0.014286
0.008248
0.000000
0.000000
0.016496
0.000000
0.000000
0.000000
0.006589
0.00000
0.00000
0.00000
Meyer, P.
Janin, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
70.000
70.000
151.770
C10 H15 N5 O10 P2
427.201
n
ADENOSINE-5'-DIPHOSPHATE
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
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
O4 P -3
94.971
PHOSPHATE ION
non-polymer
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
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
N
N
44
S
C
N
45
N
C
N
46
N
O
N
47
N
C
N
48
N
O
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
N
N
57
S
C
N
58
N
C
N
59
N
O
N
60
N
C
N
61
N
C
N
62
N
C
N
63
N
N
N
64
N
C
N
65
N
N
N
66
N
N
N
67
N
O
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
N
N
84
S
C
N
85
N
C
N
86
N
O
N
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
O
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
H
N
99
N
H
N
100
N
N
N
101
S
C
N
102
N
C
N
103
N
O
N
104
N
C
N
105
N
C
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
N
N
117
S
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
C
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
O
N
126
N
H
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
H
N
135
N
H
N
136
N
N
N
137
S
C
N
138
N
C
N
139
N
O
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
O
N
144
N
O
N
145
N
O
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
H
N
155
N
N
N
156
N
C
N
157
N
C
N
158
N
O
N
159
N
O
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
S
C
N
167
N
C
N
168
N
O
N
169
N
C
Y
170
N
C
Y
171
N
N
Y
172
N
C
Y
173
N
C
Y
174
N
N
N
175
N
O
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
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
O
N
187
N
H
N
188
N
H
N
189
N
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
S
C
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
O
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
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
N
N
212
S
C
N
213
N
C
N
214
N
O
N
215
N
C
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
O
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
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
N
N
234
S
C
N
235
N
C
N
236
N
O
N
237
N
C
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
N
N
242
N
O
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
H
N
256
N
H
N
257
N
H
N
258
N
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
S
N
265
N
C
N
266
N
O
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
H
N
277
N
H
N
278
N
MG
N
279
N
N
N
280
S
C
N
281
N
C
N
282
N
O
N
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
P
N
303
N
O
N
304
N
O
N
305
N
O
N
306
N
O
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
C
N
313
N
C
N
314
N
O
N
315
N
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
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
N
329
N
O
N
330
N
O
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
R
C
N
343
N
O
N
344
N
C
N
345
N
O
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
N
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
N
369
N
O
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
N
393
N
O
N
394
N
O
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
H
N
405
N
H
N
406
N
N
N
407
S
C
N
408
N
C
N
409
N
O
N
410
N
C
N
411
N
C
N
412
N
C
N
413
N
O
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
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
doub
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
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
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
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
doub
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
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
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
