0.009842
0.000000
0.000000
0.000000
0.009842
0.000000
0.000000
0.000000
0.020040
0.00000
0.00000
0.00000
Ostermann, N.
Schlichting, I.
Brundiers, R.
Konrad, M.
Reinstein, J.
Veit, T.
Goody, R.S.
Lavie, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
101.600
101.600
49.900
C10 H15 N5 O10 P2
427.201
n
ADENOSINE-5'-DIPHOSPHATE
non-polymer
Al F3
83.977
ALUMINUM FLUORIDE
non-polymer
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
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
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
C10 H15 N2 O8 P
322.208
THYMIDINE-5'-PHOSPHATE
non-polymer
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
S
P
N
6
N
O
N
7
N
O
N
8
N
O
N
9
N
O
N
10
N
C
N
11
R
C
N
12
N
O
N
13
S
C
N
14
N
O
N
15
R
C
N
16
N
O
N
17
R
C
Y
18
N
N
Y
19
N
C
Y
20
N
N
Y
21
N
C
Y
22
N
C
N
23
N
N
Y
24
N
N
Y
25
N
C
Y
26
N
N
Y
27
N
C
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
H
N
42
N
H
N
43
N
AL
N
44
N
F
N
45
N
F
N
46
N
F
N
47
N
N
N
48
S
C
N
49
N
C
N
50
N
O
N
51
N
C
N
52
N
O
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
N
N
61
S
C
N
62
N
C
N
63
N
O
N
64
N
C
N
65
N
C
N
66
N
C
N
67
N
N
N
68
N
C
N
69
N
N
N
70
N
N
N
71
N
O
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
N
N
88
S
C
N
89
N
C
N
90
N
O
N
91
N
C
N
92
N
C
N
93
N
O
N
94
N
N
N
95
N
O
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
N
N
105
S
C
N
106
N
C
N
107
N
O
N
108
N
C
N
109
N
C
N
110
N
O
N
111
N
O
N
112
N
O
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
N
N
121
R
C
N
122
N
C
N
123
N
O
N
124
N
C
N
125
N
S
N
126
N
O
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
N
N
135
S
C
N
136
N
C
N
137
N
O
N
138
N
C
N
139
N
C
N
140
N
C
N
141
N
O
N
142
N
N
N
143
N
O
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
N
N
155
S
C
N
156
N
C
N
157
N
O
N
158
N
C
N
159
N
C
N
160
N
C
N
161
N
O
N
162
N
O
N
163
N
O
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
N
N
174
N
C
N
175
N
C
N
176
N
O
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
Y
188
N
C
Y
189
N
N
Y
190
N
C
Y
191
N
C
Y
192
N
N
N
193
N
O
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
O
N
205
N
H
N
206
N
H
N
207
N
N
N
208
S
C
N
209
N
C
N
210
N
O
N
211
S
C
N
212
N
C
N
213
N
C
N
214
N
C
N
215
N
O
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
N
N
230
S
C
N
231
N
C
N
232
N
O
N
233
N
C
N
234
N
C
N
235
N
C
N
236
N
C
N
237
N
O
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
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
C
N
259
N
N
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
C
N
282
N
S
N
283
N
C
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
H
N
295
N
H
N
296
N
MG
N
297
N
N
N
298
S
C
N
299
N
C
N
300
N
O
N
301
N
C
Y
302
N
C
Y
303
N
C
Y
304
N
C
Y
305
N
C
Y
306
N
C
Y
307
N
C
N
308
N
O
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
C
N
326
N
C
N
327
N
O
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
N
O
N
343
N
O
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
R
C
N
356
N
O
N
357
N
C
N
358
N
O
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
H
N
367
N
H
N
368
N
P
N
369
N
O
N
370
N
O
N
371
N
O
N
372
N
O
N
373
N
C
N
374
R
C
N
375
N
O
N
376
S
C
N
377
N
O
N
378
N
C
N
379
R
C
N
380
N
N
N
381
N
C
N
382
N
O
N
383
N
N
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
H
N
390
N
H
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
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
N
Y
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
N
418
N
O
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
H
N
430
N
H
N
431
N
N
N
432
S
C
N
433
N
C
N
434
N
O
N
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
N
442
N
O
N
443
N
O
N
444
N
H
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
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
N
460
N
C
N
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
1
N
doub
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
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
Y
30
N
sing
Y
31
N
sing
Y
32
N
doub
N
33
N
sing
Y
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
doub
N
39
N
sing
N
40
N
sing
Y
41
N
sing
Y
42
N
doub
N
43
N
sing
Y
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
doub
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
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
sing
N
79
N
sing
N
80
N
doub
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
doub
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
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
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
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
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
doub
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
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
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
Y
187
N
sing
Y
188
N
doub
Y
189
N
doub
N
190
N
sing
Y
191
N
sing
N
192
N
sing
Y
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
N
203
N
sing
N
204
N
sing
N
205
N
doub
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
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
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
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
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
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
doub
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
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
Y
295
N
doub
Y
296
N
sing
Y
297
N
sing
N
298
N
sing
Y
299
N
doub
N
300
N
sing
Y
301
N
doub
N
302
N
sing
Y
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
doub
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
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
doub
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
doub
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
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
doub
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
doub
N
383
N
sing
N
384
N
sing
N
385
N
doub
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
doub
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
Y
401
N
doub
Y
402
N
sing
Y
403
N
sing
N
404
N
sing
Y
405
N
doub
Y
406
N
sing
Y
407
N
sing
N
408
N
sing
Y
409
N
sing
Y
410
N
doub
N
411
N
sing
Y
412
N
doub
N
413
N
sing
Y
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
doub
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
Y
429
N
doub
Y
430
N
sing
Y
431
N
sing
N
432
N
sing
Y
433
N
doub
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
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
doub
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
UK
Structure
STRUE6
2005
0969-2126
8
629
10.1016/S0969-2126(00)00149-0
10873853
Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate
2000
10.2210/pdb1e2e/pdb
pdb_00001e2e
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
MARRESEARCH
YES
SINGLE WAVELENGTH
M
x-ray
1
0.931
1.0
ID14-3
ESRF
0.931
SYNCHROTRON
ESRF BEAMLINE ID14-3
24052.533
THYMIDYLATE KINASE
2.7.4.9
YES
1
man
polymer
322.208
THYMIDINE-5'-PHOSPHATE
1
syn
non-polymer
427.201
ADENOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
83.977
ALUMINUM FLUORIDE
1
syn
non-polymer
18.015
water
172
nat
water
TMPK
no
no
GSHMAARRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRW
EQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQ
ERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK
GSHMAARRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRW
EQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQ
ERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
9606
HOMO SAPIENS
562
ESCHERICHIA COLI
1
2.68
54.05
VAPOR DIFFUSION
8.00
VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8.0 AND 50 MICROLITERS OF DEAD SEA WATER.
