOH
380
3
HOH
HOH
380
A
HOH
385
3
HOH
HOH
385
A
HOH
390
3
HOH
HOH
390
A
HOH
391
3
HOH
HOH
391
A
HOH
392
3
HOH
HOH
392
A
MET
1
n
1
MET
1
A
MET
2
n
2
MET
2
A
LYS
3
n
3
LYS
3
A
LYS
4
n
4
LYS
4
A
ILE
5
n
5
ILE
5
A
ASP
6
n
6
ASP
6
A
VAL
7
n
7
VAL
7
A
LYS
8
n
8
LYS
8
A
ILE
9
n
9
ILE
9
A
LEU
10
n
10
LEU
10
A
ASP
11
n
11
ASP
11
A
PRO
12
n
12
PRO
12
A
ARG
13
n
13
ARG
13
A
VAL
14
n
14
VAL
14
A
GLY
15
n
15
GLY
15
A
LYS
16
n
16
LYS
16
A
GLU
17
n
17
GLU
17
A
PHE
18
n
18
PHE
18
A
PRO
19
n
19
PRO
19
A
LEU
20
n
20
LEU
20
A
PRO
21
n
21
PRO
21
A
THR
22
n
22
THR
22
A
TYR
23
n
23
TYR
23
A
ALA
24
n
24
ALA
24
A
THR
25
n
25
THR
25
A
SER
26
n
26
SER
26
A
GLY
27
n
27
GLY
27
A
SER
28
n
28
SER
28
A
ALA
29
n
29
ALA
29
A
GLY
30
n
30
GLY
30
A
LEU
31
n
31
LEU
31
A
ASP
32
n
32
ASP
32
A
LEU
33
n
33
LEU
33
A
ARG
34
n
34
ARG
34
A
ALA
35
n
35
ALA
35
A
CYS
36
n
36
CYS
36
A
LEU
37
n
37
LEU
37
A
ASN
38
n
38
ASN
38
A
ASP
39
n
39
ASP
39
A
ALA
40
n
40
ALA
40
A
VAL
41
n
41
VAL
41
A
GLU
42
n
42
GLU
42
A
LEU
43
n
43
LEU
43
A
ALA
44
n
44
ALA
44
A
PRO
45
n
45
PRO
45
A
GLY
46
n
46
GLY
46
A
ASP
47
n
47
ASP
47
A
THR
48
n
48
THR
48
A
THR
49
n
49
THR
49
A
LEU
50
n
50
LEU
50
A
VAL
51
n
51
VAL
51
A
PRO
52
n
52
PRO
52
A
THR
53
n
53
THR
53
A
GLY
54
n
54
GLY
54
A
LEU
55
n
55
LEU
55
A
ALA
56
n
56
ALA
56
A
ILE
57
n
57
ILE
57
A
HIS
58
n
58
HIS
58
A
ILE
59
n
59
ILE
59
A
ALA
60
n
60
ALA
60
A
ASP
61
n
61
ASP
61
A
PRO
62
n
62
PRO
62
A
SER
63
n
63
SER
63
A
LEU
64
n
64
LEU
64
A
ALA
65
n
65
ALA
65
A
ALA
66
n
66
ALA
66
A
MET
67
n
67
MET
67
A
MET
68
n
68
MET
68
A
LEU
69
n
69
LEU
69
A
PRO
70
n
70
PRO
70
A
ARG
71
n
71
ARG
71
A
SER
72
n
72
SER
72
A
GLY
73
n
73
GLY
73
A
LEU
74
n
74
LEU
74
A
GLY
75
n
75
GLY
75
A
HIS
76
n
76
HIS
76
A
LYS
77
n
77
LYS
77
A
HIS
78
n
78
HIS
78
A
GLY
79
n
79
GLY
79
A
ILE
80
n
80
ILE
80
A
VAL
81
n
81
VAL
81
A
LEU
82
n
82
LEU
82
A
GLY
83
n
83
GLY
83
A
ASN
84
n
84
ASN
84
A
LEU
85
n
85
LEU
85
A
VAL
86
n
86
VAL
86
A
GLY
87
n
87
GLY
87
A
LEU
88
n
88
LEU
88
A
ILE
89
n
89
ILE
89
A
ASP
90
n
90
ASP
90
A
SER
91
n
91
SER
91
A
ASP
92
n
92
ASP
92
A
TYR
93
n
93
TYR
93
A
GLN
94
n
94
GLN
94
A
GLY
95
n
95
GLY
95
A
GLN
96
n
96
GLN
96
A
LEU
97
n
97
LEU
97
A
MET
98
n
98
MET
98
A
ILE
99
n
99
ILE
99
A
SER
100
n
100
SER
100
A
VAL
101
n
101
VAL
101
A
TRP
102
n
102
TRP
102
A
ASN
103
n
103
ASN
103
A
ARG
104
n
104
ARG
104
A
GLY
105
n
105
GLY
105
A
GLN
106
n
106
GLN
106
A
ASP
107
n
