0.005652
0.000000
0.000000
0.000000
0.005652
0.000000
0.000000
0.000000
0.010584
0.00000
0.00000
0.00000
0000-0003-2968-0081
Zhang, Y.
0000-0002-6460-4845
Baerentsen, R.L.
0000-0002-7462-4612
Gerdes, K.
0000-0002-5413-4667
Brodersen, D.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.000
90.000
90.000
176.920
176.920
94.480
2957288.851
C10 H18 N5 O20 P5
683.140
guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen 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
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
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
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
P
N
6
N
O
N
7
N
O
N
8
N
O
N
9
N
P
N
10
N
O
N
11
N
O
N
12
N
O
N
13
N
O
N
14
N
P
N
15
N
O
N
16
N
O
N
17
N
O
N
18
N
C
N
19
R
C
N
20
N
O
N
21
S
C
N
22
N
O
N
23
R
C
N
24
N
O
N
25
R
C
Y
26
N
N
Y
27
N
C
Y
28
N
N
Y
29
N
C
N
30
N
C
N
31
N
O
N
32
N
N
N
33
N
C
N
34
N
N
N
35
N
N
Y
36
N
C
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
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
H
N
57
N
H
N
58
N
H
N
59
N
N
N
60
S
C
N
61
N
C
N
62
N
O
N
63
N
C
N
64
N
O
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
N
N
73
S
C
N
74
N
C
N
75
N
O
N
76
N
C
N
77
N
C
N
78
N
C
N
79
N
N
N
80
N
C
N
81
N
N
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
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
N
N
100
S
C
N
101
N
C
N
102
N
O
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
O
N
108
N
H
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
O
N
123
N
O
N
124
N
O
N
125
N
H
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
N
N
133
R
C
N
134
N
C
N
135
N
O
N
136
N
C
N
137
N
S
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
N
N
147
S
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
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
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
O
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
N
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
N
N
196
S
C
N
197
N
C
N
198
N
O
N
199
N
C
Y
200
N
C
Y
201
N
N
Y
202
N
C
Y
203
N
C
Y
204
N
N
N
205
N
O
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
O
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
S
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
O
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
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
N
N
242
S
C
N
243
N
C
N
244
N
O
N
245
N
C
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
O
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
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
N
C
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
N
N
272
N
O
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
S
N
295
N
C
N
296
N
O
N
297
N
H
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
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
Y
318
N
C
N
319
N
O
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
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
N
336
N
C
N
337
N
C
N
338
N
O
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
O
N
354
N
O
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
N
N
363
S
C
N
364
N
C
N
365
N
O
N
366
R
C
N
367
N
O
N
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
N
N
380
S
C
N
381
N
C
N
382
N
O
N
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
N
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
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
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
Y
411
N
C
Y
412
N
C
Y
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
N
417
N
O
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
N
N
431
S
C
N
432
N
C
N
433
N
O
N
434
N
C
N
435
N
C
N
436
N
C
N
437
N
O
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
1
N
doub
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
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
doub
Y
19
N
doub
Y
20
N
sing
N
21
N
sing
N
22
N
sing
Y
23
N
sing
N
24
N
sing
N
25
N
sing
Y
26
N
sing
N
27
N
sing
N
28
N
doub
Y
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
doub
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
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
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
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
doub
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
doub
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
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
sing
N
121
N
doub
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
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
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
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
sing
N
167
N
sing
N
168
N
doub
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
doub
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
doub
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
doub
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
Y
200
N
sing
Y
201
N
doub
Y
202
N
doub
N
203
N
sing
Y
204
N
sing
N
205
N
sing
Y
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
doub
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
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
doub
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
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
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
doub
N
313
N
sing
Y
314
N
doub
N
315
N
sing
Y
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
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
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
sing
N
354
N
sing
N
355
N
sing
N
356
N
doub
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
doub
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
Y
377
N
doub
Y
378
N
sing
Y
379
N
sing
N
380
N
sing
Y
381
N
doub
Y
382
N
sing
Y
383
N
sing
N
384
N
sing
Y
385
N
sing
Y
386
N
doub
N
387
N
sing
Y
388
N
doub
N
389
N
sing
Y
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
sing
N
400
N
doub
N
401
N
sing
N
402
N
sing
N
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
doub
N
410
N
sing
Y
411
N
doub
N
412
N
sing
Y
413
N
sing
N
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
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
sing
US
Mol.Cell
MOCEFL
2168
1097-2765
74
1239
10.1016/j.molcel.2019.03.035
31023582
(p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.