293
database_PDB_rev
database_PDB_rev_record
exptl_crystal_grow
pdbx_database_proc
pdbx_database_status
pdbx_struct_special_symmetry
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Derived calculations
Experimental preparation
Other
Data collection
Database references
Derived calculations
Other
1
0
2001-05-17
1
1
2011-05-08
1
2
2011-07-13
1
3
2019-03-06
1
4
2024-05-08
_exptl_crystal_grow.method
_exptl_crystal_grow.temp
_pdbx_database_status.recvd_author_approval
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_struct_conn.pdbx_dist_value
_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_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.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION
YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)
YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP)
HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION
HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION
HUMAN THYMIDYLATE KINASE COMPLEXED WITH TP5A AND A MAGNESIUM-ION
HUMAN THYMIDYLATE KINASE COMPLEXED WITH ADP, TDP AND A MAGNESIUM-ION
WILD TYPE HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND ADP
HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND ADP
HUMAN THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR AZTP5A
HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND APPNP
MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND APPNP
MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH AZTMP AND ADP
MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH DTMP AND ADP
MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND ADP
PDBE
Y
PDBE
2000-05-22
REL
REL
1
A
O
HOH
2002
7.18
1
A
O
HOH
2064
6.48
TMP
THYMIDINE-5'-PHOSPHATE
ADP
ADENOSINE-5'-DIPHOSPHATE
MG
MAGNESIUM ION
AF3
ALUMINUM FLUORIDE
HOH
water
CHAIN A ENGINEERED MUTATION ARG200ALA
GLY, SER, HIS INSERTED AT THE N-TERMINUS
SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191
(CONFIRMED BY THE DNA SEQUENCE AND ELECTRON DENSITY OF
SIDE-CHAINS). POSSIBLE ERROR IN SWISSPROT ENTRY.
TMP
301
2
TMP
TMP
301
A
ADP
302
3
ADP
ADP
302
A
MG
401
4
MG
MG
401
A
MG
402
4
MG
MG
402
A
AF3
901
5
AF3
AF3
901
A
HOH
2001
6
HOH
HOH
2001
A
HOH
2002
6
HOH
HOH
2002
A
HOH
2003
6
HOH
HOH
2003
A
HOH
2004
6
HOH
HOH
2004
A
HOH
2005
6
HOH
HOH
2005
A
HOH
2006
6
HOH
HOH
2006
A
HOH
2007
6
HOH
HOH
2007
A
HOH
2008
6
HOH
HOH
2008
A
HOH
2009
6
HOH
HOH
2009
A
HOH
2010
6
HOH
HOH
2010
A
HOH
2011
6
HOH
HOH
2011
A
HOH
2012
6
HOH
HOH
2012
A
HOH
2013
6
HOH
HOH
2013
A
HOH
2014
6
HOH
HOH
2014
A
HOH
2015
6
HOH
HOH
2015
A
HOH
2016
6
HOH
HOH
2016
A
HOH
2017
6
HOH
HOH
2017
A
HOH
2018
6
HOH
HOH
2018
A
HOH
2019
6
HOH
HOH
2019
A
HOH
2020
6
HOH
HOH
2020
A
HOH
2021
6
HOH
HOH
2021
A
HOH
2022
6
HOH
HOH
2022
A
HOH
2023
6
HOH
HOH
2023
A
HOH
2024
6
HOH
HOH
2024
A
HOH
2025
6
HOH
HOH
2025
A
HOH
2026
6
HOH
HOH
2026
A
HOH
2027
6
HOH
HOH
2027
A
HOH
2028
6
HOH
HOH
2028
A
HOH
2029
6
HOH
HOH
2029
A
HOH
2030
6
HOH
HOH
2030
A
HOH
2031
6
HOH
HOH
2031
A
HOH
2032
6
HOH
HOH
2032
A
HOH
2033
6
HOH
HOH
2033
A
HOH
2034
6
HOH
HOH
2034
A
HOH
2035
6
HOH
HOH
2035
A
HOH
2036
6
HOH
HOH
2036
A
HOH
2037
6
HOH
HOH
2037
A
HOH
2038
6
HOH
HOH
2038
A
HOH
2039
6
HOH
HOH
2039
A
HOH
2040
6
HOH
HOH
2040
A
HOH
2041
6
HOH
HOH
2041
A
HOH
2042
6
HOH
HOH
2042
A
HOH
2043
6
HOH
HOH
2043
A
HOH
2044
6
HOH
HOH
2044
A
HOH
2045
6
HOH
HOH
