0.015999
0.000000
0.000000
0.000000
0.013598
0.000000
0.000000
0.000000
0.008421
0.00000
0.00000
0.00000
Poncet-Montange, G.
Assairi, L.
Arold, S.
Pochet, S.
Labesse, G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
62.503
73.538
118.745
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
C6 H8 O7
192.124
CITRIC ACID
non-polymer
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
C21 H27 N7 O14 P2
663.425
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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
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
C
N
75
N
O
N
76
N
O
N
77
N
C
N
78
N
C
N
79
N
O
N
80
N
C
N
81
N
C
N
82
N
O
N
83
N
O
N
84
N
C
N
85
N
O
N
86
N
O
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
H
N
95
N
N
N
96
R
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
S
N
101
N
O
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
N
N
118
N
O
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
N
N
130
S
C
N
131
N
C
N
132
N
O
N
133
N
C
N
134
N
C
N
135
N
C
N
136
N
O
N
137
N
O
N
138
N
O
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
N
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
N
C
Y
163
N
C
Y
164
N
N
Y
165
N
C
Y
166
N
C
Y
167
N
N
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
N
N
183
S
C
N
184
N
C
N
185
N
O
N
186
S
C
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
O
N
191
N
H
N
192
N
H
N
193
N
H
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
N
N
205
S
C
N
206
N
C
N
207
N
O
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
O
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
N
N
227
S
C
N
228
N
C
N
229
N
O
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
N
N
235
N
O
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
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
S
N
258
N
C
N
259
N
O
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
S
P
N
272
N
O
N
273
N
O
N
274
N
O
N
275
N
C
N
276
R
C
N
277
N
O
N
278
S
C
N
279
N
O
N
280
R
C
N
281
N
O
N
282
R
C
Y
283
N
N
Y
284
N
C
Y
285
N
N
Y
286
N
C
Y
287
N
C
N
288
N
N
Y
289
N
N
Y
290
N
C
Y
291
N
N
Y
292
N
C
N
293
N
O
N
294
N
P
N
295
N
O
N
296
N
O
N
297
N
O
N
298
N
C
N
299
R
C
N
300
N
O
N
301
S
C
N
302
N
O
N
303
R
C
N
304
N
O
N
305
R
C
Y
306
N
N
Y
307
N
C
Y
308
N
C
N
309
N
C
N
310
N
O
N
311
N
N
Y
312
N
C
Y
313
N
C
Y
314
N
C
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
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
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
N
353
N
O
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
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
N
387
N
O
N
388
N
O
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
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
R
C
N
401
N
O
N
402
N
C
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
N
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
N
427
N
O
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
N
451
N
O
N
452
N
O
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
N
N
465
S
C
N
466
N
C
N
467
N
O
N
468
N
C
N
469
N
C
N
470
N
C
N
471
N
O
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
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
doub
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
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
doub
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
sing
N
96
N
doub
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
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
Y
160
N
sing
Y
161
N
doub
Y
162
N
doub
N
163
N
sing
Y
164
N
sing
N
165
N
sing
Y
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
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
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
doub
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
doub
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
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
doub
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
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
Y
280
N
sing
Y
281
N
sing
Y
282
N
doub
N
283
N
sing
Y
284
N
sing
Y
285
N
sing
Y
286
N
doub
N
287
N
sing
Y
288
N
doub
N
289
N
sing
N
290
N
sing
Y
291
N
sing
Y
292
N
doub
N
293
N
sing
Y
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
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
Y
317
N
sing
Y
318
N
doub
Y
319
N
doub
N
320
N
sing
N
321
N
sing
Y
322
N
sing
N
323
N
doub
N
324
N
sing
N
325
N
sing
N
326
N
sing
Y
327
N
doub
N
328
N
sing
Y
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
Y
343
N
doub
Y
344
N
sing
Y
345
N
sing
N
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
doub
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
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
doub
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
doub
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
Y
412
N
doub
Y
413
N
sing
Y
414
N
sing
N
415
N
sing
Y
416
N
doub
Y
417
N
sing
Y
418
N
sing
N
419
N
sing
Y
420
N
sing
Y
421
N
doub
N
422
N
sing
Y
423
N
doub
N
424
N
sing
Y
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
doub
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
Y
440
N
doub
Y
441
N
sing
Y
442
N
sing
N
443
N
sing
Y
444
N
doub
N
445
N
sing
Y
446
N
doub
N
447
N
sing
Y
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
doub
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
282
33925
33934
10.1074/jbc.M701394200
17686780
NAD kinases use substrate-assisted catalysis for specific recognition of NAD.