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
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
sing
N
156
N
sing
N
157
N
doub
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
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
Y
171
N
sing
Y
172
N
doub
Y
173
N
doub
N
174
N
sing
Y
175
N
sing
N
176
N
sing
Y
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
doub
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
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
doub
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
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
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
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
doub
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
Y
279
N
doub
Y
280
N
sing
Y
281
N
sing
N
282
N
sing
Y
283
N
doub
N
284
N
sing
Y
285
N
doub
N
286
N
sing
Y
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
doub
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
sing
N
300
N
sing
N
301
N
doub
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
doub
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
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
Y
352
N
doub
Y
353
N
sing
Y
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
sing
Y
361
N
doub
N
362
N
sing
Y
363
N
doub
N
364
N
sing
Y
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
doub
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
Y
380
N
doub
Y
381
N
sing
Y
382
N
sing
N
383
N
sing
Y
384
N
doub
N
385
N
sing
Y
386
N
doub
N
387
N
sing
Y
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
38
4701
4711
10.1021/bi9827565
10200157
Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
1999
US
Biochemistry
BICHAW
0033
0006-2960
34
11062
Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium
1995
US
Biochemistry
BICHAW
0033
0006-2960
33
459
Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
1994
10.2210/pdb1b4s/pdb
pdb_00001b4s
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
IMAGE PLATE
1998-07
MARRESEARCH
M
x-ray
1
1.375
1.0
D41A
LURE
1.375
SYNCHROTRON
LURE BEAMLINE D41A
16735.242
NUCLEOSIDE DIPHOSPHATE KINASE
2.7.4.6
H122G
3
man
polymer
94.971
PHOSPHATE ION
3
syn
non-polymer
24.305
MAGNESIUM ION
3
syn
non-polymer
427.201
ADENOSINE-5'-DIPHOSPHATE
3
syn
non-polymer
18.015
water
108
nat
water
NDPK
no
no
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
A,B,C
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
Dictyostelium
Escherichia
sample
44689
Dictyostelium discoideum
562
Escherichia coli
1
2.14
42.44
7.5
pH 7.5
database_2
pdbx_database_status
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
pdbx_initial_refinement_model
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Refinement description
Data collection
1
0
1999-06-15
1
1
2008-03-24
1
2
2011-07-13
1
3
2021-11-03
1
4
2023-08-02
1
5
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-12-28
REL
PO4
PHOSPHATE ION
MG
MAGNESIUM ION
ADP
ADENOSINE-5'-DIPHOSPHATE
HOH
water
1KDN
PDB
experimental model
PO4
161
2
PO4
PO4
161
A
MG
162
3
MG
MG
162
A
ADP
160
4
ADP
ADP
160
A
PO4
161
2
PO4
PO4
161
B
MG
162
3
MG
MG
162
B
ADP
160
4
ADP
ADP
160
B
PO4
161
2
PO4
PO4
161
C
MG
162
3
MG
MG
162
C
ADP
160
4
ADP
ADP
160
C
HOH
1
5
HOH
HOH
163
A
HOH
5
5
HOH
HOH
164
A
HOH
6
5
HOH
HOH
165
A
HOH
7
5
HOH
HOH
166
A
HOH
10
5
HOH
HOH
167
A
HOH
12
5
HOH
HOH
168
A
HOH
19
5
HOH
HOH
169
A
HOH
23
5
HOH
HOH
170
A
HOH
24
5
HOH
HOH
171
A
HOH
29
5
HOH
HOH
172
A
HOH
31
5
HOH
HOH
173
A
HOH
33
5
HOH
HOH
174
A
HOH
37
5
HOH
HOH
175
A
HOH
39
5
HOH
HOH
176
A
HOH
45
5
HOH
HOH
177
A
HOH
48
5
HOH
HOH
178
A
HOH
49
5
HOH
HOH
179
A
HOH
50
5
HOH
HOH
180
A
HOH
51
5
HOH
HOH
181
A
HOH
66
5
HOH
HOH
182
A
HOH
67
5
HOH
HOH
183
A
HOH
68
5
HOH
HOH
184
A
HOH
70
5
HOH
HOH
185
A
HOH
71
5
HOH
HOH
186
A
HOH
75
5
HOH
HOH
187
A
HOH
78
5
HOH
HOH
188
A
HOH
81
5
HOH
HOH
189