2045
A
HOH
2046
6
HOH
HOH
2046
A
HOH
2047
6
HOH
HOH
2047
A
HOH
2048
6
HOH
HOH
2048
A
HOH
2049
6
HOH
HOH
2049
A
HOH
2050
6
HOH
HOH
2050
A
HOH
2051
6
HOH
HOH
2051
A
HOH
2052
6
HOH
HOH
2052
A
HOH
2053
6
HOH
HOH
2053
A
HOH
2054
6
HOH
HOH
2054
A
HOH
2055
6
HOH
HOH
2055
A
HOH
2056
6
HOH
HOH
2056
A
HOH
2057
6
HOH
HOH
2057
A
HOH
2058
6
HOH
HOH
2058
A
HOH
2059
6
HOH
HOH
2059
A
HOH
2060
6
HOH
HOH
2060
A
HOH
2061
6
HOH
HOH
2061
A
HOH
2062
6
HOH
HOH
2062
A
HOH
2063
6
HOH
HOH
2063
A
HOH
2064
6
HOH
HOH
2064
A
HOH
2065
6
HOH
HOH
2065
A
HOH
2066
6
HOH
HOH
2066
A
HOH
2067
6
HOH
HOH
2067
A
HOH
2068
6
HOH
HOH
2068
A
HOH
2069
6
HOH
HOH
2069
A
HOH
2070
6
HOH
HOH
2070
A
HOH
2071
6
HOH
HOH
2071
A
HOH
2072
6
HOH
HOH
2072
A
HOH
2073
6
HOH
HOH
2073
A
HOH
2074
6
HOH
HOH
2074
A
HOH
2075
6
HOH
HOH
2075
A
HOH
2076
6
HOH
HOH
2076
A
HOH
2077
6
HOH
HOH
2077
A
HOH
2078
6
HOH
HOH
2078
A
HOH
2079
6
HOH
HOH
2079
A
HOH
2080
6
HOH
HOH
2080
A
HOH
2081
6
HOH
HOH
2081
A
HOH
2082
6
HOH
HOH
2082
A
HOH
2083
6
HOH
HOH
2083
A
HOH
2084
6
HOH
HOH
2084
A
HOH
2085
6
HOH
HOH
2085
A
HOH
2086
6
HOH
HOH
2086
A
HOH
2087
6
HOH
HOH
2087
A
HOH
2088
6
HOH
HOH
2088
A
HOH
2089
6
HOH
HOH
2089
A
HOH
2090
6
HOH
HOH
2090
A
HOH
2091
6
HOH
HOH
2091
A
HOH
2092
6
HOH
HOH
2092
A
HOH
2093
6
HOH
HOH
2093
A
HOH
2094
6
HOH
HOH
2094
A
HOH
2095
6
HOH
HOH
2095
A
HOH
2096
6
HOH
HOH
2096
A
HOH
2097
6
HOH
HOH
2097
A
HOH
2098
6
HOH
HOH
2098
A
HOH
2099
6
HOH
HOH
2099
A
HOH
2100
6
HOH
HOH
2100
A
HOH
2101
6
HOH
HOH
2101
A
HOH
2102
6
HOH
HOH
2102
A
HOH
2103
6
HOH
HOH
2103
A
HOH
2104
6
HOH
HOH
2104
A
HOH
2105
6
HOH
HOH
2105
A
HOH
2106
6
HOH
HOH
2106
A
HOH
2107
6
HOH
HOH
2107
A
HOH
2108
6
HOH
HOH
2108
A
HOH
2109
6
HOH
HOH
2109
A
HOH
2110
6
HOH
HOH
2110
A
HOH
2111
6
HOH
HOH
2111
A
HOH
2112
6
HOH
HOH
2112
A
HOH
2113
6
HOH
HOH
2113
A
HOH
2114
6
HOH
HOH
2114
A
HOH
2115
6
HOH
HOH
2115
A
HOH
2116
6
HOH
HOH
2116
A
HOH
2117
6
HOH
HOH
2117
A
HOH
2118
6
HOH
HOH
2118
A
HOH
2119
6
HOH
HOH
2119
A
HOH
2120
6
HOH
HOH
2120
A
HOH
2121
6
HOH
HOH
2121
A
HOH
2122
6
HOH
HOH
2122
A
HOH
2123
6
HOH
HOH
2123
A
HOH
2124
6
HOH
HOH
2124
A
HOH
2125
6
HOH
HOH
2125
A
HOH
2126
6
HOH
HOH
2126
A
HOH
2127
6
HOH
HOH
2127
A
HOH
2128
6
HOH
HOH
2128
A
HOH
2129
6
HOH
HOH
2129
A
HOH
2130
6
HOH
HOH
2130
A
HOH
2131
6
HOH
HOH
2131
A
HOH
2132
6
HOH
HOH
2132
A
HOH
2133
6
HOH
HOH
2133
A
HOH
2134
6
HOH
HOH
2134
A
HOH
2135
6
HOH
HOH
2135
A
HOH
2136
6
HOH
HOH
2136
A
HOH
2137
6
HOH
HOH
2137
A
HOH
2138
6
HOH
HOH
2138
A
HOH
2139
6
HOH
HOH
2139
A
HOH
2140
6
HOH
HOH
2140
A
HOH
2141
6
HOH
HOH
2141
A
HOH
2142
6
HOH
HOH
2142
A
HOH
2143
6
HOH
HOH
2143
A
HOH
2144
6
HOH
HOH
2144
A
HOH
2145
6
HOH
HOH
2145
A
HOH
2146
6
HOH
HOH
2146
A
HOH
2147
6
HOH
HOH
2147
A
HOH
2148
6
HOH
HOH
2148
A
HOH
2149
6
HOH
HOH
2149
A
HOH
2150
6
HOH
HOH
2150
A
HOH
2151
6
HOH
HOH
2151
A
HOH
2152
6
HOH
HOH
2152
A
HOH
2153
6
HOH
HOH
2153
A
HOH
2154
6
HOH
HOH
2154
A
HOH
2155
6
HOH
HOH
2155
A
HOH
2156
6
HOH
HOH
2156
A
HOH
2157
6
HOH
HOH
2157
A
HOH
2158
6
HOH
HOH
2158
A
HOH
2159
6
HOH
HOH
2159
A
HOH
2160
6
HOH
HOH
2160
A
HOH
2161
6
HOH
HOH
2161
A
HOH
2162
6
HOH
HOH
2162
A
HOH
2163
6
HOH
HOH
2163
A
HOH
2164
6
HOH
HOH
2164
A
HOH
2165
6
HOH
HOH
2165
A
HOH
2166
6
HOH
HOH
2166
A
HOH
2167
6
HOH
HOH
2167
A
HOH
2168
6
HOH
HOH
2168
A
HOH
2169
6
HOH
HOH
2169
A
HOH
2170
6
HOH
HOH
2170
A
HOH
2171
6
HOH
HOH
2171
A
HOH
2172
6
HOH
HOH
2172