2019
10.2210/pdb6gfm/pdb
pdb_00006gfm
100
1
PIXEL
2017-10-20
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.97623
1.0
P13 (MX1)
PETRA III, EMBL c/o DESY
0.97623
SYNCHROTRON
PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
53244.168
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
3.2.2.-,3.2.2.10,3.2.2.4
1
man
polymer
683.140
guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
1
syn
non-polymer
18.015
water
99
nat
water
AMP nucleosidase,CMP nucleosidase,GMP nucleosidase,IMP nucleosidase,UMP nucleosidase,dTMP nucleosidase
no
no
RGSHHHHHHTDPALRAITHISPLGSMDMLSQLEVDMLKRTASSDLYQLFRNCSLAVLNSGSLTDNSKELLSRFENFDINV
LRRERGVKLELINPPEEAFVDGRIIRALQANLFAVLRDILFVYGQIHNTVRFPNLNLDNSVHITNLVFSILRNARALHVG
EAPNMVVCWGGHSINENEYLYARRVGNQLGLRELNICTGCGPGAMEAPMKGAAVGHAQQRYKDSRFIGMTEPSIIAAEPP
NPLVNELIIMPDIEKRLEAFVRIAHGIIIFPGGVGTAEELLYLLGILMNPANKDQVLPLILTGPKESADYFRVLDEFVVH
TLGENARRHYRIIIDDAAEVARQMKKSMPLVKENRRDTGDAYSFNWSMRIAPDLQMPFEPSHENMANLKLYPDQPVEVLA
ADLRRAFSGIVAGNVKEVGIRAIEEFGPYKINGDKEIMRRMDDLLQGFVAQHRMKLPGSAYIPCYEICTGLCGR
RGSHHHHHHTDPALRAITHISPLGSMDMLSQLEVDMLKRTASSDLYQLFRNCSLAVLNSGSLTDNSKELLSRFENFDINV
LRRERGVKLELINPPEEAFVDGRIIRALQANLFAVLRDILFVYGQIHNTVRFPNLNLDNSVHITNLVFSILRNARALHVG
EAPNMVVCWGGHSINENEYLYARRVGNQLGLRELNICTGCGPGAMEAPMKGAAVGHAQQRYKDSRFIGMTEPSIIAAEPP
NPLVNELIIMPDIEKRLEAFVRIAHGIIIFPGGVGTAEELLYLLGILMNPANKDQVLPLILTGPKESADYFRVLDEFVVH
TLGENARRHYRIIIDDAAEVARQMKKSMPLVKENRRDTGDAYSFNWSMRIAPDLQMPFEPSHENMANLKLYPDQPVEVLA
ADLRRAFSGIVAGNVKEVGIRAIEEFGPYKINGDKEIMRRMDDLLQGFVAQHRMKLPGSAYIPCYEICTGLCGR
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
K12
sample
1
474
ppnN, ygdH, b2795, JW2766
83333
Escherichia coli K-12
469008
Escherichia coli BL21(DE3)
plasmid
Biological sequence
1
3.48
64.64
VAPOR DIFFUSION, SITTING DROP
7.0
0.4M KNa tartrate hydrate
277.15
atom_site
citation
citation_author
database_PDB_rev
database_PDB_rev_record
diffrn_source
pdbx_data_processing_status
pdbx_database_proc
citation
citation_author
pdbx_database_proc
citation
database_PDB_rev
database_PDB_rev_record
pdbx_database_proc
citation_author
diffrn_source
chem_comp_atom
chem_comp_bond
database_2
entity_src_gen
pdbx_initial_refinement_model
repository
Initial release
Atomic model