A
HOH
86
5
HOH
HOH
190
A
HOH
87
5
HOH
HOH
191
A
HOH
90
5
HOH
HOH
192
A
HOH
94
5
HOH
HOH
193
A
HOH
96
5
HOH
HOH
194
A
HOH
100
5
HOH
HOH
195
A
HOH
101
5
HOH
HOH
196
A
HOH
105
5
HOH
HOH
197
A
HOH
3
5
HOH
HOH
163
B
HOH
4
5
HOH
HOH
164
B
HOH
8
5
HOH
HOH
165
B
HOH
13
5
HOH
HOH
166
B
HOH
16
5
HOH
HOH
167
B
HOH
17
5
HOH
HOH
168
B
HOH
18
5
HOH
HOH
169
B
HOH
21
5
HOH
HOH
170
B
HOH
25
5
HOH
HOH
171
B
HOH
30
5
HOH
HOH
172
B
HOH
34
5
HOH
HOH
173
B
HOH
35
5
HOH
HOH
174
B
HOH
40
5
HOH
HOH
175
B
HOH
41
5
HOH
HOH
176
B
HOH
43
5
HOH
HOH
177
B
HOH
44
5
HOH
HOH
178
B
HOH
46
5
HOH
HOH
179
B
HOH
47
5
HOH
HOH
180
B
HOH
52
5
HOH
HOH
181
B
HOH
62
5
HOH
HOH
182
B
HOH
63
5
HOH
HOH
183
B
HOH
65
5
HOH
HOH
184
B
HOH
69
5
HOH
HOH
185
B
HOH
73
5
HOH
HOH
186
B
HOH
77
5
HOH
HOH
187
B
HOH
80
5
HOH
HOH
188
B
HOH
84
5
HOH
HOH
189
B
HOH
85
5
HOH
HOH
190
B
HOH
88
5
HOH
HOH
191
B
HOH
89
5
HOH
HOH
192
B
HOH
91
5
HOH
HOH
193
B
HOH
97
5
HOH
HOH
194
B
HOH
99
5
HOH
HOH
195
B
HOH
103
5
HOH
HOH
196
B
HOH
104
5
HOH
HOH
197
B
HOH
107
5
HOH
HOH
198
B
HOH
110
5
HOH
HOH
199
B
HOH
114
5
HOH
HOH
200
B
HOH
116
5
HOH
HOH
201
B
HOH
119
5
HOH
HOH
202
B
HOH
102
5
HOH
HOH
203
B
HOH
108
5
HOH
HOH
204
B
HOH
111
5
HOH
HOH
205
B
HOH
2
5
HOH
HOH
163
C
HOH
9
5
HOH
HOH
164
C
HOH
11
5
HOH
HOH
165
C
HOH
20
5
HOH
HOH
166
C
HOH
22
5
HOH
HOH
167
C
HOH
27
5
HOH
HOH
168
C
HOH
28
5
HOH
HOH
169
C
HOH
32
5
HOH
HOH
170
C
HOH
36
5
HOH
HOH
171
C
HOH
38
5
HOH
HOH
172
C
HOH
53
5
HOH
HOH
173
C
HOH
60
5
HOH
HOH
174
C
HOH
61
5
HOH
HOH
175
C
HOH
64
5
HOH
HOH
176
C
HOH
72
5
HOH
HOH
177
C
HOH
74
5
HOH
HOH
178
C
HOH
76
5
HOH
HOH
179
C
HOH
79
5
HOH
HOH
180
C
HOH
82
5
HOH
HOH
181
C
HOH
83
5
HOH
HOH
182
C
HOH
92
5
HOH
HOH
183
C
HOH
93
5
HOH
HOH
184
C
HOH
95
5
HOH
HOH
185
C
HOH
98
5
HOH
HOH
186
C
HOH
106
5
HOH
HOH
187
C
HOH
109
5
HOH
HOH
188
C
HOH
113
5
HOH
HOH
189
C
HOH
115
5
HOH
HOH
190
C
HOH
117
5
HOH
HOH
191
C
HOH
121
5
HOH
HOH
192
C
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
VAL
6
n
6
VAL
6
A
ASN
7
n
7
ASN
7
A
LYS
8
n
8
LYS
8
A
GLU
9
n
9
GLU
9
A
ARG
10
n
10
ARG
10
A
THR
11
n
11
THR
11
A
PHE
12
n
12
PHE
12
A
LEU
13
n
13
LEU
13
A
ALA
14
n
14
ALA
14
A
VAL
15
n
15
VAL
15
A
LYS
16
n
16
LYS
16
A
PRO
17
n
17
PRO
17
A
ASP
18
n
18
ASP
18
A
GLY
19
n
19
GLY
19
A
VAL
20
n
20
VAL
20
A
ALA
21
n
21
ALA
21
A
ARG
22
n
22
ARG
22
A
GLY
23
n
23
GLY
23
A
LEU
24
n
24
LEU
24
A
VAL
25
n
25
VAL
25
A
GLY
26
n
26
GLY
26
A
GLU
27
n
27
GLU
27
A
ILE
28
n
28
ILE
28
A
ILE
29
n
29
ILE
29
A
ALA
30
n
30
ALA
30
A
ARG
31
n
31
ARG
31
A
TYR
32
n
32
TYR
32
A
GLU
33
n
33
GLU
33
A
LYS
34
n
34
LYS
34
A
LYS
35
n
35
LYS
35
A
GLY
36
n
36
GLY
36
A
PHE
37
n
37
PHE
37
A
VAL
38
n
38
VAL
38
A
LEU
39
n
39
LEU
39
A
VAL
40
n
40
VAL
40
A
GLY
41
n
41
GLY
41
A
LEU
42
n
42
LEU
42
A
LYS
43
n
43
LYS
43
A
GLN
44
n
44
GLN
44
A
LEU
45
n
45
LEU
45
A
VAL
46
n
46
VAL
46
A
PRO
47
n
47
PRO
47
A
THR
48
n
48
THR
48
A
LYS
49
n
49
LYS
49
A
ASP
50
n
50
ASP
50
A
LEU
51
n
51
LEU
51
A
ALA
52
n
52
ALA
52
A
GLU
53
n
53
GLU
53
A
SER
54
n
54
SER
54
A
HIS
55
n
55
HIS
55
A
TYR
56
n
56
TYR
56
A
ALA
57
n
57
ALA
57
A
GLU
58
n
58
GLU
58
A
HIS
59
n
59
HIS
59
A
LYS
60
n
60
LYS
60
A
GLU
61
n
61
GLU
61
A
ARG
62
n
62
ARG
62
A
PRO
63
n
63
PRO
63
A
PHE
64
n
64
PHE
64
A
PHE
65
n
65
PHE
65
A
GLY
66
n
66
GLY
66
A
GLY
67
n
67
GLY
67
A
LEU
68
n
68
LEU
68
A
VAL
69
n
69
VAL
69
A
SER
70
n
70
SER
70
A
PHE
71
n
71
PHE
71
A
ILE
72
n
72
ILE
72
A
THR
73
n
73
THR
73
A
SER
74
n
74
SER
74
A
GLY
75
n
75
GLY
75
A
PRO
76
n
76
PRO
76
A
VAL
77
n
77
VAL
77
A
VAL
78
n
78
VAL
78
A
ALA
79
n
79
ALA
79
A
MET
80
n
80
MET
80
A
VAL
81
n
81
VAL
81
A
PHE
82
n
82
PHE
82
A
GLU
83
n
83
GLU
83
A
GLY
84
n
84
GLY
84
A
LYS
85
n
85
LYS
85
A
GLY
86
n
86
GLY
86
A
VAL
87
n
87
VAL
87
A
VAL
88
n
88
VAL
88
A
ALA
89
n
89
ALA
89
A
SER
90
n
90
SER
90
A
ALA
91
n
91
ALA
91
A
ARG
92
n
92
ARG
92
A
LEU
93
n
93
LEU
93
A
MET
94
n
94
MET
94
A
ILE
95
n
95
ILE
95