2007
10.2210/pdb2i29/pdb
pdb_00002i29
ASP A 77 HAS WRONG CHIRALITY AT ATOM CA
100
1
CCD
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
ID14-2
ESRF
0.979
SYNCHROTRON
ESRF BEAMLINE ID14-2
31045.279
Probable inorganic polyphosphate/ATP-NAD kinase 1
2.7.1.23
1
man
polymer
663.425
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
1
syn
non-polymer
192.124
CITRIC ACID
1
syn
non-polymer
18.015
water
77
nat
water
PolyP, /ATP NAD kinase 1
no
no
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRP
AEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGT
TAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSA
KKIHFARFRSFPFWRRVHDSFIEDLEHHHHHH
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRP
AEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGT
TAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSA
KKIHFARFRSFPFWRRVHDSFIEDLEHHHHHH
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Listeria
Listeria monocytogenes
EGD-E
Escherichia
sample
ppnK1
169963
Listeria monocytogenes EGD-e
562
Escherichia coli
PLASMID
PET22B
1
2.28
45.94
VAPOR DIFFUSION, HANGING DROP
5.4
0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP
audit_author
exptl_crystal_grow
database_PDB_caveat
pdbx_struct_assembly
pdbx_struct_assembly_gen
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Advisory
Derived calculations
Refinement description
Version format compliance
Structure summary
Experimental preparation
Advisory
Database references
Derived calculations
Data collection
Database references
Derived calculations
Refinement description
1
0
2007-08-07
1
1
2011-07-13
1
2
2018-01-24
1
3
2018-02-14
1
4
2020-06-24
1
5
2023-08-30
_audit_author.name
_exptl_crystal_grow.pdbx_details
_exptl_crystal_grow.temp
_struct_ref_seq_dif.details
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of NAD kinase 1 from Listeria monocytogenes
Crystal structure of LmNADK1 from Listeria monocytogenes
Crystal structure of LmNADK1 from Listeria monocytogenes
Crystal structure of LmNADK1
Crystal structure of LmNADK1
Crystal structure of LmNADK1
Crystal structure of LmNADK1
RCSB
Y
RCSB
2006-08-16
REL
REL
NAD
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
CIT
CITRIC ACID
HOH
water
2I1W
PDB ENTRY 2I1W
PDB
experimental model
NAD
101
2
NAD
NAD
273
A
CIT
201
3
CIT
CIT
274
A
HOH
1
4
HOH
HOH
275
A
HOH
2
4
HOH
HOH
276
A
HOH
3
4
HOH
HOH
277
A
HOH
4
4
HOH
HOH
278
A
HOH
5
4
HOH
HOH
279
A
HOH
6
4
HOH
HOH
280
A
HOH
7
4
HOH
HOH
281
A
HOH
8
4
HOH
HOH
282
A
HOH
9
4
HOH
HOH
283
A
HOH
10
4
HOH
HOH
284
A
HOH
11
4
HOH
HOH
285
A
HOH
12
4
HOH
HOH
286
A
HOH
13
4
HOH
HOH
287
A
HOH
14
4
HOH
HOH
288
A
HOH
15
4
HOH
HOH
289
A
HOH
16
4
HOH
HOH
290
A
HOH
17
4
HOH
HOH
291
A
HOH
18
4
HOH
HOH
292
A
HOH
19
4
HOH
HOH
293
A
HOH
20
4
HOH
HOH
294
A
HOH
21
4
HOH
HOH
295
A
HOH
22
4
HOH
HOH
296
A