A
n
1
-2
A
n
2
-1
A
n
3
0
A
n
4
1
A
n
5
2
A
n
6
3
A
ARG
4
n
7
ARG
4
A
ARG
5
n
8
ARG
5
A
GLY
6
n
9
GLY
6
A
ALA
7
n
10
ALA
7
A
LEU
8
n
11
LEU
8
A
ILE
9
n
12
ILE
9
A
VAL
10
n
13
VAL
10
A
LEU
11
n
14
LEU
11
A
GLU
12
n
15
GLU
12
A
GLY
13
n
16
GLY
13
A
VAL
14
n
17
VAL
14
A
ASP
15
n
18
ASP
15
A
ARG
16
n
19
ARG
16
A
ALA
17
n
20
ALA
17
A
GLY
18
n
21
GLY
18
A
LYS
19
n
22
LYS
19
A
SER
20
n
23
SER
20
A
THR
21
n
24
THR
21
A
GLN
22
n
25
GLN
22
A
SER
23
n
26
SER
23
A
ARG
24
n
27
ARG
24
A
LYS
25
n
28
LYS
25
A
LEU
26
n
29
LEU
26
A
VAL
27
n
30
VAL
27
A
GLU
28
n
31
GLU
28
A
ALA
29
n
32
ALA
29
A
LEU
30
n
33
LEU
30
A
CYS
31
n
34
CYS
31
A
ALA
32
n
35
ALA
32
A
ALA
33
n
36
ALA
33
A
GLY
34
n
37
GLY
34
A
HIS
35
n
38
HIS
35
A
ARG
36
n
39
ARG
36
A
ALA
37
n
40
ALA
37
A
GLU
38
n
41
GLU
38
A
LEU
39
n
42
LEU
39
A
LEU
40
n
43
LEU
40
A
ARG
41
n
44
ARG
41
A
PHE
42
n
45
PHE
42
A
PRO
43
n
46
PRO
43
A
GLU
44
n
47
GLU
44
A
ARG
45
n
48
ARG
45
A
SER
46
n
49
SER
46
A
THR
47
n
50
THR
47
A
GLU
48
n
51
GLU
48
A
ILE
49
n
52
ILE
49
A
GLY
50
n
53
GLY
50
A
LYS
51
n
54
LYS
51
A
LEU
52
n
55
LEU
52
A
LEU
53
n
56
LEU
53
A
SER
54
n
57
SER
54
A
SER
55
n
58
SER
55
A
TYR
56
n
59
TYR
56
A
LEU
57
n
60
LEU
57
A
GLN
58
n
61
GLN
58
A
LYS
59
n
62
LYS
59
A
LYS
60
n
63
LYS
60
A
SER
61
n
64
SER
61
A
ASP
62
n
65
ASP
62
A
VAL
63
n
66
VAL
63
A
GLU
64
n
67
GLU
64
A
ASP
65
n
68
ASP
65
A
HIS
66
n
69
HIS
66
A
SER
67
n
70
SER
67
A
VAL
68
n
71
VAL
68
A
HIS
69
n
72
HIS
69
A
LEU
70
n
73
LEU
70
A
LEU
71
n
74
LEU
71
A
PHE
72
n
75
PHE
72
A
SER
73
n
76
SER
73
A
ALA
74
n
77
ALA
74
A
ASN
75
n
78
ASN
75
A
ARG
76
n
79
ARG
76
A
TRP
77
n
80
TRP
77
A
GLU
78
n
81
GLU
78
A
GLN
79
n
82
GLN
79
A
VAL
80
n
83
VAL
80
A
PRO
81
n
84
PRO
81
A
LEU
82
n
85
LEU
82
A
ILE
83
n
86
ILE
83
A
LYS
84
n
87
LYS
84
A
GLU
85
n
88
GLU
85
A
LYS
86
n
89
LYS
86
A
LEU
87
n
90
LEU
87
A
SER
88
n
91
SER
88
A
GLN
89
n
92
GLN
89
A
GLY
90
n
93
GLY
90
A
VAL
91
n
94
VAL
91
A
THR
92
n
95
THR
92
A
LEU
93
n
96
LEU
93
A
VAL
94
n
97
VAL
94
A
VAL
95
n
98
VAL
95
A
ASP
96
n
99
ASP
96
A
ARG
97
n
100
ARG
97
A
TYR
98
n
101
TYR
98
A
ALA
99
n
102
ALA
99
A
PHE
100
n
103
PHE
100
A
SER
101
n
104
SER
101
A
GLY
102
n
105
GLY
102
A
VAL
103
n
106
VAL
103
A
ALA
104
n
107
ALA
104
A
PHE
105
n
108
PHE
105
A
THR
106
n
109
THR
106
A
GLY
107
n
110
GLY
107
A
ALA
108
n
111
ALA
108
A
LYS
109
n
112
LYS
109
A
GLU
110
n
113
GLU
110
A
ASN
111
n
114
ASN
111
A
PHE
112
n
115
PHE
112
A
SER
113
n
116
SER
113
A
LEU
114
n
117
LEU
114
A
ASP
115
n
118
ASP
115
A
TRP
116
n
119
TRP
116
A
CYS
117
n
120
CYS
117
A
LYS
118
n
121
LYS
118
A
GLN
119
n
122
GLN
119
A
PRO
120
n
123
PRO
120
A
ASP
121
n
124
ASP
121
A
VAL
122
n
125
VAL
122
A
GLY
123
n
126
GLY
123
A
LEU
124
n
127
LEU
124
A
PRO
125
n
128
PRO
125
A
LYS
126
n
129
LYS
126
A
PRO
127
n
130
PRO
127
A
ASP
128
n
131
ASP
128
A
LEU
129
n
132
LEU
129
A
VAL
130
n
133
VAL
130
A
LEU
131
n
134
LEU
131
A
PHE
132
n
135
PHE
132
A
LEU
133
n
136
LEU
133
A
GLN
134
n
137
GLN
134
A
LEU
135
n
138
LEU
135
A
GLN
136
n
139
GLN
136
A
LEU
137
n
140
LEU
137
A
ALA
138
n
141
ALA
138
A
ASP
139
n
142
ASP
139
A
ALA
140
n
143
ALA
140
A
ALA
141
n
144
ALA
141
A
LYS
142
n
145
LYS
142
A
ARG
143
n
146
ARG
143
A
GLY
144
n
147
GLY
144
A
ALA
145
n
148
ALA
145
A
PHE
146
n
149
PHE
146
A
GLY
147
n
150
GLY
147
A
HIS
148
n
151
HIS
148
A
GLU
149
n
152
GLU
149
A
ARG
150
n
153
ARG
150
A
TYR
151
n
154
TYR
151
A
GLU
