0.013333
0.007698
0.000000
0.000000
0.015396
0.000000
0.000000
0.000000
0.009419
0.00000
0.00000
0.00000
Admiraal, S.J.
Meyer, P.
Schneider, B.
Deville-Bonne, D.
Janin, J.
Herschlag, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
75.001
75.001
106.169
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
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
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
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
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
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
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
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
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
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
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
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
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
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
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
O
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
R
C
N
295
N
O
N
296
N
C
N
297
N
O
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
N
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
N
321
N
O
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
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
N
345
N
O
N
346
N
O
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
N
363
N
C
N
364
N
C
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
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
doub
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
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
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
doub
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
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
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
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
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
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
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
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
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
doub
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
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
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
doub
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
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
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
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
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
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
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
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
US
Biochemistry
BICHAW
0033
0006-2960
40
403
413
10.1021/bi002472w
11148034
Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis.
2001
10.2210/pdb1hlw/pdb
pdb_00001hlw
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
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
RIGAKU
16749.268
NUCLEOSIDE DIPHOSPHATE KINASE
2.7.4.6
H122A
1
man
polymer
18.015
water
126
nat
water
no
no
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIAGSDSVESANREIALWFKPEELLTEVKPNPNLYE
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIAGSDSVESANREIALWFKPEELLTEVKPNPNLYE
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
Dictyostelium
Escherichia
sample
44689
Dictyostelium discoideum
562
Escherichia coli
1
2.57
52.17
VAPOR DIFFUSION, HANGING DROP
7.5
PEG 600, Magnesium Chloride, Tris Hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
290
database_2
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Database references
Data collection
1
0
2001-02-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2000-12-04
REL
HOH
water
WAT
200
2
HOH
HOH
200
A
WAT
201
2
HOH
HOH
201
A
WAT
202
2
HOH
HOH
202
A
WAT
203
2
HOH
HOH
203
A
WAT
204
2
HOH
HOH
204
A
WAT
205
2
HOH
HOH
205
A
WAT
206
2
HOH
HOH
206
A
WAT
207
2
HOH
HOH
207
A
WAT
208
2
HOH
HOH
208
A
WAT
209
2
HOH
HOH
209
A
WAT
210
2
HOH
HOH
210
A
WAT
211
2
HOH
HOH
211
A
WAT
212
2
HOH
HOH
212
A
WAT
213
2
HOH
HOH
213
A
WAT
214
2
HOH
HOH
214
A
WAT
215
2
HOH
HOH
215
A
WAT
216
2
HOH
HOH
216
A
WAT
217
2
HOH
HOH
217
A
WAT
218
2
HOH
HOH
218
A
WAT
219
2
HOH
HOH
219
A
WAT
220
2
HOH
HOH
220
A
WAT
221
2
HOH
HOH
221
A
WAT
222
2
HOH
HOH
222
A
WAT
223
2
HOH
HOH
223
A
WAT
224
2
HOH
HOH
224
A
WAT
225
2
HOH
HOH
225
A
WAT
226
2
HOH
HOH
226
A
WAT
227
2
HOH
HOH
227
A
WAT
228
2
HOH
HOH
228
A
WAT
229
2
HOH
HOH
229
A
WAT
230
2
HOH
HOH
230
A
WAT
231
2
HOH
HOH
231
A
WAT
232
2
HOH
HOH
232
A
WAT
233
2
HOH
HOH
233
A
WAT
234
2
HOH
HOH
234
A
WAT
235
2
HOH
HOH
235
A
WAT
237
2
HOH
HOH
237
A
WAT
238
2
HOH
HOH
238
A
WAT
239
2
HOH
HOH
239
A
WAT
240
2
HOH
HOH
240
A
WAT
241
2
HOH
HOH
241
A
WAT
242
2
HOH
HOH
242
A
WAT
243
2
HOH
HOH
243
A
WAT
244
2
HOH
HOH
244
A
WAT
245
2
HOH
HOH
245
A
WAT
246
2
HOH
HOH
246
A
WAT
247
2
HOH
HOH
247
A
WAT
248
2
HOH
HOH
248
A
WAT
249
2
HOH
HOH
249
A
WAT
250
2
HOH
HOH
250
A
WAT
252
2
HOH
HOH
252
A
WAT
253
2
HOH
HOH
253
A
WAT
254
2
HOH
HOH
254
A
WAT
255
2
HOH
HOH
255
A
WAT
256
2
HOH
HOH
256
A
WAT
257
2
HOH
HOH
257
A
WAT
258
2
HOH
HOH
258
A
WAT
259
2
HOH
HOH
259
A
WAT
260
2
HOH
HOH
260
A
WAT
261
2
HOH
HOH
261
A
WAT
262
2
HOH
HOH
262
A
WAT
263
2
HOH
HOH
263
A
WAT
264
2
HOH
HOH
264
A
WAT
265
2
HOH
HOH
265
A
WAT
266
2
HOH
HOH
266
A
WAT
267
2
HOH
HOH
267
A
WAT
268
2
HOH
HOH
268
A
WAT
270
2
HOH
HOH
270
A
WAT
271
2
HOH
HOH
271
A
WAT
272
2
HOH
HOH
272
A
WAT
273
2
HOH
HOH
273
A
WAT
274
2
HOH
HOH
274
A
WAT
275
2
HOH
HOH
275
A
WAT
276
2
HOH
HOH
276
A
WAT
277
2
HOH
HOH
277
A
WAT
278
2
HOH
HOH
278
A
WAT
280
2
HOH
HOH
280
A
WAT
281
2
HOH
HOH
281
A
WAT
282
2
HOH
HOH
282
A
WAT
283
2
HOH
HOH
283
A
WAT
284
2
HOH
HOH
284
A
WAT
286
2
HOH
HOH
286
A
WAT
287
2
HOH
HOH
287
A
WAT
288
2
HOH
HOH
288
A
WAT
289
2
HOH
HOH
289
A
WAT
290
2
HOH
HOH
290
A
WAT
291
2
HOH
HOH
291
A
WAT
292
2
HOH
HOH
292
A
WAT
293
2
HOH
HOH
293
A
WAT
294
2
HOH
HOH
294
A
WAT
295
2
HOH
HOH
295
A
WAT
296
2
HOH
HOH
296
A
WAT
297
2
HOH
HOH
297
A
WAT
298
2
HOH
HOH
298
A
WAT
299
2
HOH
HOH
299
A
WAT
300
2
HOH
HOH
300
A
WAT
301
2
HOH
HOH
301
A
WAT
302
2
HOH
HOH
302
A
WAT
303
2
HOH
HOH
303
A
WAT
304
2
HOH
HOH
304
A
WAT
306
2
HOH
HOH
306
A
WAT
308
2
HOH
HOH