HOH
23
4
HOH
HOH
297
A
HOH
24
4
HOH
HOH
298
A
HOH
25
4
HOH
HOH
299
A
HOH
26
4
HOH
HOH
300
A
HOH
27
4
HOH
HOH
301
A
HOH
28
4
HOH
HOH
302
A
HOH
29
4
HOH
HOH
303
A
HOH
30
4
HOH
HOH
304
A
HOH
31
4
HOH
HOH
305
A
HOH
32
4
HOH
HOH
306
A
HOH
33
4
HOH
HOH
307
A
HOH
34
4
HOH
HOH
308
A
HOH
35
4
HOH
HOH
309
A
HOH
36
4
HOH
HOH
310
A
HOH
37
4
HOH
HOH
311
A
HOH
38
4
HOH
HOH
312
A
HOH
39
4
HOH
HOH
313
A
HOH
40
4
HOH
HOH
314
A
HOH
41
4
HOH
HOH
315
A
HOH
42
4
HOH
HOH
316
A
HOH
43
4
HOH
HOH
317
A
HOH
44
4
HOH
HOH
318
A
HOH
45
4
HOH
HOH
319
A
HOH
46
4
HOH
HOH
320
A
HOH
47
4
HOH
HOH
321
A
HOH
48
4
HOH
HOH
322
A
HOH
49
4
HOH
HOH
323
A
HOH
50
4
HOH
HOH
324
A
HOH
51
4
HOH
HOH
325
A
HOH
52
4
HOH
HOH
326
A
HOH
53
4
HOH
HOH
327
A
HOH
54
4
HOH
HOH
328
A
HOH
55
4
HOH
HOH
329
A
HOH
56
4
HOH
HOH
330
A
HOH
57
4
HOH
HOH
331
A
HOH
58
4
HOH
HOH
332
A
HOH
59
4
HOH
HOH
333
A
HOH
60
4
HOH
HOH
334
A
HOH
61
4
HOH
HOH
335
A
HOH
62
4
HOH
HOH
336
A
HOH
63
4
HOH
HOH
337
A
HOH
64
4
HOH
HOH
338
A
HOH
65
4
HOH
HOH
339
A
HOH
66
4
HOH
HOH
340
A
HOH
67
4
HOH
HOH
341
A
HOH
68
4
HOH
HOH
342
A
HOH
69
4
HOH
HOH
343
A
HOH
70
4
HOH
HOH
344
A
HOH
71
4
HOH
HOH
345
A
HOH
72
4
HOH
HOH
346
A
HOH
73
4
HOH
HOH
347
A
HOH
74
4
HOH
HOH
348
A
HOH
75
4
HOH
HOH
349
A
HOH
76
4
HOH
HOH
350
A
HOH
77
4
HOH
HOH
351
A
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
TYR
3
n
3
TYR
3
A
MET
4
n
4
MET
4
A
ILE
5
n
5
ILE
5
A
THR
6
n
6
THR
6
A
SER
7
n
7
SER
7
A
LYS
8
n
8
LYS
8
A
GLY
9
n
9
GLY
9
A
ASP
10
n
10
ASP
10
A
GLU
11
n
11
GLU
11
A
LYS
12
n
12
LYS
12
A
SER
13
n
13
SER
13
A
ASP
14
n
14
ASP
14
A
LEU
15
n
15
LEU
15
A
LEU
16
n
16
LEU
16
A
ARG
17
n
17
ARG
17
A
LEU
18
n
18
LEU
18
A
ASN
19
n
19
ASN
19
A
MET
20
n
20
MET
20
A
ILE
21
n
21
ILE
21
A
ALA
22
n
22
ALA
22
A
GLY
23
n
23
GLY
23
A
PHE
24
n
24
PHE
24
A
GLY
25
n
25
GLY
25
A
GLU
26
n
26
GLU
26
A
TYR
27
n
27
TYR
27
A
ASP
28
n
28
ASP
28
A
MET
29
n
29
MET
29
A
GLU
30
n
30
GLU
30
A
TYR
31
n
31
TYR
31
A
ASP
32
n
32
ASP
32
A
ASP
33
n
33
ASP
33
A
VAL
34
n
34
VAL
34
A
GLU
35
n
35
GLU
35
A
PRO
36
n
36
PRO
36
A
GLU
37
n
37
GLU
37
A
ILE
38
n
38
ILE
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
SER
41
n
41
SER
41
A
ILE
42
n
42
ILE
42
A
GLY
43
n
43
GLY
43
A
GLY
44
n
44
GLY
44
A
ASP
45
n
45
ASP
45
A
GLY
46
n
46
GLY
46
A
THR
47
n
47
THR
47
A
PHE
48
n
48
PHE
48
A
LEU
49
n
49
LEU
49
A
SER
50
n
50
SER
50
A
ALA
51
n
51
ALA
51
A
PHE
52
n
52
PHE
52
A
HIS
53
n
53
HIS
53
A
GLN
54
n
54
GLN
54
A
TYR
55
n
55
TYR
55
A
GLU
56
n
56
GLU
56
A
GLU
57
n
57
GLU
57
A
ARG
58
n
58
ARG
58
A
LEU
59
n
59
LEU
59
A
ASP
60
n
60
ASP
60
A
GLU
61
n
61
GLU
61
A
ILE
62
n
62
ILE
62
A
ALA
63
n
63
ALA
63
A
PHE
64
n
64
PHE
64
A
ILE
65
n
65
ILE
65
A
GLY
66
n
66
GLY
66
A
ILE
67
n
67
ILE
67
A
HIS
68
n
68
HIS
68
A
THR
69
n
69
THR
69
A
n
70
70
A
n
71
71
A
n
72
72
A
GLY
73
n
73
GLY
73
A
PHE
74
n
74
PHE