152
n
155
GLU
152
A
ASN
153
n
156
ASN
153
A
GLY
154
n
157
GLY
154
A
ALA
155
n
158
ALA
155
A
PHE
156
n
159
PHE
156
A
GLN
157
n
160
GLN
157
A
GLU
158
n
161
GLU
158
A
ARG
159
n
162
ARG
159
A
ALA
160
n
163
ALA
160
A
LEU
161
n
164
LEU
161
A
ARG
162
n
165
ARG
162
A
CYS
163
n
166
CYS
163
A
PHE
164
n
167
PHE
164
A
HIS
165
n
168
HIS
165
A
GLN
166
n
169
GLN
166
A
LEU
167
n
170
LEU
167
A
MET
168
n
171
MET
168
A
LYS
169
n
172
LYS
169
A
ASP
170
n
173
ASP
170
A
THR
171
n
174
THR
171
A
THR
172
n
175
THR
172
A
LEU
173
n
176
LEU
173
A
ASN
174
n
177
ASN
174
A
TRP
175
n
178
TRP
175
A
LYS
176
n
179
LYS
176
A
MET
177
n
180
MET
177
A
VAL
178
n
181
VAL
178
A
ASP
179
n
182
ASP
179
A
ALA
180
n
183
ALA
180
A
SER
181
n
184
SER
181
A
LYS
182
n
185
LYS
182
A
SER
183
n
186
SER
183
A
ILE
184
n
187
ILE
184
A
GLU
185
n
188
GLU
185
A
ALA
186
n
189
ALA
186
A
VAL
187
n
190
VAL
187
A
HIS
188
n
191
HIS
188
A
GLU
189
n
192
GLU
189
A
ASP
190
n
193
ASP
190
A
ILE
191
n
194
ILE
191
A
ARG
192
n
195
ARG
192
A
VAL
193
n
196
VAL
193
A
LEU
194
n
197
LEU
194
A
SER
195
n
198
SER
195
A
GLU
196
n
199
GLU
196
A
ASP
197
n
200
ASP
197
A
ALA
198
n
201
ALA
198
A
ILE
199
n
202
ILE
199
A
ALA
200
n
203
ALA
200
A
THR
201
n
204
THR
201
A
ALA
202
n
205
ALA
202
A
THR
203
n
206
THR
203
A
GLU
204
n
207
GLU
204
A
LYS
205
n
208
LYS
205
A
PRO
206
n
209
PRO
206
A
LEU
207
n
210
LEU
207
A
GLY
208
n
211
GLY
208
A
GLU
209
n
212
GLU
209
A
LEU
210
n
213
LEU
210
A
TRP
211
n
214
TRP
211
A
LYS
212
n
215
LYS
212
A
author_and_software_defined_assembly
PQS
2
dimeric
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
ADP
302
C
O2B
ADP
1_555
93.4
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
F1
AF3
1_555
152.9
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
F1
AF3
1_555
86.5
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
AL
AF3
1_555
166.0
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
AL
AF3
1_555
74.9
A
AF3
901
F
F1
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
AL
AF3
1_555
22.2
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2012
G
O
HOH
1_555
79.3
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2012
G
O
HOH
1_555
100.1
A
AF3
901
F
F1
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2012
G
O
HOH
1_555
74.0
A
AF3
901
F
AL
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2012
G
O
HOH
1_555
94.8
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
94.3
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
171.2
A
AF3
901
F
F1
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
88.6
A
AF3
901
F
AL
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
98.0
A
HOH
2012
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
85.5
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
91.1
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
89.9
A
AF3
901
F
F1
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
116.0
A
AF3
901
F
AL
AF3
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
96.6
A
HOH
2012
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
166.5
A
HOH
2013
G
O
HOH
1_555
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
85.7
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F1
AF3
1_555
61.4
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F2
AF3
1_555
119.7
A
AF3
901
F
F1
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F2
AF3
1_555
126.4