308
A
WAT
309
2
HOH
HOH
309
A
WAT
310
2
HOH
HOH
310
A
WAT
311
2
HOH
HOH
311
A
WAT
312
2
HOH
HOH
312
A
WAT
314
2
HOH
HOH
314
A
WAT
315
2
HOH
HOH
315
A
WAT
317
2
HOH
HOH
317
A
WAT
318
2
HOH
HOH
318
A
WAT
319
2
HOH
HOH
319
A
WAT
320
2
HOH
HOH
320
A
WAT
321
2
HOH
HOH
321
A
WAT
322
2
HOH
HOH
322
A
WAT
323
2
HOH
HOH
323
A
WAT
324
2
HOH
HOH
324
A
WAT
325
2
HOH
HOH
325
A
WAT
326
2
HOH
HOH
326
A
WAT
327
2
HOH
HOH
327
A
WAT
328
2
HOH
HOH
328
A
WAT
330
2
HOH
HOH
330
A
WAT
331
2
HOH
HOH
331
A
WAT
332
2
HOH
HOH
332
A
WAT
333
2
HOH
HOH
333
A
WAT
334
2
HOH
HOH
334
A
WAT
335
2
HOH
HOH
335
A
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
ALA
122
n
122
ALA
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
author_and_software_defined_assembly
PISA,PQS
6
hexameric
12810
-62
36090
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
37.5005000000
64.9527713092
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
-37.5005000000
64.9527713092
0.0000000000
0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
10_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
37.5005000000
64.9527713092
53.0845000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
11_555
-x+y,y,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
53.0845000000
0.5000000000
0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
12_565
x,x-y+1,-z+1/2
crystal symmetry operation
-37.5005000000
64.9527713092
53.0845000000
A
O
LEU
45
A
O
LEU
45
A
N
VAL
77
A
N
VAL
77
A
O
PHE
82
A
O
PHE
82
A
N
THR
11
A
N
THR
11
A
N
ALA
14
A
N
ALA
14
A
O
ALA
122
A
O
ALA
122
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
A
ILE
120
69.60
-50.59
28.6
0.76
2.69
0.00
0.76
0.00
-1.53
0.2080000
0.006
0.1660000
0.1660000
1.90
30.00
1137
13909
8.2
95.8
RANDOM
2300066.55
0.00
1
RESTRAINED
THROUGHOUT
0.0
FLAT MODEL
54.57
0.319
0.23
0.18
5.00
0.14
0.13
1.90
30.00
126
1268
0
0
1142
0.014
1.9
23.8
1.16
2.91
1.50
3.74
2.00
5.89
2.00
7.93
2.50
0.2500000
0.018
0.2140000
2.02
198
1876
6
9.5
88.0
18.6
1.9
30.0
1HLW
110350
13910
0.0690000
1
95.8
1.9
2.02
1
88.0
phasing
AMoRE
refinement
CNS
0.5
data reduction
DENZO
data scaling
SCALEPACK
STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE
1
N
N
2
N
N
The biological assembly is a homohexamer
A
LYS
16
A
LYS
16
HELX_P
A
ARG
22
A
ARG
22
1
1
7
A
LEU
24
A
LEU
24
HELX_P
A
GLY
36
A
GLY
36
1
2
13
A
THR
48
A
THR
48
HELX_P
A
TYR
56
A
TYR
56
1
3
9
A
ALA
57
A
ALA
57
HELX_P
A
LYS
60
A
LYS
60
5
4
4
A
PHE
64
A
PHE
64
HELX_P
A
THR
73
A
THR
73
1
5
10
A
GLY
86
A
GLY
86
HELX_P
A
GLY
96
A
GLY
96
1
6
11
A
ASN
99
A
ASN
99
HELX_P
A
SER
103
A
SER
103
5
7
5
A
SER
107
A
SER
107
HELX_P
A
GLY
113
A
GLY
113
1
8
7
A
SER
126
A
SER
126
HELX_P
A
PHE
138
A
PHE
138
1
9
13
A
LYS
139
A
LYS
139
HELX_P
A
LEU
143
A
LEU
143
5
10
5
TRANSFERASE
PHOSPHOTRANSFERASE, KINASE, ATP-BINDING, TRANSFERASE
NDKC_DICDI
UNP
1
1
P22887
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
1
155
1HLW
1
155
P22887
A
1
1
155
1
HIS
engineered mutation
ALA
122
1HLW
A
P22887
UNP
122
122
4
anti-parallel
anti-parallel
anti-parallel
A
VAL
38
A
VAL
38
A
LEU
45
A
LEU
45
A
VAL
77
A
VAL
77
A
GLU
83
A
GLU
83
A
ARG
10
A
ARG
10
A
VAL
15
A
VAL
15
A
ILE
121
A
ILE
121
A
GLY
123
A
GLY
123
182
P 63 2 2