74
A
TYR
75
n
75
TYR
75
A
ALA
76
n
76
ALA
76
A
ASP
77
n
77
ASP
77
A
TRP
78
n
78
TRP
78
A
ARG
79
n
79
ARG
79
A
PRO
80
n
80
PRO
80
A
ALA
81
n
81
ALA
81
A
GLU
82
n
82
GLU
82
A
ALA
83
n
83
ALA
83
A
ASP
84
n
84
ASP
84
A
LYS
85
n
85
LYS
85
A
LEU
86
n
86
LEU
86
A
VAL
87
n
87
VAL
87
A
LYS
88
n
88
LYS
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
ALA
91
n
91
ALA
91
A
LYS
92
n
92
LYS
92
A
GLY
93
n
93
GLY
93
A
GLU
94
n
94
GLU
94
A
TYR
95
n
95
TYR
95
A
GLN
96
n
96
GLN
96
A
LYS
97
n
97
LYS
97
A
VAL
98
n
98
VAL
98
A
SER
99
n
99
SER
99
A
TYR
100
n
100
TYR
100
A
PRO
101
n
101
PRO
101
A
LEU
102
n
102
LEU
102
A
LEU
103
n
103
LEU
103
A
LYS
104
n
104
LYS
104
A
THR
105
n
105
THR
105
A
THR
106
n
106
THR
106
A
VAL
107
n
107
VAL
107
A
LYS
108
n
108
LYS
108
A
TYR
109
n
109
TYR
109
A
n
110
110
A
n
111
111
A
n
112
112
A
n
113
113
A
n
114
114
A
GLU
115
n
115
GLU
115
A
ALA
116
n
116
ALA
116
A
THR
117
n
117
THR
117
A
TYR
118
n
118
TYR
118
A
LEU
119
n
119
LEU
119
A
ALA
120
n
120
ALA
120
A
LEU
121
n
121
LEU
121
A
ASN
122
n
122
ASN
122
A
GLU
123
n
123
GLU
123
A
SER
124
n
124
SER
124
A
THR
125
n
125
THR
125
A
VAL
126
n
126
VAL
126
A
LYS
127
n
127
LYS
127
A
SER
128
n
128
SER
128
A
SER
129
n
129
SER
129
A
GLY
130
n
130
GLY
130
A
GLY
131
n
131
GLY
131
A
PRO
132
n
132
PRO
132
A
PHE
133
n
133
PHE
133
A
VAL
134
n
134
VAL
134
A
VAL
135
n
135
VAL
135
A
ASP
136
n
136
ASP
136
A
VAL
137
n
137
VAL
137
A
VAL
138
n
138
VAL
138
A
ILE
139
n
139
ILE
139
A
ASN
140
n
140
ASN
140
A
ASP
141
n
141
ASP
141
A
ILE
142
n
142
ILE
142
A
HIS
143
n
143
HIS
143
A
PHE
144
n
144
PHE
144
A
GLU
145
n
145
GLU
145
A
ARG
146
n
146
ARG
146
A
PHE
147
n
147
PHE
147
A
ARG
148
n
148
ARG
148
A
GLY
149
n
149
GLY
149
A
ASP
150
n
150
ASP
150
A
GLY
151
n
151
GLY
151
A
LEU
152
n
152
LEU
152
A
CYS
153
n
153
CYS
153
A
MET
154
n
154
MET
154
A
SER
155
n
155
SER
155
A
THR
156
n
156
THR
156
A
PRO
157
n
157
PRO
157
A
SER
158
n
158
SER
158
A
GLY
159
n
159
GLY
159
A
THR
160
n
160
THR
160
A
THR
161
n
161
THR
161
A
ALA
162
n
162
ALA
162
A
TYR
163
n
163
TYR
163
A
ASN
164
n
164
ASN
164
A
LYS
165
n
165
LYS
165
A
SER
166
n
166
SER
166
A
LEU
167
n
167
LEU
167
A
GLY
168
n
168
GLY
168
A
GLY
169
n
169
GLY
169
A
ALA
170
n
170
ALA
170
A
LEU
171
n
171
LEU
171
A
MET
172
n
172
MET
172
A
HIS
173
n
173
HIS
173
A
PRO
174
n
174
PRO
174
A
SER
175
n
175
SER
175
A
ILE
176
n
176
ILE
176
A
GLU
177
n
177
GLU
177
A
ALA
178
n
178
ALA
178
A
MET
179
n
179
MET
179
A
GLN
180
n
180
GLN
180
A
LEU
181
n
181
LEU
181
A
THR
182
n
182
THR
182
A
GLU
183
n
183
GLU
183
A
MET
184
n
184
MET
184
A
ALA
185
n
185
ALA
185
A
SER
186
n
186
SER
186
A
ILE
187
n
187
ILE
187
A
ASN
188
n
188
ASN
188
A
ASN
189
n
189
ASN
189
A
ARG
190
n
190
ARG
190
A
VAL
191
n
191
VAL
191
A
TYR
192
n
192
TYR
192
A
ARG
193
n
193
ARG
193
A
THR
194
n
194
THR
194
A
ILE
195
n
195
ILE
195