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F3
AF3
1_555
81.0
A
AF3
901
F
F1
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F3
AF3
1_555
106.8
A
AF3
901
F
F2
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
AF3
901
F
F3
AF3
1_555
126.7
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O3B
ADP
1_555
158.8
A
AF3
901
F
F1
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O3B
ADP
1_555
102.5
A
AF3
901
F
F2
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O3B
ADP
1_555
80.5
A
AF3
901
F
F3
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O3B
ADP
1_555
91.7
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O2B
ADP
1_555
113.5
A
AF3
901
F
F1
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O2B
ADP
1_555
52.9
A
AF3
901
F
F2
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O2B
ADP
1_555
106.7
A
AF3
901
F
F3
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O2B
ADP
1_555
107.3
A
ADP
302
C
O3B
ADP
1_555
A
AF3
901
F
AL
AF3
1_555
A
ADP
302
C
O2B
ADP
1_555
49.7
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
96.3
A
AF3
901
F
F1
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
156.0
A
AF3
901
F
F2
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
71.1
A
AF3
901
F
F3
AF3
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
57.4
A
ADP
302
C
O3B
ADP
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
96.4
A
ADP
302
C
O2B
ADP
1_555
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
144.7
A
HOH
2050
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2050
G
O
HOH
1_555
87.3
A
HOH
2050
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
1_555
82.5
A
HOH
2050
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
1_555
161.2
A
HOH
2050
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
8_665
172.9
A
HOH
2050
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
8_665
91.5
A
HOH
2100
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
8_665
100.4
A
HOH
2050
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
8_665
84.4
A
HOH
2050
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
8_665
84.6
A
HOH
2100
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
8_665
110.0
A
HOH
2100
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
8_665
88.5
A
HOH
2050
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
76.7
A
HOH
2050
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
83.9
A
HOH
2100
G
O
HOH
1_555
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
78.4
A
HOH
2100
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
110.2
A
HOH
2102
G
O
HOH
8_665
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
158.3
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
101.6000000000
101.6000000000
24.9500000000
A
O
LYS
176
A
O
LYS
179
A
N
VAL
130
A
N
VAL
133
A
O
LEU
129
A
O
LEU
132
A
N
VAL
10
A
N
VAL
13
A
O
ILE
9
A
O
ILE
12
A
N
LEU
93
A
N
LEU
96
A
O
THR
92
A
O
THR
95
A
N
GLU
38
A
N
GLU
41
1
A
MG
402
E
MG
1
A
CG
ARG
4
A
CG
ARG
7
1
Y
1
A
CD
ARG
4
A
CD
ARG
7
1
Y
1
A
NE
ARG
4
A
NE
ARG
7
1
Y
1
A
CZ
ARG
4
A
CZ
ARG
7
1
Y
1
A
NH1
ARG
4
A
NH1
ARG
7
1
Y
1
A
NH2
ARG
4
A
NH2
ARG
7
1
Y
1
A
CG
ARG
41
A
CG
ARG
44
1
Y
1
A
CD
ARG
41
A
CD
ARG
44
1
Y
1
A
NE
ARG
41
A
NE
ARG
44
1
Y
1
A
CZ
ARG
41
A
CZ
ARG
44
1
Y
1
A
NH1
ARG
41
A
NH1
ARG
44
1
Y
1
A
NH2
ARG
41
A
NH2
ARG
44
1
Y
1
A
CG
GLU
110
A
CG
GLU
113
1
Y
1
A
CD