Data collection
Database references
Data collection
Database references
Data collection
Database references
Data collection
Database references
Data collection
Database references
Source and taxonomy
Refinement description
1
0
2019-04-24
2
0
2019-05-01
2
1
2019-05-08
2
2
2019-07-03
2
3
2019-07-31
2
4
2023-09-27
2
5
2024-01-17
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_atom_site.pdbx_auth_atom_name
_citation.country
_citation.journal_abbrev
_citation.journal_id_ASTM
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.pdbx_database_id_DOI
_citation.title
_citation.year
_diffrn_source.pdbx_synchrotron_site
_citation.pdbx_database_id_PubMed
_citation.title
_citation_author.identifier_ORCID
_citation_author.name
_citation.journal_volume
_citation.page_first
_citation_author.name
_diffrn_source.pdbx_synchrotron_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity_src_gen.pdbx_gene_src_scientific_name
Denmark
Danish National Research Foundation
DNRF120
apo form
N
PDBE
Y
PDBE
2018-05-01
REL
REL
0O2
guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
HOH
water
6GFL
PDB
experimental model
PGP
461
2
0O2
0O2
501
A
HOH
66
3
HOH
HOH
601
A
HOH
13
3
HOH
HOH
602
A
HOH
12
3
HOH
HOH
603
A
HOH
60
3
HOH
HOH
604
A
HOH
92
3
HOH
HOH
605
A
HOH
136
3
HOH
HOH
606
A
HOH
101
3
HOH
HOH
607
A
HOH
33
3
HOH
HOH
608
A
HOH
97
3
HOH
HOH
609
A
HOH
126
3
HOH
HOH
610
A
HOH
39
3
HOH
HOH
611
A
HOH
19
3
HOH
HOH
612
A
HOH
153
3
HOH
HOH
613
A
HOH
6
3
HOH
HOH
614
A
HOH
98
3
HOH
HOH
615
A
HOH
93
3
HOH
HOH
616
A
HOH
1
3
HOH
HOH
617
A
HOH
7
3
HOH
HOH
618
A
HOH
9
3
HOH
HOH
619
A
HOH
38
3
HOH
HOH
620
A
HOH
132
3
HOH
HOH
621
A
HOH
75
3
HOH
HOH
622
A
HOH
56
3
HOH
HOH
623
A
HOH
124
3
HOH
HOH
624
A
HOH
2
3
HOH
HOH
625
A
HOH
42
3
HOH
HOH
626
A
HOH
41
3
HOH
HOH
627
A
HOH
118
3
HOH
HOH
628
A
HOH
79
3
HOH
HOH
629
A
HOH
49
3
HOH
HOH
630
A
HOH
111
3
HOH
HOH
631
A
HOH
65
3
HOH
HOH
632
A
HOH
21
3
HOH
HOH
633
A
HOH
43
3
HOH
HOH
634
A
HOH
5
3
HOH
HOH
635
A
HOH
59
3
HOH
HOH
636
A
HOH
120
3
HOH
HOH
637
A
HOH
34
3
HOH
HOH
638
A
HOH
105
3
HOH
HOH
639
A
HOH
122
3
HOH
HOH
640
A
HOH
27
3
HOH
HOH
641
A
HOH
112
3
HOH
HOH
642
A
HOH
4
3
HOH
HOH
643
A
HOH
103
3
HOH
HOH
644
A
HOH
22
3
HOH
HOH
645
A
HOH
78
3
HOH
HOH