A
GLY
196
n
196
GLY
196
A
SER
197
n
197
SER
197
A
PRO
198
n
198
PRO
198
A
LEU
199
n
199
LEU
199
A
VAL
200
n
200
VAL
200
A
PHE
201
n
201
PHE
201
A
PRO
202
n
202
PRO
202
A
LYS
203
n
203
LYS
203
A
HIS
204
n
204
HIS
204
A
HIS
205
n
205
HIS
205
A
VAL
206
n
206
VAL
206
A
VAL
207
n
207
VAL
207
A
SER
208
n
208
SER
208
A
LEU
209
n
209
LEU
209
A
GLN
210
n
210
GLN
210
A
PRO
211
n
211
PRO
211
A
VAL
212
n
212
VAL
212
A
ASN
213
n
213
ASN
213
A
ASP
214
n
214
ASP
214
A
LYS
215
n
215
LYS
215
A
ASP
216
n
216
ASP
216
A
PHE
217
n
217
PHE
217
A
GLN
218
n
218
GLN
218
A
ILE
219
n
219
ILE
219
A
SER
220
n
220
SER
220
A
VAL
221
n
221
VAL
221
A
ASP
222
n
222
ASP
222
A
HIS
223
n
223
HIS
223
A
LEU
224
n
224
LEU
224
A
SER
225
n
225
SER
225
A
ILE
226
n
226
ILE
226
A
LEU
227
n
227
LEU
227
A
HIS
228
n
228
HIS
228
A
ARG
229
n
229
ARG
229
A
ASP
230
n
230
ASP
230
A
VAL
231
n
231
VAL
231
A
GLN
232
n
232
GLN
232
A
GLU
233
n
233
GLU
233
A
ILE
234
n
234
ILE
234
A
ARG
235
n
235
ARG
235
A
TYR
236
n
236
TYR
236
A
GLU
237
n
237
GLU
237
A
VAL
238
n
238
VAL
238
A
SER
239
n
239
SER
239
A
ALA
240
n
240
ALA
240
A
LYS
241
n
241
LYS
241
A
LYS
242
n
242
LYS
242
A
ILE
243
n
243
ILE
243
A
HIS
244
n
244
HIS
244
A
PHE
245
n
245
PHE
245
A
ALA
246
n
246
ALA
246
A
ARG
247
n
247
ARG
247
A
PHE
248
n
248
PHE
248
A
ARG
249
n
249
ARG
249
A
SER
250
n
250
SER
250
A
PHE
251
n
251
PHE
251
A
PRO
252
n
252
PRO
252
A
PHE
253
n
253
PHE
253
A
TRP
254
n
254
TRP
254
A
ARG
255
n
255
ARG
255
A
ARG
256
n
256
ARG
256
A
VAL
257
n
257
VAL
257
A
HIS
258
n
258
HIS
258
A
ASP
259
n
259
ASP
259
A
SER
260
n
260
SER
260
A
PHE
261
n
261
PHE
261
A
ILE
262
n
262
ILE
262
A
GLU
263
n
263
GLU
263
A
n
264
264
A
n
265
265
A
n
266
266
A
n
267
267
A
n
268
268
A
n
269
269
A
n
270
270
A
n
271
271
A
n
272
272
A
3.0171
-0.3055
-1.5985
0.6746
1.6187
6.7790
-0.0522
-0.1731
0.1379
0.0156
0.0578
0.0787
-0.1871
-0.2483
-0.0056
0.0184
0.0465
0.0434
0.0561
-0.0664
-0.0448
refined
10.8536
23.2133
21.9260
X-RAY DIFFRACTION
1.8804
0.8737
0.1633
0.4556
0.5159
3.9143
-0.0498
-0.5712
0.3461
0.0845
0.2446
-0.1960
-0.2550
0.2500
-0.1949
0.1640
0.0351
0.0733
0.1199
-0.1111
0.0591
refined
21.8585
25.6166
25.8639
X-RAY DIFFRACTION
3.5343
3.9782
-2.4174
13.7830
2.6839
7.1481
0.1645
-0.5491
0.1494
0.6995
-0.0788
-0.0115
-0.0402
-0.0301
-0.0857
-0.0923
-0.0169
-0.0194
-0.0357
-0.0482
-0.1711
refined
31.0908
13.7001
16.6672
X-RAY DIFFRACTION
1.4690
-0.1463
0.0957
1.8902
0.4699
2.8995
0.0926
0.0484
0.1337
-0.0799
-0.1318
0.2879
-0.1911
-0.3211
0.0391
-0.1271
0.0518
0.0064
-0.1202
0.0104
-0.1037
refined
17.5327
13.3537
-4.2049
X-RAY DIFFRACTION
0.0316
0.6405
0.0599
12.9867
1.2135
0.1134
-0.0127
-2.0793
-0.4061
0.9707
0.0526
0.6092
0.1179
-1.4235
-0.0400
0.0463
0.0114
0.0836
0.2020
0.0380
0.0554
refined
17.1313
8.7296
11.1169
X-RAY DIFFRACTION
148.7147