A
GLY
96
n
96
GLY
96
A
VAL
97
n
97
VAL
97
A
THR
98
n
98
THR
98
A
ASN
99
n
99
ASN
99
A
PRO
100
n
100
PRO
100
A
LEU
101
n
101
LEU
101
A
ALA
102
n
102
ALA
102
A
SER
103
n
103
SER
103
A
ALA
104
n
104
ALA
104
A
PRO
105
n
105
PRO
105
A
GLY
106
n
106
GLY
106
A
SER
107
n
107
SER
107
A
ILE
108
n
108
ILE
108
A
ARG
109
n
109
ARG
109
A
GLY
110
n
110
GLY
110
A
ASP
111
n
111
ASP
111
A
PHE
112
n
112
PHE
112
A
GLY
113
n
113
GLY
113
A
VAL
114
n
114
VAL
114
A
ASP
115
n
115
ASP
115
A
VAL
116
n
116
VAL
116
A
GLY
117
n
117
GLY
117
A
ARG
118
n
118
ARG
118
A
ASN
119
n
119
ASN
119
A
ILE
120
n
120
ILE
120
A
ILE
121
n
121
ILE
121
A
GLY
122
n
122
GLY
122
A
GLY
123
n
123
GLY
123
A
SER
124
n
124
SER
124
A
ASP
125
n
125
ASP
125
A
SER
126
n
126
SER
126
A
VAL
127
n
127
VAL
127
A
GLU
128
n
128
GLU
128
A
SER
129
n
129
SER
129
A
ALA
130
n
130
ALA
130
A
ASN
131
n
131
ASN
131
A
ARG
132
n
132
ARG
132
A
GLU
133
n
133
GLU
133
A
ILE
134
n
134
ILE
134
A
ALA
135
n
135
ALA
135
A
LEU
136
n
136
LEU
136
A
TRP
137
n
137
TRP
137
A
PHE
138
n
138
PHE
138
A
LYS
139
n
139
LYS
139
A
PRO
140
n
140
PRO
140
A
GLU
141
n
141
GLU
141
A
GLU
142
n
142
GLU
142
A
LEU
143
n
143
LEU
143
A
LEU
144
n
144
LEU
144
A
THR
145
n
145
THR
145
A
GLU
146
n
146
GLU
146
A
VAL
147
n
147
VAL
147
A
LYS
148
n
148
LYS
148
A
PRO
149
n
149
PRO
149
A
ASN
150
n
150
ASN
150
A
PRO
151
n
151
PRO
151
A
ASN
152
n
152
ASN
152
A
LEU
153
n
153
LEU
153
A
TYR
154
n
154
TYR
154
A
GLU
155
n
155
GLU
155
A
n
1
1
B
n
2
2
B
n
3
3
B
n
4
4
B
n
5
5
B
VAL
6
n
6
VAL
6
B
ASN
7
n
7
ASN
7
B
LYS
8
n
8
LYS
8
B
GLU
9
n
9
GLU
9
B
ARG
10
n
10
ARG
10
B
THR
11
n
11
THR
11
B
PHE
12
n
12
PHE
12
B
LEU
13
n
13
LEU
13
B
ALA
14
n
14
ALA
14
B
VAL
15
n
15
VAL
15
B
LYS
16
n
16
LYS
16
B
PRO
17
n
17
PRO
17
B
ASP
18
n
18
ASP
18
B
GLY
19
n
19
GLY
19
B
VAL
20
n
20
VAL
20
B
ALA
21
n
21
ALA
21
B
ARG
22
n
22
ARG
22
B
GLY
23
n
23
GLY
23
B
LEU
24
n
24
LEU
24
B
VAL
25
n
25
VAL
25
B
GLY
26
n
26
GLY
26
B
GLU
27
n
27
GLU
27
B
ILE
28
n
28
ILE
28
B
ILE
29
n
29
ILE
29
B
ALA
30
n
30
ALA
30
B
ARG
31
n
31
ARG
31
B
TYR
32
n
32
TYR
32
B
GLU
33
n
33
GLU
33
B
LYS
34
n
34
LYS
34
B
LYS
35
n
35
LYS
35
B
GLY
36
n
36
GLY
36
B
PHE
37
n
37
PHE
37
B
VAL
38
n
38
VAL
38
B
LEU
39
n
39
LEU
39
B
VAL
40
n
40
VAL
40
B
GLY
41
n
41
GLY
41
B
LEU
42
n
42
LEU
42
B
LYS
43
n
43
LYS
43
B
GLN
44
n
44
GLN
44
B
LEU
45
n
45
LEU
45
B
VAL
46
n
46
VAL
46
B
PRO
47
n
47
PRO
47
B
THR
48
n
48
THR
48
B
LYS
49
n
49
LYS
49
B
ASP
50
n
50
ASP
50
B
LEU
51
n
51
LEU
51
B
ALA
52
n
52
ALA
52
B
GLU
53
n
53
GLU
53
B
SER
54
n
54
SER
54
B
HIS
55
n
55
HIS
55
B
TYR
56
n
56
TYR
56
B
ALA
57
n
57
ALA
57
B
GLU
58
n
58
GLU
58
B
HIS
59
n
59
HIS
59
B
LYS
60
n
60
LYS
60
B
GLU
61
n
61
GLU
61
B
ARG
62
n
62
ARG
62
B
PRO
63
n
63
PRO
63
B
PHE
64
n
64
PHE
64
B
PHE
65
n
65
PHE
65
B
GLY
66
n
66
GLY
66
B
GLY
67
n
67
GLY
67
B
LEU
68
n
68
LEU
68
B
VAL
69
n
69
VAL
69
B
SER
70
n
70
SER
70
B
PHE
71
n
71
PHE
71
B
ILE
72
n
72
ILE
72
B
THR
73
n
73
THR
73
B
SER
74
n
74
SER
74
B
GLY
75
n
75
GLY
75
B
PRO
76
n
76
PRO
76
B
VAL
77
n
77
VAL
77
B
VAL
78
n
78
VAL
78
B
ALA
79
n
79
ALA
79
B
MET
80
n
80
MET
80
B
VAL
81
n
81
VAL
81
B
PHE
82
n
82
PHE
82
B
GLU
83
n
83
GLU
83
B
GLY
84
n
84
GLY
84
B
LYS
85
n
85
LYS
85
B
GLY
86
n
86
GLY
86
B
VAL
87
n
87
VAL
87
B
VAL
88
n
88
VAL
88
B
ALA
89
n
89
ALA
89
B
SER
90
n
90
SER
90
B
ALA
91
n
91
ALA
91
B
ARG
92
n
92
ARG
92
B
LEU
93
n
93
LEU
93
B
MET
94
n
94
MET
94
B
ILE
95
n
95
ILE
95
B
GLY
96
n
96
GLY
96
B
VAL
97
n
97
VAL
97
B
THR
98
n
98
THR
98
B
ASN
99
n
99
ASN
99
B
PRO
100
n
100
PRO
100
B
LEU
101
n
101
LEU
101
B
ALA
102
n
102
ALA
102
B
SER
103
n
103
SER
103
B
ALA
104
n
104
ALA
104
B
PRO
105
n
105
PRO
105
B
GLY
106
n
106
GLY
106
B
SER
107
n
107
SER
107
B
ILE
108
n
108
ILE
108
B
ARG
109
n
109
ARG
109
B
GLY
110
n
110
GLY
110
B
ASP
111
n
111
ASP
111
B
PHE
112
n
112
PHE
112
B
GLY
113
n
113
GLY
113
B
VAL
114
n
114
VAL
114
B
ASP
115
n
115
ASP