107
ASP
107
A
SER
108
n
108
SER
108
A
PHE
109
n
109
PHE
109
A
THR
110
n
110
THR
110
A
ILE
111
n
111
ILE
111
A
GLN
112
n
112
GLN
112
A
PRO
113
n
113
PRO
113
A
GLY
114
n
114
GLY
114
A
GLU
115
n
115
GLU
115
A
ARG
116
n
116
ARG
116
A
ILE
117
n
117
ILE
117
A
ALA
118
n
118
ALA
118
A
GLN
119
n
119
GLN
119
A
MET
120
n
120
MET
120
A
ILE
121
n
121
ILE
121
A
PHE
122
n
122
PHE
122
A
VAL
123
n
123
VAL
123
A
PRO
124
n
124
PRO
124
A
VAL
125
n
125
VAL
125
A
VAL
126
n
126
VAL
126
A
GLN
127
n
127
GLN
127
A
ALA
128
n
128
ALA
128
A
GLU
129
n
129
GLU
129
A
PHE
130
n
130
PHE
130
A
ASN
131
n
131
ASN
131
A
LEU
132
n
132
LEU
132
A
VAL
133
n
133
VAL
133
A
GLU
134
n
134
GLU
134
A
ASP
135
n
135
ASP
135
A
PHE
136
n
136
PHE
136
A
n
137
137
A
n
138
138
A
n
139
139
A
n
140
140
A
n
141
141
A
n
142
142
A
n
143
143
A
n
144
144
A
n
145
145
A
n
146
146
A
n
147
147
A
n
148
148
A
n
149
149
A
n
150
150
A
n
151
151
A
n
152
152
A
author_and_software_defined_assembly
PISA,PQS
3
trimeric
11920
-74
15890
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_665
-y+1,x-y+1,z
crystal symmetry operation
43.3200000000
75.0324409839
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_565
-x+y,-x+1,z
crystal symmetry operation
-43.3200000000
75.0324409839
0.0000000000
A
O
ASP
6
A
O
ASP
6
A
N
HIS
58
A
N
HIS
58
A
O
VAL
51
A
O
VAL
51
A
N
MET
98
A
N
MET
98
A
O
SER
100
A
O
SER
100
A
N
GLY
83
A
N
GLY
83
A
O
LEU
31
A
O
LEU
31
A
N
MET
120
A
N
MET
120
A
O
VAL
123
A
O
VAL
123
A
N
ALA
65
A
N
ALA
65
A
O
MET
68
A
O
MET
68
A
N
GLY
87
A
N
GLY
87
A
O
LEU
43
A
O
LEU
43
A
N
PHE
109
A
N
PHE
109
1
A
ASP
137
A
ASP
137
1
Y
1
A
ALA
138
A
ALA
138
1
Y
1
A
THR
139
A
THR
139
1
Y
1
A
ASP
140
A
ASP
140
1
Y
1
A
ARG
141
A
ARG
141
1
Y
1
A
GLY
142
A
GLY
142
1
Y
1
A
GLU
143
A
GLU
143
1
Y
1
A
GLY
144
A
GLY
144
1
Y
1
A
GLY
145
A
GLY
145
1
Y
1
A
PHE
146
A
PHE
146
1
Y
1
A
GLY
147
A
GLY
147
1
Y
1
A
HIS
148
A
HIS
148
1
Y
1
A
SER
149
A
SER
149
1
Y
1
A
GLY
150
A
GLY
150
1
Y
1
A
ARG
151
A
ARG
151
1
Y
1
A
GLN
152
A
GLN
152
1
Y
1
-4.00
0.50
120.30
116.30
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
34
34
34
N
1
-9.73
1.60
100.20
90.47
A
A
A
CG
SD
CE
MET
MET
MET
67
67
67
N
1
3.44
0.50
120.30
123.74
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
71
71
71
N
1
-5.39
0.50
120.30
114.91
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
71
71
71
N
1
-11.30
1.60
110.90
99.60
A
A
A
CG1
CB