43.0319
33.1290
154.4411
20.4373
8.2094
-1.4729
3.9824
1.6678
0.4382
3.4690
0.5662
1.1516
-6.1270
-1.9961
0.1035
0.0489
0.0189
0.0434
-0.0759
0.0087
refined
30.8602
24.9193
13.5940
X-RAY DIFFRACTION
A
1
A
76
X-RAY DIFFRACTION
1
A
77
A
97
X-RAY DIFFRACTION
2
A
245
A
251
X-RAY DIFFRACTION
2
A
252
A
263
X-RAY DIFFRACTION
3
A
98
A
244
X-RAY DIFFRACTION
4
A
273
A
273
X-RAY DIFFRACTION
5
A
274
A
274
X-RAY DIFFRACTION
6
author_and_software_defined_assembly
PISA
4
tetrameric
12670
-70
37880
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_655
-x+1,-y,z
crystal symmetry operation
62.5030000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_655
-x+1,y,-z
crystal symmetry operation
62.5030000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
x,-y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
THR
6
A
N
THR
6
A
O
ILE
40
A
O
ILE
40
A
N
SER
41
A
N
SER
41
A
O
ILE
67
A
O
ILE
67
A
O
ALA
116
A
O
ALA
116
A
N
VAL
107
A
N
VAL
107
A
N
GLN
96
A
N
GLN
96
A
O
ARG
247
A
O
ARG
247
A
O
TYR
236
A
O
TYR
236
A
N
VAL
207
A
N
VAL
207
A
O
SER
208
A
O
SER
208
A
N
VAL
138
A
N
VAL
138
A
N
VAL
137
A
N
VAL
137
A
O
GLU
145
A
O
GLU
145
A
O
PHE
201
A
O
PHE
201
A
N
MET
179
A
N
MET
179
A
O
THR
182
A
O
THR
182
A
N
CYS
153
A
N
CYS
153
A
O
MET
154
A
O
MET
154
A
N
SER
124
A
N
SER
124
A
N
THR
125
A
N
THR
125
A
O
SER
220
A
O
SER
220
A
N
PHE
217
A
N
PHE
217
A
O
HIS
228
A
O
HIS
228
1
A
CG
GLU
11
A
CG
GLU
11
1
Y
1
A
CD
GLU
11
A
CD
GLU
11
1
Y
1
A
OE1
GLU
11
A
OE1
GLU
11
1
Y
1
A
OE2
GLU
11
A
OE2
GLU
11
1
Y
1
A
CG
LYS
12
A
CG
LYS
12
1
Y
1
A
CD
LYS
12
A
CD
LYS
12
1
Y
1
A
CE
LYS
12
A
CE
LYS
12
1
Y
1
A
NZ
LYS
12
A
NZ
LYS
12
1
Y
1
A
CG
LEU
15
A
CG
LEU
15
1
Y
1
A
CD1
LEU
15
A
CD1
LEU
15
1
Y
1
A
CD2
LEU
15
A
CD2
LEU
15
1
Y
1
A
CB
ASP
28
A
CB
ASP
28
1
Y
1
A
CG
ASP
28
A
CG
ASP
28
1
Y
1
A
OD1
ASP
28
A
OD1
ASP
28
1
Y
1
A
OD2
ASP
28
A
OD2
ASP
28
1
Y
1
A
CG
GLU
35
A
CG
GLU
35
1
Y
1
A
CD
GLU
35
A
CD
GLU
35
1
Y
1
A
OE1
GLU
35
A
OE1
GLU
35
1
Y
1
A
OE2
GLU
35
A
OE2
GLU
35
1
Y
1
A
CG
ARG
58
A
CG
ARG
58
1
Y
1
A
CD
ARG
58
A
CD
ARG
58
1
Y
1
A
NE
ARG
58
A
NE
ARG
58
1
Y
1
A
CZ
ARG
58
A
CZ
ARG
58
1
Y
1
A
NH1
ARG
58
A
NH1
ARG
58
1
Y
1
A
NH2
ARG
58
A
NH2
ARG
58
1
Y
1
A
CG
LYS
85
A
CG
LYS
85
1
Y
1
A
CD
LYS
85
A
CD
LYS
85
1
Y
1
A
CE
LYS
85
A
CE
LYS
85
1
Y
1
A
NZ
LYS
85
A
NZ
LYS
85
1
Y
1
A
CG
LYS
88
A
CG
LYS
88
1
Y
1
A
CD
LYS
88
A
CD
LYS
88
1
Y
1
A
CE
LYS
88
A
CE
LYS
88
1
Y
1
A
NZ
LYS
88
A
NZ
LYS
88
1
Y
1
A
CB
ALA
91
A
CB
ALA
91
1
Y
1
A
CG
LYS
92
A
CG
LYS
92
1
Y
1
A
CD
LYS
92
A
CD
LYS
92
1
Y
1
A
CE
LYS
92
A
CE
LYS
92
1
Y
1
A
NZ
LYS
92
A
NZ
LYS
92
1
Y
1
A
CG
GLN
96
A
CG
GLN
96
1
Y
1
A
CD
GLN
96
A
CD
GLN
96
1
Y
1
A
OE1
GLN
96
A
OE1
GLN
96
1
Y
1
A
NE2
GLN
96
A
NE2
GLN
96
1
Y
1
A
CG
ARG
190
A
CG
ARG
190
1
Y
1
A
CD
ARG
190
A
CD
ARG
190
1
Y
1
A
NE
ARG
190
A
NE
ARG
190
1
Y
1
A
CZ
ARG
190
A
CZ
ARG
190
1