115
B
VAL
116
n
116
VAL
116
B
GLY
117
n
117
GLY
117
B
ARG
118
n
118
ARG
118
B
ASN
119
n
119
ASN
119
B
ILE
120
n
120
ILE
120
B
ILE
121
n
121
ILE
121
B
GLY
122
n
122
GLY
122
B
GLY
123
n
123
GLY
123
B
SER
124
n
124
SER
124
B
ASP
125
n
125
ASP
125
B
SER
126
n
126
SER
126
B
VAL
127
n
127
VAL
127
B
GLU
128
n
128
GLU
128
B
SER
129
n
129
SER
129
B
ALA
130
n
130
ALA
130
B
ASN
131
n
131
ASN
131
B
ARG
132
n
132
ARG
132
B
GLU
133
n
133
GLU
133
B
ILE
134
n
134
ILE
134
B
ALA
135
n
135
ALA
135
B
LEU
136
n
136
LEU
136
B
TRP
137
n
137
TRP
137
B
PHE
138
n
138
PHE
138
B
LYS
139
n
139
LYS
139
B
PRO
140
n
140
PRO
140
B
GLU
141
n
141
GLU
141
B
GLU
142
n
142
GLU
142
B
LEU
143
n
143
LEU
143
B
LEU
144
n
144
LEU
144
B
THR
145
n
145
THR
145
B
GLU
146
n
146
GLU
146
B
VAL
147
n
147
VAL
147
B
LYS
148
n
148
LYS
148
B
PRO
149
n
149
PRO
149
B
ASN
150
n
150
ASN
150
B
PRO
151
n
151
PRO
151
B
ASN
152
n
152
ASN
152
B
LEU
153
n
153
LEU
153
B
TYR
154
n
154
TYR
154
B
GLU
155
n
155
GLU
155
B
n
1
1
C
n
2
2
C
n
3
3
C
n
4
4
C
n
5
5
C
VAL
6
n
6
VAL
6
C
ASN
7
n
7
ASN
7
C
LYS
8
n
8
LYS
8
C
GLU
9
n
9
GLU
9
C
ARG
10
n
10
ARG
10
C
THR
11
n
11
THR
11
C
PHE
12
n
12
PHE
12
C
LEU
13
n
13
LEU
13
C
ALA
14
n
14
ALA
14
C
VAL
15
n
15
VAL
15
C
LYS
16
n
16
LYS
16
C
PRO
17
n
17
PRO
17
C
ASP
18
n
18
ASP
18
C
GLY
19
n
19
GLY
19
C
VAL
20
n
20
VAL
20
C
ALA
21
n
21
ALA
21
C
ARG
22
n
22
ARG
22
C
GLY
23
n
23
GLY
23
C
LEU
24
n
24
LEU
24
C
VAL
25
n
25
VAL
25
C
GLY
26
n
26
GLY
26
C
GLU
27
n
27
GLU
27
C
ILE
28
n
28
ILE
28
C
ILE
29
n
29
ILE
29
C
ALA
30
n
30
ALA
30
C
ARG
31
n
31
ARG
31
C
TYR
32
n
32
TYR
32
C
GLU
33
n
33
GLU
33
C
LYS
34
n
34
LYS
34
C
LYS
35
n
35
LYS
35
C
GLY
36
n
36
GLY
36
C
PHE
37
n
37
PHE
37
C
VAL
38
n
38
VAL
38
C
LEU
39
n
39
LEU
39
C
VAL
40
n
40
VAL
40
C
GLY
41
n
41
GLY
41
C
LEU
42
n
42
LEU
42
C
LYS
43
n
43
LYS
43
C
GLN
44
n
44
GLN
44
C
LEU
45
n
45
LEU
45
C
VAL
46
n
46
VAL
46
C
PRO
47
n
47
PRO
47
C
THR
48
n
48
THR
48
C
LYS
49
n
49
LYS
49
C
ASP
50
n
50
ASP
50
C
LEU
51
n
51
LEU
51
C
ALA
52
n
52
ALA
52
C
GLU
53
n
53
GLU
53
C
SER
54
n
54
SER
54
C
HIS
55
n
55
HIS
55
C
TYR
56
n
56
TYR
56
C
ALA
57
n
57
ALA
57
C
GLU
58
n
58
GLU
58
C
HIS
59
n
59
HIS
59
C
LYS
60
n
60
LYS
60
C
GLU
61
n
61
GLU
61
C
ARG
62
n
62
ARG
62
C
PRO
63
n
63
PRO
63
C
PHE
64
n
64
PHE
64
C
PHE
65
n
65
PHE
65
C
GLY
66
n
66
GLY
66
C
GLY
67
n
67
GLY
67
C
LEU
68
n
68
LEU
68
C
VAL
69
n
69
VAL
69
C
SER
70
n
70
SER
70
C
PHE
71
n
71
PHE
71
C
ILE
72
n
72
ILE
72
C
THR
73
n
73
THR
73
C
SER
74
n
74
SER
74
C
GLY
75
n
75
GLY
75
C
PRO
76
n
76
PRO
76
C
VAL
77
n
77
VAL
77
C
VAL
78
n
78
VAL
78
C
ALA
79
n
79
ALA
79
C
MET
80
n
80
MET
80
C
VAL
81
n
81
VAL
81
C
PHE
82
n
82
PHE
82
C
GLU
83
n
83
GLU
83
C
GLY
84
n
84
GLY
84
C
LYS
85
n
85
LYS
85
C
GLY
86
n
86
GLY
86
C
VAL
87
n
87
VAL
87
C
VAL
88
n
88
VAL
88
C
ALA
89
n
89
ALA
89
C
SER
90
n
90
SER
90
C
ALA
91
n
91
ALA
91
C
ARG
92
n
92
ARG
92
C
LEU
93
n
93
LEU
93
C
MET
94
n
94
MET
94
C
ILE
95
n
95
ILE
95
C
GLY
96
n
96
GLY
96
C
VAL
97
n
97
VAL
97
C
THR
98
n
98
THR
98
C
ASN
99
n
99
ASN
99
C
PRO
100
n
100
PRO
100
C
LEU
101
n
101
LEU
101
C
ALA
102
n
102
ALA
102
C
SER
103
n
103
SER
103
C
ALA
104
n
104
ALA
104
C
PRO
105
n
105
PRO
105
C
GLY
106
n
106
GLY
106
C
SER
107
n
107
SER
107
C
ILE
108
n
108
ILE
108
C
ARG
109
n
109
ARG
109
C
GLY
110
n
110
GLY
110
C
ASP
111
n
111
ASP
111
C
PHE
112
n
112
PHE
112
C
GLY
113
n
113
GLY
113
C
VAL
114
n
114
VAL
114
C
ASP
115
n
115
ASP
115
C
VAL
116
n
116
VAL
116
C
GLY
117
n
117
GLY
117
C
ARG
118
n
118
ARG
118
C
ASN
119
n
119
ASN
119
C
ILE
120
n
120
ILE
120
C
ILE
121
n
121
ILE
121
C
GLY
122
n
122
GLY
122
C
GLY
123
n
123
GLY
123
C
SER
124
n
124
SER
124
C
ASP
125
n
125
ASP
125
C
SER
126
n
126
SER
126
C
VAL
127
n
127
VAL
127
C
GLU
128
n
128
GLU
128
C
SER
129
n
129
SER
129
C
ALA
130
n
130
ALA
130
C
ASN
131
n
131
ASN
131
C
ARG
132
n
132
ARG
132
C
GLU
133
n
133
GLU
133
C
ILE
134
n
134
ILE
134
C