GLU
110
A
CD
GLU
113
1
Y
1
A
OE1
GLU
110
A
OE1
GLU
113
1
Y
1
A
OE2
GLU
110
A
OE2
GLU
113
1
Y
1
A
CG
GLN
136
A
CG
GLN
139
1
Y
1
A
CD
GLN
136
A
CD
GLN
139
1
Y
1
A
OE1
GLN
136
A
OE1
GLN
139
1
Y
1
A
NE2
GLN
136
A
NE2
GLN
139
1
Y
1
A
CG
LYS
142
A
CG
LYS
145
1
Y
1
A
CD
LYS
142
A
CD
LYS
145
1
Y
1
A
CE
LYS
142
A
CE
LYS
145
1
Y
1
A
NZ
LYS
142
A
NZ
LYS
145
1
Y
1
A
CG
GLU
152
A
CG
GLU
155
1
Y
1
A
CD
GLU
152
A
CD
GLU
155
1
Y
1
A
OE1
GLU
152
A
OE1
GLU
155
1
Y
1
A
OE2
GLU
152
A
OE2
GLU
155
1
Y
1
A
CG
ARG
162
A
CG
ARG
165
1
Y
1
A
CD
ARG
162
A
CD
ARG
165
1
Y
1
A
NE
ARG
162
A
NE
ARG
165
1
Y
1
A
CZ
ARG
162
A
CZ
ARG
165
1
Y
1
A
NH1
ARG
162
A
NH1
ARG
165
1
Y
1
A
NH2
ARG
162
A
NH2
ARG
165
1
Y
1
A
CG
LYS
205
A
CG
LYS
208
1
Y
1
A
CD
LYS
205
A
CD
LYS
208
1
Y
1
A
CE
LYS
205
A
CE
LYS
208
1
Y
1
A
NZ
LYS
205
A
NZ
LYS
208
1
Y
1
A
GLY
-2
A
GLY
1
1
Y
1
A
SER
-1
A
SER
2
1
Y
1
A
HIS
0
A
HIS
3
1
Y
1
A
MET
1
A
MET
4
1
Y
1
A
ALA
2
A
ALA
5
1
Y
1
A
ALA
3
A
ALA
6
1
Y
1
A
A
N
O
VAL
HOH
14
2006
1.96
1
A
A
O
O
HOH
HOH
2130
2166
2.02
1
A
A
OD1
O
ASP
HOH
197
2156
2.19
1
A
A
O
O
HOH
HOH
2106
2164
2.19
1
11.28
0.90
118.30
129.58
A
A
A
CB
CG
OD2
ASP
ASP
ASP
15
15
15
N
1
9.75
1.40
123.60
133.35
A
A
A
CD
NE
CZ
ARG
ARG
ARG
16
16
16
N
1
10.41
0.50
120.30
130.71
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
1
-7.87
0.50
120.30
112.43
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
16
16
16
N
1
-3.29
0.50
120.30
117.01
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
24
24
24
N
1
-3.08
0.50
120.30
117.22
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
36
36
36
N
1
4.38
0.50
120.30
124.68
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
45
45
45
N
1
7.50
0.90
118.30
125.80
A
A
A
CB
CG
OD1
ASP
ASP
ASP
62
62
62
N
1
-5.53
0.50
120.30
114.77
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
97
97
97
N
1
5.78
0.90
118.30
124.08
A
A
A
CB
CG
OD2
ASP
ASP
ASP
115
115
115
N
1
7.51
1.10
119.40
126.91
A
A
A
NH1
CZ
NH2
ARG
ARG
ARG
143
143
143
N
1
-5.04
0.50
120.30
115.26
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
143
143
143
N
1
-3.46
0.50
120.30
116.84
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
192
192
192
N
1
A
ARG
97
79.62
145.90
1
A
TYR
98
-148.21
-145.00
1
A
LEU
137
-36.94
-36.09
1
A
ALA
145
-179.59
141.67
1
A
TYR
151
76.15
-14.74
1
A
THR
203
-52.65
10.66
GLU 152 MODELED AS ALA DUE TO WEAK SIDE-CHAIN ELECTRON DENSITY
0.272
0.214
2.0
71.8
930
17782
5.2
99.0
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
2.0
71.8
172
1842
54
0
1616
0.018
1.6
2.000
71.800
1E2E
17782
0.07900
1
11.7000
5.200
99.0
2.00
2.10
3.000
0.32900
1
4.60
98.7
refinement
REFMAC
data reduction
XDS
data scaling
XSCALE
phasing
AMoRE
Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate,a magnesium-ion and ALf3
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
6
N
N
A
GLY
18
A
GLY
21
HELX_P
A
ALA
33
A
ALA
36
1
1
16
A
THR
47
A
THR
50
HELX_P
A
GLN
58
A
GLN
61
1
2
12
A
GLU
64
A
GLU
67
HELX_P
A
GLU
78
A
GLU
81
1
3
15
A
GLN
79
A
GLN
82
HELX_P
A
GLN
89
A
GLN
92
1
4
11
A
TYR
98
A
TYR
101
HELX_P
A
GLY
107
A
GLY
110
1
5
10
A
SER
113
A
SER
116
HELX_P
A
GLN
119
A
GLN
122
1
6
7
A
PRO
120
A
PRO
123
HELX_P
A
VAL
122
A
VAL
125
5
7
3
A
ASN
153
A
ASN
156
HELX_P
A
MET
168
A
MET
171
1
8
16
A
SER
183
A
SER
186
HELX_P
A
THR
203
A
THR
206
1
9
21
metalc
2.062
A
SER
20
A
OG
SER
23