CG2
VAL
VAL
VAL
81
81
81
N
1
-4.07
0.60
121.00
116.93
A
A
A
CB
CG
CD1
TYR
TYR
TYR
93
93
93
N
1
6.39
0.80
106.30
112.69
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
102
102
102
N
1
-6.18
0.80
107.30
101.12
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
102
102
102
N
1
3.86
0.50
120.30
124.16
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
104
104
104
N
1
-3.27
0.50
120.30
117.03
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
104
104
104
N
1
A
A
NE2
CD2
HIS
HIS
58
58
-0.076
0.011
1.373
1.297
N
1
A
A
NE2
CD2
HIS
HIS
76
76
-0.067
0.011
1.373
1.306
N
1
A
A
NE2
CD2
HIS
HIS
78
78
-0.079
0.011
1.373
1.294
N
1
A
LYS
16
-102.15
-64.87
1
A
ALA
60
54.24
-14.71
1
A
LEU
85
60.71
-55.08
PARAM119X.PRO
TOPH19X.PRO
PARAM11.DNA
TOPH11.DNA
23.4
0.2000000
0.2000000
2.3
10.0
7520
98.2
1
1.0
10.0
0.23
2.3
10.0
94
1145
24
0
1027
0.017
3.3
27.9
1.35
1.5
2.0
2.0
2.5
0.2580000
2.40
924
96.
24.9
2.25
1DUD
7520
0.0720000
1
67.
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
data reduction
XDS
phasing
X-PLOR
3.1
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)
1
N
N
2
N
N
3
N
N
A
SER
72
A
SER
72
HELX_P
A
HIS
78
A
HIS
78
1
H1
7
HYDROLASE
HYDROLASE, NUCLEOTIDE METABOLISM, D-UTPASE, SUBSTRATE ANALOGUE, D-UDP COMPLEX
DUT_ECOLI
UNP
1
1
P06968
MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIV
LGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ
1
151
1DUD
2
152
P06968
A
1
2
152
4
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
3
A
LYS
3
A
LEU
10
A
LEU
10
A
ASP
47
A
ASP
47
A
HIS
58
A
HIS
58
A
LEU
97
A
LEU
97
A
ARG
104
A
ARG
104
A
GLY
79
A
GLY
79
A
GLY
83
A
GLY
83
A
LEU
31
A
LEU
31
A
ALA
35
A
ALA
35
A
GLY
114
A
GLY
114
A
VAL
125
A
VAL
125
A
SER
63
A
SER
63
A
LEU
69
A
LEU
69
A
GLY
87
A
GLY
87
A
ILE
89
A
ILE
89
A
VAL
41
A
VAL
41
A
LEU
43
A
LEU
43
A
PHE
109
A
PHE
109
A
ILE
111
A
ILE
111
BINDING SITE FOR RESIDUE DUD A 153
A
DUD
153
Software
17
A
MET
68
A
MET
68
17
1_555
A
SER
72
A
SER
72
17
3_565
A
GLY
73
A
GLY
73
17
3_565
A
ASN
84
A
ASN
84
17
1_555
A
GLY
87
A
GLY
87
17
1_555
A
LEU
88
A
LEU
88
17
1_555
A
ILE
89
A
ILE
89
17
1_555
A
ASP
90
A
ASP
90
17
1_555
A
TYR
93
A
TYR
93
17
1_555
A
GLN
96
A
GLN
96
17
1_555
A
MET
98
A
MET
98
17
1_555
A
GLN
119
A
GLN
119
17
3_565
A
HOH
235
C
HOH
17
3_565
A
HOH
271
C
HOH
17
1_555
A
HOH
359
C
HOH
17
1_555
A
HOH
390
C
HOH
17
1_555
A
HOH
392
C
HOH
17
1_555
146
H 3