ALA
135
n
135
ALA
135
C
LEU
136
n
136
LEU
136
C
TRP
137
n
137
TRP
137
C
PHE
138
n
138
PHE
138
C
LYS
139
n
139
LYS
139
C
PRO
140
n
140
PRO
140
C
GLU
141
n
141
GLU
141
C
GLU
142
n
142
GLU
142
C
LEU
143
n
143
LEU
143
C
LEU
144
n
144
LEU
144
C
THR
145
n
145
THR
145
C
GLU
146
n
146
GLU
146
C
VAL
147
n
147
VAL
147
C
LYS
148
n
148
LYS
148
C
PRO
149
n
149
PRO
149
C
ASN
150
n
150
ASN
150
C
PRO
151
n
151
PRO
151
C
ASN
152
n
152
ASN
152
C
LEU
153
n
153
LEU
153
C
TYR
154
n
154
TYR
154
C
GLU
155
n
155
GLU
155
C
author_defined_assembly
6
hexameric
A
ADP
160
F
O1B
ADP
1_555
A
MG
162
E
MG
MG
1_555
A
ADP
160
F
O1A
ADP
1_555
65.0
A
ADP
160
F
O1B
ADP
1_555
A
MG
162
E
MG
MG
1_555
A
PO4
161
D
O1
PO4
1_555
80.2
A
ADP
160
F
O1A
ADP
1_555
A
MG
162
E
MG
MG
1_555
A
PO4
161
D
O1
PO4
1_555
78.7
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
ADP
160
I
O1A
ADP
1_555
73.8
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
PO4
161
G
O2
PO4
1_555
79.5
B
ADP
160
I
O1A
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
PO4
161
G
O2
PO4
1_555
86.4
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
203
N
O
HOH
1_555
99.0
B
ADP
160
I
O1A
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
203
N
O
HOH
1_555
172.3
B
PO4
161
G
O2
PO4
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
203
N
O
HOH
1_555
89.4
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
204
N
O
HOH
1_555
89.1
B
ADP
160
I
O1A
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
204
N
O
HOH
1_555
80.4
B
PO4
161
G
O2
PO4
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
204
N
O
HOH
1_555
164.6
B
HOH
203
N
O
HOH
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
204
N
O
HOH
1_555
102.7
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
148.5
B
ADP
160
I
O1A
ADP
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
76.9
B
PO4
161
G
O2
PO4
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
87.4
B
HOH
203
N
O
HOH
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
109.4
B
HOH
204
N
O
HOH
1_555
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
97.3
C
ADP
160
L
O1A
ADP
1_555
C
MG
162
K
MG
MG
1_555
C
ADP
160
L
O1B
ADP
1_555
73.3
C
ADP
160
L
O1A
ADP
1_555
C
MG
162
K
MG
MG
1_555
C
PO4
161
J
O1
PO4
1_555
92.5
C
ADP
160
L
O1B
ADP
1_555
C
MG
162
K
MG
MG
1_555
C
PO4
161
J
O1
PO4
1_555
79.2
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
6_765
-x+2,-x+y+1,-z+1/3
crystal symmetry operation
105.0000000000
60.6217782649
50.5900000000
A
O
GLY
122
A
O
GLY
122
A
N
ALA
14
A
N
ALA
14
A
O
THR
11
A
O
THR
11
A
N
PHE
82
A
N
PHE
82
A
O
VAL
77
A
O
VAL
77
A
N
LEU
45
A
N
LEU
45
B
O
GLY
122
B
O
GLY
122
B
N
ALA
14
B
N
ALA
14
B
O
THR
11
B
O
THR
11
B
N
PHE
82
B
N
PHE
82
B
O
VAL
77
B
O
VAL
77
B
N
LEU
45
B
N
LEU
45
C
O
GLY
122
C
O
GLY
122
C
N
ALA
14
C
N
ALA
14
C
O
THR
11
C
O
THR
11
C
N
PHE
82
C
N
PHE
82
C
O
VAL
77
C
O
VAL
77
C
N
LEU
45
C
N
LEU
45
1
A
MET
1
A
MET
1
1
Y
1
A
SER
2
A
SER
2
1
Y
1
A
THR
3
A
THR
3
1
Y
1
A
ASN
4
A
ASN
4
1
Y
1
A
LYS
5
A
LYS
5
1
Y
1
B
MET
1
B
MET
1
1
Y
1
B
SER
2
B
SER
2
1
Y
1
B
THR
3
B
THR
3
1
Y
1
B
ASN
4
B
ASN
4
1
Y
1
B
LYS
5
B
LYS
5
1
Y
1
C
MET
1
C
MET
1
1
Y
1
C
SER
2
C
SER
2
1
Y
1
C
THR
3
C
THR
3
1
Y
1
C
ASN
4
C
ASN
4
1
Y
1
C
LYS
5
C
LYS
5
1
Y
1
9.39
1.50
119.30
128.69
C
C
C
C
N
CA
GLY
PRO
PRO
75
76
76
Y
1
A
VAL
114
-138.28
-35.36
1
A
ASN
119
-92.20
33.56
1
A
ILE
120
55.83
-42.44
1
B
LYS
43
-172.33
144.57
1
B
VAL
114
-140.43
-34.18
1
B
ASN
119
-96.22
37.60
1
B
ILE
120
53.93
-47.28
1
C
ASN
7
-63.68
57.23
1
C
TYR
56
-99.17
33.56
1
C
VAL
114
-137.83
-43.27
1
C
ARG
118
-118.85
59.45
1
C
ASN
119
-94.99
34.92
1
C
ILE
120
56.08
-48.71
22.0
MUTANT HAS LOST NDPK ACTIVITY, BUT EFFICIENTLY
PHOSPHORYLATES IMIDAZOLE AND OTHER PHOSPHATE ACCEPTOR
MOLECULES (AMINES AND ALCOHOLS). THE PROTEIN WAS
CRYSTALLIZED WITH ATP, BUT THE NUCLEOTIDE IS SEEN TO BE
HYDROLYZED TO ADP+PO4 IN THE CRYSTAL.