646
A
HOH
44
3
HOH
HOH
647
A
HOH
95
3
HOH
HOH
648
A
HOH
113
3
HOH
HOH
649
A
HOH
87
3
HOH
HOH
650
A
HOH
15
3
HOH
HOH
651
A
HOH
14
3
HOH
HOH
652
A
HOH
154
3
HOH
HOH
653
A
HOH
11
3
HOH
HOH
654
A
HOH
23
3
HOH
HOH
655
A
HOH
96
3
HOH
HOH
656
A
HOH
18
3
HOH
HOH
657
A
HOH
144
3
HOH
HOH
658
A
HOH
45
3
HOH
HOH
659
A
HOH
58
3
HOH
HOH
660
A
HOH
114
3
HOH
HOH
661
A
HOH
85
3
HOH
HOH
662
A
HOH
67
3
HOH
HOH
663
A
HOH
53
3
HOH
HOH
664
A
HOH
145
3
HOH
HOH
665
A
HOH
68
3
HOH
HOH
666
A
HOH
91
3
HOH
HOH
667
A
HOH
69
3
HOH
HOH
668
A
HOH
40
3
HOH
HOH
669
A
HOH
28
3
HOH
HOH
670
A
HOH
146
3
HOH
HOH
671
A
HOH
24
3
HOH
HOH
672
A
HOH
148
3
HOH
HOH
673
A
HOH
31
3
HOH
HOH
674
A
HOH
57
3
HOH
HOH
675
A
HOH
72
3
HOH
HOH
676
A
HOH
73
3
HOH
HOH
677
A
HOH
89
3
HOH
HOH
678
A
HOH
135
3
HOH
HOH
679
A
HOH
139
3
HOH
HOH
680
A
HOH
152
3
HOH
HOH
681
A
HOH
29
3
HOH
HOH
682
A
HOH
99
3
HOH
HOH
683
A
HOH
55
3
HOH
HOH
684
A
HOH
88
3
HOH
HOH
685
A
HOH
10
3
HOH
HOH
686
A
HOH
77
3
HOH
HOH
687
A
HOH
37
3
HOH
HOH
688
A
HOH
32
3
HOH
HOH
689
A
HOH
86
3
HOH
HOH
690
A
HOH
149
3
HOH
HOH
691
A
HOH
47
3
HOH
HOH
692
A
HOH
83
3
HOH
HOH
693
A
HOH
100
3
HOH
HOH
694
A
HOH
138
3
HOH
HOH
695
A
HOH
137
3
HOH
HOH
696
A
HOH
141
3
HOH
HOH
697
A
HOH
25
3
HOH
HOH
698
A
HOH
127
3
HOH
HOH
699
A
n
1
-16
A
n
2
-15
A
n
3
-14
A
n
4
-13
A
n
5
-12
A
n
6
-11
A
n
7
-10
A
n
8
-9
A
n
9
-8
A
n
10
-7
A
n
11
-6
A
n
12
-5
A
n
13
-4
A
LEU
-3
n
14
LEU
-3
A
ARG
-2
n
15
ARG
-2
A
ALA
-1
n
16
ALA
-1
A
ILE
1
n
17
ILE
1
A
THR
2
n
18
THR
2
A
HIS
3
n
19
HIS
3
A
ILE
4
n
20
ILE
4
A
SER
5
n
21
SER
5
A
PRO
6
n
22
PRO
6
A
LEU
7
n
23
LEU
7
A
GLY
8
n
24
GLY
8
A
SER
9
n
25
SER
9
A
MET
10
n
26
MET
10
A
ASP
11
n
27
ASP
11
A
MET
12
n
28
MET
12
A
LEU
13
n
29
LEU
13
A
SER
14
n
30
SER
14
A
GLN
15
n
31
GLN
15
A
LEU
16
n
32
LEU
16
A
GLU
17
n
33
GLU
17
A
VAL
18
n
34
VAL
18
A
ASP
19
n
35
ASP
19
A
MET
20
n
36
MET
20
A
LEU
21
n
37
LEU
21
A
LYS
22
n
38
LYS
22
A
ARG
23
n
39
ARG
23
A
THR
24
n
40
THR
24
A
ALA
25
n
41
ALA
25
A
SER
26
n
42
SER
26
A
SER
27
n
43
SER
27
A
ASP
28
n
44
ASP
28
A
LEU
29
n
45
LEU
29
A
TYR
30
n
46
TYR
30
A
GLN
31
n
47
GLN
31
A
LEU
32
n
48
LEU
32
A
PHE
33
n
49
PHE
33
A
ARG
34
n
50
ARG
34
A
ASN
35
n
51
ASN
35
A
CYS
36
n
52
CYS
36
A
SER
37
n
53
SER
37
A
LEU