Y
1
A
NH1
ARG
190
A
NH1
ARG
190
1
Y
1
A
NH2
ARG
190
A
NH2
ARG
190
1
Y
1
A
CB
VAL
191
A
CB
VAL
191
1
Y
1
A
CG1
VAL
191
A
CG1
VAL
191
1
Y
1
A
CG2
VAL
191
A
CG2
VAL
191
1
Y
1
A
CG
ARG
193
A
CG
ARG
193
1
Y
1
A
CD
ARG
193
A
CD
ARG
193
1
Y
1
A
NE
ARG
193
A
NE
ARG
193
1
Y
1
A
CZ
ARG
193
A
CZ
ARG
193
1
Y
1
A
NH1
ARG
193
A
NH1
ARG
193
1
Y
1
A
NH2
ARG
193
A
NH2
ARG
193
1
Y
1
A
CG
GLN
232
A
CG
GLN
232
1
Y
1
A
CD
GLN
232
A
CD
GLN
232
1
Y
1
A
OE1
GLN
232
A
OE1
GLN
232
1
Y
1
A
NE2
GLN
232
A
NE2
GLN
232
1
Y
1
A
CG
ARG
249
A
CG
ARG
249
1
Y
1
A
CD
ARG
249
A
CD
ARG
249
1
Y
1
A
NE
ARG
249
A
NE
ARG
249
1
Y
1
A
CZ
ARG
249
A
CZ
ARG
249
1
Y
1
A
NH1
ARG
249
A
NH1
ARG
249
1
Y
1
A
NH2
ARG
249
A
NH2
ARG
249
1
Y
1
A
CG
GLU
263
A
CG
GLU
263
1
Y
1
A
CD
GLU
263
A
CD
GLU
263
1
Y
1
A
OE1
GLU
263
A
OE1
GLU
263
1
Y
1
A
OE2
GLU
263
A
OE2
GLU
263
1
Y
1
A
GLY
70
A
GLY
70
1
Y
1
A
HIS
71
A
HIS
71
1
Y
1
A
LEU
72
A
LEU
72
1
Y
1
A
GLY
110
A
GLY
110
1
Y
1
A
ILE
111
A
ILE
111
1
Y
1
A
GLY
112
A
GLY
112
1
Y
1
A
LYS
113
A
LYS
113
1
Y
1
A
LYS
114
A
LYS
114
1
Y
1
A
ASP
264
A
ASP
264
1
Y
1
A
LEU
265
A
LEU
265
1
Y
1
A
GLU
266
A
GLU
266
1
Y
1
A
HIS
267
A
HIS
267
1
Y
1
A
HIS
268
A
HIS
268
1
Y
1
A
HIS
269
A
HIS
269
1
Y
1
A
HIS
270
A
HIS
270
1
Y
1
A
HIS
271
A
HIS
271
1
Y
1
A
HIS
272
A
HIS
272
1
Y
1
A
CA
ASP
77
PLANAR
1
A
A
O
O
ALA
HOH
76
338
2.17
1
A
A
ALA
ASP
76
77
35.23
1
A
A
ASN
ASP
213
214
84.40
1
A
A
ARG
PHE
247
248
-67.25
1
19.46
2.70
111.00
130.46
A
A
A
N
CA
C
ASP
ASP
ASP
77
77
77
N
1
7.01
0.90
118.30
125.31
A
A
A
CB
CG
OD2
ASP
ASP
ASP
222
222
222
N
1
A
A
O
O
HOH
HOH
325
325
2.01
1_555
4_555
1
A
TYR
27
-103.70
-153.12
1
A
ASP
28
174.57
103.82
1
A
MET
29
93.14
58.69
1
A
ASP
77
74.21
-74.22
1
A
ASN
122
-100.61
-72.62
1
A
ASP
141
72.30
-4.86
1
A
ALA
162
-99.53
-126.05
1
A
PRO
174
-68.75
3.31
1
A
ASN
213
-97.30
-103.75
1
A
ASP
214
35.66
91.29
1
A
ASP
222
51.49
-116.39
1
A
PHE
248
163.60
-47.21
39.011
0.680
0.000
0.000
3.790
0.000
-4.470
0.948
0.917
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.254
0.205
0.206
0.206
2.100
34.86
478
16111
15633
3.000
98.450
11.179
0.148
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
0.241
0.201
0.800
0.800
1.200
PDB ENTRY 2I1W
MAXIMUM LIKELIHOOD
MASK
2.100
34.86
77
2110
57
0
1976
0.009
0.021
2122
1.478
1.964
2887
9.342
5.000
256
33.082
23.438
96
15.741
15.000
329
19.956
15.000
11
0.163
0.200
314
0.004
0.020
1617
0.212
0.200
889
0.309
0.200
1383
0.299
0.200
115
0.170
0.200
34
0.296
0.200
10
0.455
1.500
1320
0.707
2.000
2041
1.055
3.000
930
1.244
4.500
844
0.277
0.283
2.154
31
981
1012
20
85.190
37.7
2.1
37.14
2I29
16111
15633
0.0
0.0
0.071
1
17.2
6.0
98.7
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0005
data extraction
PDB
sw-help@rcsb.rutgers.edu
April. 3, 2006
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
2.000