0.3050000
0.2030000
0.2030000
2.5
8
14555
99.9
RANDOM
1
2.0
MOLECULAR REPLACEMENT
1KDN
2.5
8
108
3633
3
99
3423
0.012
1.9
2.0
2.5
8.0
1B4S
14555
3.0
0.0830000
1
9.8
99.9
model building
X-PLOR
refinement
X-PLOR
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
2
N
N
3
N
N
4
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
PRO
17
A
PRO
17
HELX_P
A
ALA
21
A
ALA
21
1
A0
5
A
VAL
25
A
VAL
25
HELX_P
A
LYS
35
A
LYS
35
1
A1
11
A
LYS
49
A
LYS
49
HELX_P
A
HIS
55
A
HIS
55
1
A2
7
A
ALA
57
A
ALA
57
HELX_P
A
HIS
59
A
HIS
59
5
A3
3
A
PHE
65
A
PHE
65
HELX_P
A
PHE
71
A
PHE
71
1
A5
7
A
VAL
87
A
VAL
87
HELX_P
A
ILE
95
A
ILE
95
1
A6
9
A
PRO
100
A
PRO
100
HELX_P
A
ALA
102
A
ALA
102
5
A7
3
A
ILE
108
A
ILE
108
HELX_P
A
PHE
112
A
PHE
112
1
A8
5
A
VAL
127
A
VAL
127
HELX_P
A
TRP
137
A
TRP
137
1
A9
11
A
PRO
140
A
PRO
140
HELX_P
A
GLU
142
A
GLU
142
5
A10
3
B
PRO
17
B
PRO
17
HELX_P
B
ALA
21
B
ALA
21
1
B0
5
B
VAL
25
B
VAL
25
HELX_P
B
LYS
34
B
LYS
34
1
B1
10
B
LYS
49
B
LYS
49
HELX_P
B
HIS
55
B
HIS
55
1
B2
7
B
ALA
57
B
ALA
57
HELX_P
B
HIS
59
B
HIS
59
5
B3
3
B
PHE
65
B
PHE
65
HELX_P
B
ILE
72
B
ILE
72
1
B4
8
B
VAL
87
B
VAL
87
HELX_P
B
ILE
95
B
ILE
95
1
B5
9
B
ILE
108
B
ILE
108
HELX_P
B
PHE
112
B
PHE
112
1
B6
5
B
VAL
127
B
VAL
127
HELX_P
B
TRP
137
B
TRP
137
1
B7
11
B
PRO
140
B
PRO
140
HELX_P
B
GLU
142
B
GLU
142
5
B8
3
C
PRO
17
C
PRO
17
HELX_P
C
ALA
21
C
ALA
21
1
C0
5
C
VAL
25
C
VAL
25
HELX_P
C
LYS
35
C
LYS
35
1
C1
11
C
LYS
49
C
LYS
49
HELX_P
C
HIS
55
C
HIS
55
1
C2
7
C
ALA
57
C
ALA
57
HELX_P
C
HIS
59
C
HIS
59
5
C3
3
C
PHE
65
C
PHE
65
HELX_P
C
ILE
72
C
ILE
72
1
C4
8
C
VAL
87
C
VAL
87
HELX_P
C
ILE
95
C
ILE
95
1
C5
9
C
PRO
100
C
PRO
100
HELX_P
C
ALA
102
C
ALA
102
5
C6
3
C
ILE
108
C
ILE
108
HELX_P
C
PHE
112
C
PHE
112
1
C7
5
C
VAL
127
C
VAL
127
HELX_P
C
TRP
137
C
TRP
137
1
C8
11
C
PRO
140
C
PRO
140
HELX_P
C
GLU
142
C
GLU
142
5
C9
3
metalc
2.556
A
ADP
160
F
O1B
ADP
1_555
A
MG
162
E
MG
MG
1_555
metalc
2.525
A
ADP
160
F
O1A
ADP
1_555
A
MG
162
E
MG
MG
1_555
metalc
2.236
A
PO4
161
D
O1
PO4
1_555
A
MG
162
E
MG
MG
1_555
metalc
2.217
B
ADP
160
I
O1B
ADP
1_555
B
MG
162
H
MG
MG
1_555
metalc
2.274
B
ADP
160
I
O1A
ADP
1_555
B
MG
162
H
MG
MG
1_555
metalc
2.044
B
PO4
161
G
O2
PO4
1_555
B
MG
162
H
MG
MG
1_555
metalc
2.113
B
MG
162
H
MG
MG
1_555
B
HOH
203
N
O
HOH
1_555
metalc
2.070
B
MG
162
H
MG
MG
1_555
B
HOH
204
N
O
HOH
1_555
metalc
1.845
B
MG
162
H
MG
MG
1_555
B
HOH
205
N
O
HOH
1_555
metalc
2.145
C
ADP
160
L
O1A
ADP
1_555
C
MG
162
K
MG
MG
1_555
metalc
2.558
C
ADP
160
L
O1B
ADP
1_555
C
MG
162
K
MG
MG
1_555
metalc
2.401
C
PO4
161
J
O1
PO4
1_555
C
MG
162
K
MG
MG
1_555
PHOSPHOTRANSFERASE
TRANSFERASE, KINASE, ATP-BINDING, PHOSPHOTRANSFERASE
NDKC_DICDI
UNP
1
1
P22887
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
1
155
1B4S
1
155
P22887
A
1
1
155
1
155
1B4S
1
155
P22887
B
1
1
155
1
155
1B4S
1
155
P22887
C
1
1
155
1
HIS
engineered mutation
GLY
122
1B4S
A
P22887
UNP
122
122
2
HIS
engineered mutation
GLY
122
1B4S
B
P22887
UNP
122
122
3
HIS
engineered mutation
GLY
122
1B4S
C
P22887
UNP
122
122
4