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.637
A
TMP
301
B
O2P
TMP
1_555
A
AF3
901
F
AL
AF3
1_555
metalc
1.981
A
ADP
302
C
O2B
ADP
1_555
A
MG
401
D
MG
MG
1_555
metalc
2.217
A
ADP
302
C
O3B
ADP
1_555
A
AF3
901
F
AL
AF3
1_555
metalc
3.326
A
ADP
302
C
O2B
ADP
1_555
A
AF3
901
F
AL
AF3
1_555
metalc
1.931
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
F1
AF3
1_555
metalc
3.237
A
MG
401
D
MG
MG
1_555
A
AF3
901
F
AL
AF3
1_555
metalc
2.131
A
MG
401
D
MG
MG
1_555
A
HOH
2012
G
O
HOH
1_555
metalc
1.975
A
MG
401
D
MG
MG
1_555
A
HOH
2013
G
O
HOH
1_555
metalc
2.090
A
MG
401
D
MG
MG
1_555
A
HOH
2172
G
O
HOH
1_555
metalc
2.416
A
MG
402
E
MG
MG
1_555
A
HOH
2050
G
O
HOH
8_665
metalc
2.256
A
MG
402
E
MG
MG
1_555
A
HOH
2050
G
O
HOH
1_555
metalc
2.197
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
1_555
metalc
1.986
A
MG
402
E
MG
MG
1_555
A
HOH
2100
G
O
HOH
8_665
metalc
2.004
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
8_665
metalc
2.209
A
MG
402
E
MG
MG
1_555
A
HOH
2102
G
O
HOH
1_555
metalc
3.664
A
AF3
901
F
AL
AF3
1_555
A
HOH
2058
G
O
HOH
1_555
THYMIDYLATE KINASE
THYMIDYLATE KINASE, P-LOOP
A
PHE
42
A
PHE
45
1
A
PRO
43
A
PRO
46
-5.81
1E2E
PDB
1
1E2E
KTHY_HUMAN
UNP
1
P23919
-2
0
1E2E
-2
0
1E2E
A
1
1
3
1
212
1E2E
1
212
P23919
A
2
4
215
1
ARG
engineered mutation
ALA
200
1E2E
A
P23919
UNP
200
203
1
ARG
conflict
SER
183
1E2E
A
P23919
UNP
183
186
1
LEU
conflict
ILE
184
1E2E
A
P23919
UNP
184
187
1
GLU
conflict
ASP
190
1E2E
A
P23919
UNP
190
193
1
LEU
conflict
ILE
191
1E2E
A
P23919
UNP
191
194
5
parallel
parallel
parallel
parallel
A
TRP
175
A
TRP
178
A
ASP
179
A
ASP
182
A
LEU
129
A
LEU
132
A
GLN
134
A
GLN
137
A
LEU
8
A
LEU
11
A
GLY
13
A
GLY
16
A
THR
92
A
THR
95
A
ASP
96
A
ASP
99
A
ALA
37
A
ALA
40
A
ARG
41
A
ARG
44
BINDING SITE FOR RESIDUE MG A 401
A
MG
401
Software
6
BINDING SITE FOR RESIDUE MG A 402
A
MG
402
Software
3
BINDING SITE FOR RESIDUE TMP A 301
A
TMP
301
Software
15
BINDING SITE FOR RESIDUE ADP A 302
A
ADP
302
Software
16
BINDING SITE FOR RESIDUE AF3 A 901
A
AF3
901
Software
9
A
SER
20
A
SER
23
6
1_555
A
ADP
302
C
ADP
6
1_555
A
AF3
901
F
AF3
6
1_555
A
HOH
2012
G
HOH
6
1_555
A
HOH
2013
G
HOH
6
1_555
A
HOH
2172
G
HOH
6
1_555
A
HOH
2050
G
HOH
3
1_555
A
HOH
2100
G
HOH
3
1_555
A
HOH
2102
G
HOH
3
1_555
A
ASP
15
A
ASP
18
15
1_555
A
PHE
42
A
PHE
45
15
1_555
A
ARG
45
A
ARG
48
15
1_555
A
PHE
72
A
PHE
75
15
1_555
A
ARG
76
A
ARG
79
15
1_555
A
ARG
97
A
ARG
100
15
1_555
A
GLY
102
A
GLY
105
15
1_555
A
PHE
105
A
PHE
108
15
1_555
A
TYR
151
A
TYR
154
15
1_555
A
AF3
901
F
AF3
15
1_555
A
HOH
2013
G
HOH
15
1_555
A
HOH
2091
G
HOH
15
1_555
A
HOH
2168
G
HOH
15
1_555
A
HOH
2170
G
HOH
15
1_555
A
HOH
2171
G
HOH
15
1_555
A
ARG
16
A
ARG
19
16
1_555
A
ALA
17
A
ALA
20
16
1_555
A
GLY
18
A
GLY
21
16
1_555
A
LYS
19
A
LYS
22
16
1_555
A
SER
20
A
SER
23
16
1_555
A
THR
21
A
THR
24
16
1_555
A
ARG
143
A
ARG
146
16
1_555
A
LYS
182
A
LYS
185
16
1_555
A
SER
183
A
SER
186
16
1_555
A
ILE
184
A
ILE
187
16
1_555
A
ARG
192
A
ARG
195
16
1_555
A
MG
401
D
MG
16
1_555
A
AF3
901
F
AF3
16
1_555
A
HOH
2017
G
HOH
16
1_555
A
HOH
2151
G
HOH
16
1_555
A
HOH
2172
G
HOH
16
1_555
A
ASP
15
A
ASP
18
9
1_555
A
ARG
16
A
ARG
19
9
1_555
A
LYS
19
A
LYS
22
9
1_555
A
ARG
97
A
ARG
100
9
1_555
A
TMP
301
B
TMP
9
1_555
A
ADP
302
C
ADP
9
1_555
A
MG
401
D
MG
9
1_555
A
HOH
2012
G
HOH
9
1_555
A
HOH
2013
G
HOH
9
1_555
96
P 43 21 2