data collection
ADSC
Quantum
data reduction
MOSFLM
data scaling
SCALA
phasing
MOLREP
Crystal structure of NAD kinase 1 from Listeria monocytogenes
1
N
N
2
N
N
3
N
N
4
N
N
A
ASP
10
A
ASP
10
HELX_P
A
GLU
26
A
GLU
26
1
1
17
A
GLY
44
A
GLY
44
HELX_P
A
TYR
55
A
TYR
55
1
2
12
A
ARG
79
A
ARG
79
HELX_P
A
ALA
81
A
ALA
81
5
3
3
A
GLU
82
A
GLU
82
HELX_P
A
GLY
93
A
GLY
93
1
4
12
A
PRO
157
A
PRO
157
HELX_P
A
THR
161
A
THR
161
5
5
5
A
ALA
162
A
ALA
162
HELX_P
A
LEU
167
A
LEU
167
1
6
6
A
PRO
252
A
PRO
252
HELX_P
A
ILE
262
A
ILE
262
1
7
11
TRANSFERASE
NAD-bound NAD kinase in orthorhombic form, TRANSFERASE
A
ASP
28
A
ASP
28
1
A
MET
29
A
MET
29
-10.61
A
GLY
130
A
GLY
130
1
A
GLY
131
A
GLY
131
-13.37
PPNK1_LISMO
UNP
1
1
Q8Y8D7
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRP
AEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGT
TAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSA
KKIHFARFRSFPFWRRVHDSFIED
1
264
2I29
1
264
Q8Y8D7
A
1
1
264
1
cloning artifact
LEU
265
2I29
A
Q8Y8D7
UNP
265
1
cloning artifact
GLU
266
2I29
A
Q8Y8D7
UNP
266
1
expression tag
HIS
267
2I29
A
Q8Y8D7
UNP
267
1
expression tag
HIS
268
2I29
A
Q8Y8D7
UNP
268
1
expression tag
HIS
269
2I29
A
Q8Y8D7
UNP
269
1
expression tag
HIS
270
2I29
A
Q8Y8D7
UNP
270
1
expression tag
HIS
271
2I29
A
Q8Y8D7
UNP
271
1
expression tag
HIS
272
2I29
A
Q8Y8D7
UNP
272
3
6
6
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
3
A
TYR
3
A
SER
7
A
SER
7
A
ILE
38
A
ILE
38
A
GLY
43
A
GLY
43
A
ALA
63
A
ALA
63
A
HIS
68
A
HIS
68
A
ALA
116
A
ALA
116
A
ALA
120
A
ALA
120
A
GLN
96
A
GLN
96
A
LYS
108
A
LYS
108
A
GLU
233
A
GLU
233
A
ARG
247
A
ARG
247
A
VAL
207
A
VAL
207
A
PRO
211
A
PRO
211
A
PHE
133
A
PHE
133
A
ILE
139
A
ILE
139
A
ILE
142
A
ILE
142
A
GLY
149
A
GLY
149
A
LEU
199
A
LEU
199
A
PRO
202
A
PRO
202
A
ALA
178
A
ALA
178
A
MET
184
A
MET
184
A
GLY
151
A
GLY
151
A
SER
155
A
SER
155
A
GLU
123
A
GLU
123
A
SER
128
A
SER
128
A
PHE
217
A
PHE
217
A
VAL
221
A
VAL
221
A
LEU
224
A
LEU
224
A
HIS
228
A
HIS
228
BINDING SITE FOR RESIDUE NAD A 273
A
NAD
273
Software
18
BINDING SITE FOR RESIDUE CIT A 274
A
CIT
274
Software
7
A
ASP
45
A
ASP
45
18
1_555
A
GLY
46
A
GLY
46
18
1_555
A
PHE
74
A
PHE
74
18
1_555
A
TYR
75
A
TYR
75
18
1_555
A
ASN
122
A
ASN
122
18
1_555
A
GLU
123
A
GLU
123
18
1_555
A
ASP
150
A
ASP
150
18
4_555
A
SER
158
A
SER
158
18
1_555
A
THR
161
A
THR
161
18
1_555
A
ALA
162
A
ALA
162
18
1_555
A
TYR
163
A
TYR
163
18
1_555
A
SER
166
A
SER
166
18
1_555
A
ALA
185
A
ALA
185
18
4_555
A
ILE
187
A
ILE
187
18
4_555
A
TYR
192
A
TYR
192
18
4_555
A
HIS
223
A
HIS
223
18
1_555
A
HOH
314
D
HOH
18
1_555
A
HOH
321
D
HOH
18
1_555
A
TYR
100
A
TYR
100
7
1_555
A
HIS
173
A
HIS
173
7
1_555
A
HIS
205
A
HIS
205
7
3_655
A
ARG
247
A
ARG
247
7
1_555
A
PHE
251
A
PHE
251
7
1_555
A
PHE
253
A
PHE
253
7
1_555
A
HOH
302
D
HOH
7
1_555
23
I 2 2 2