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
121
A
ILE
121
A
GLY
123
A
GLY
123
A
ARG
10
A
ARG
10
A
VAL
15
A
VAL
15
A
PRO
76
A
PRO
76
A
GLU
83
A
GLU
83
A
VAL
38
A
VAL
38
A
VAL
46
A
VAL
46
B
ILE
121
B
ILE
121
B
GLY
123
B
GLY
123
B
ARG
10
B
ARG
10
B
VAL
15
B
VAL
15
B
PRO
76
B
PRO
76
B
GLU
83
B
GLU
83
B
VAL
38
B
VAL
38
B
VAL
46
B
VAL
46
C
ILE
121
C
ILE
121
C
GLY
123
C
GLY
123
C
ARG
10
C
ARG
10
C
VAL
15
C
VAL
15
C
VAL
77
C
VAL
77
C
GLU
83
C
GLU
83
C
VAL
38
C
VAL
38
C
LEU
45
C
LEU
45
BINDING SITE FOR RESIDUE PO4 A 161
A
PO4
161
Software
9
BINDING SITE FOR RESIDUE MG A 162
A
MG
162
Software
2
BINDING SITE FOR RESIDUE PO4 B 161
B
PO4
161
Software
11
BINDING SITE FOR RESIDUE MG B 162
B
MG
162
Software
5
BINDING SITE FOR RESIDUE PO4 C 161
C
PO4
161
Software
8
BINDING SITE FOR RESIDUE MG C 162
C
MG
162
Software
2
BINDING SITE FOR RESIDUE ADP A 160
A
ADP
160
Software
12
BINDING SITE FOR RESIDUE ADP B 160
B
ADP
160
Software
15
BINDING SITE FOR RESIDUE ADP C 160
C
ADP
160
Software
13
A
LYS
16
A
LYS
16
9
1_555
A
HIS
55
A
HIS
55
9
1_555
A
TYR
56
A
TYR
56
9
1_555
A
ARG
92
A
ARG
92
9
1_555
A
ARG
109
A
ARG
109
9
1_555
A
GLY
122
A
GLY
122
9
1_555
A
GLY
123
A
GLY
123
9
1_555
A
ADP
160
F
ADP
9
1_555
A
MG
162
E
MG
9
1_555
A
ADP
160
F
ADP
2
1_555
A
PO4
161
D
PO4
2
1_555
B
LYS
16
B
LYS
16
11
1_555
B
HIS
55
B
HIS
55
11
1_555
B
TYR
56
B
TYR
56
11
1_555
B
ARG
92
B
ARG
92
11
1_555
B
GLY
122
B
GLY
122
11
1_555
B
GLY
123
B
GLY
123
11
1_555
B
ADP
160
I
ADP
11
1_555
B
MG
162
H
MG
11
1_555
B
HOH
182
N
HOH
11
1_555
B
HOH
203
N
HOH
11
1_555
B
HOH
205
N
HOH
11
1_555
B
ADP
160
I
ADP
5
1_555
B
PO4
161
G
PO4
5
1_555
B
HOH
203
N
HOH
5
1_555
B
HOH
204
N
HOH
5
1_555
B
HOH
205
N
HOH
5
1_555
C
LYS
16
C
LYS
16
8
1_555
C
HIS
55
C
HIS
55
8
1_555
C
TYR
56
C
TYR
56
8
1_555
C
ARG
92
C
ARG
92
8
1_555
C
GLY
122
C
GLY
122
8
1_555
C
GLY
123
C
GLY
123
8
1_555
C
ADP
160
L
ADP
8
1_555
C
MG
162
K
MG
8
1_555
C
ADP
160
L
ADP
2
1_555
C
PO4
161
J
PO4
2
1_555
A
LYS
16
A
LYS
16
12
1_555
A
TYR
56
A
TYR
56
12
1_555
A
HIS
59
A
HIS
59
12
1_555
A
PHE
64
A
PHE
64
12
1_555
A
LEU
68
A
LEU
68
12
1_555
A
ARG
92
A
ARG
92
12
1_555
A
THR
98
A
THR
98
12
1_555
A
ARG
109
A
ARG
109
12
1_555
A
VAL
116
A
VAL
116
12
1_555
A
ASN
119
A
ASN
119
12
1_555
A
PO4
161
D
PO4
12
1_555
A
MG
162
E
MG
12
1_555
B
LYS
16
B
LYS
16
15
1_555
B
TYR
56
B
TYR
56
15
1_555
B
HIS
59
B
HIS
59
15
1_555
B
PHE
64
B
PHE
64
15
1_555
B
LEU
68
B
LEU
68
15
1_555
B
ARG
92
B
ARG
92
15
1_555
B
THR
98
B
THR
98
15
1_555
B
ARG
109
B
ARG
109
15
1_555
B
VAL
116
B
VAL
116
15
1_555
B
ASN
119
B
ASN
119
15
1_555
B
PO4
161
G
PO4
15
1_555
B
MG
162
H
MG
15
1_555
B
HOH
175
N
HOH
15
1_555
B
HOH
204
N
HOH
15
1_555
B
HOH
205
N
HOH
15
1_555
C
LYS
16
C
LYS
16
13
1_555
C
TYR
56
C
TYR
56
13
1_555
C
HIS
59
C
HIS
59
13
1_555
C
ARG
62
C
ARG
62
13
1_555
C
PHE
64
C
PHE
64
13
1_555
C
LEU
68
C
LEU
68
13
1_555
C
ARG
92
C
ARG
92
13
1_555
C
THR
98
C
THR
98
13
1_555
C
ARG
109
C
ARG
109
13
1_555
C
VAL
116
C
VAL
116
13
1_555
C
ASN
119
C
ASN
119
13
1_555
C
PO4
161
J
PO4
13
1_555
C
MG
162
K
MG
13
1_555
152
P 31 2 1