38
n
54
LEU
38
A
ALA
39
n
55
ALA
39
A
VAL
40
n
56
VAL
40
A
LEU
41
n
57
LEU
41
A
ASN
42
n
58
ASN
42
A
SER
43
n
59
SER
43
A
GLY
44
n
60
GLY
44
A
SER
45
n
61
SER
45
A
LEU
46
n
62
LEU
46
A
THR
47
n
63
THR
47
A
ASP
48
n
64
ASP
48
A
ASN
49
n
65
ASN
49
A
SER
50
n
66
SER
50
A
LYS
51
n
67
LYS
51
A
GLU
52
n
68
GLU
52
A
LEU
53
n
69
LEU
53
A
LEU
54
n
70
LEU
54
A
SER
55
n
71
SER
55
A
ARG
56
n
72
ARG
56
A
PHE
57
n
73
PHE
57
A
GLU
58
n
74
GLU
58
A
ASN
59
n
75
ASN
59
A
PHE
60
n
76
PHE
60
A
ASP
61
n
77
ASP
61
A
ILE
62
n
78
ILE
62
A
ASN
63
n
79
ASN
63
A
VAL
64
n
80
VAL
64
A
LEU
65
n
81
LEU
65
A
ARG
66
n
82
ARG
66
A
ARG
67
n
83
ARG
67
A
GLU
68
n
84
GLU
68
A
ARG
69
n
85
ARG
69
A
GLY
70
n
86
GLY
70
A
VAL
71
n
87
VAL
71
A
LYS
72
n
88
LYS
72
A
LEU
73
n
89
LEU
73
A
GLU
74
n
90
GLU
74
A
LEU
75
n
91
LEU
75
A
ILE
76
n
92
ILE
76
A
ASN
77
n
93
ASN
77
A
PRO
78
n
94
PRO
78
A
PRO
79
n
95
PRO
79
A
GLU
80
n
96
GLU
80
A
GLU
81
n
97
GLU
81
A
ALA
82
n
98
ALA
82
A
PHE
83
n
99
PHE
83
A
VAL
84
n
100
VAL
84
A
ASP
85
n
101
ASP
85
A
GLY
86
n
102
GLY
86
A
ARG
87
n
103
ARG
87
A
ILE
88
n
104
ILE
88
A
ILE
89
n
105
ILE
89
A
ARG
90
n
106
ARG
90
A
ALA
91
n
107
ALA
91
A
LEU
92
n
108
LEU
92
A
GLN
93
n
109
GLN
93
A
ALA
94
n
110
ALA
94
A
ASN
95
n
111
ASN
95
A
LEU
96
n
112
LEU
96
A
PHE
97
n
113
PHE
97
A
ALA
98
n
114
ALA
98
A
VAL
99
n
115
VAL
99
A
LEU
100
n
116
LEU
100
A
ARG
101
n
117
ARG
101
A
ASP
102
n
118
ASP
102
A
ILE
103
n
119
ILE
103
A
LEU
104
n
120
LEU
104
A
PHE
105
n
121
PHE
105
A
VAL
106
n
122
VAL
106
A
TYR
107
n
123
TYR
107
A
GLY
108
n
124
GLY
108
A
GLN
109
n
125
GLN
109
A
ILE
110
n
126
ILE
110
A
HIS
111
n
127
HIS
111
A
ASN
112
n
128
ASN
112
A
THR
113
n
129
THR
113
A
VAL
114
n
130
VAL
114
A
ARG
115
n
131
ARG
115
A
PHE
116
n
132
PHE
116
A
PRO
117
n
133
PRO
117
A
ASN
118
n
134
ASN
118
A
LEU
119
n
135
LEU
119
A
ASN
120
n
136
ASN
120
A
LEU
121
n
137
LEU
121
A
ASP
122
n
138
ASP
122
A
ASN
123
n
139
ASN
123
A
SER
124
n
140
SER
124
A
VAL
125
n
141
VAL
125
A
HIS
126
n
142
HIS
126
A
ILE
127
n
143
ILE
127
A
THR
128
n
144
THR
128
A
ASN
129
n
145
ASN
129
A
LEU
130
n
146
LEU
130
A
VAL
131
n
147
VAL
131
A
PHE
132
n
148
PHE
132
A
SER
133
n
149
SER
133
A
ILE
134
n
150
ILE
134
A
LEU
135
n
151
LEU
135
A
ARG
136
n
152
ARG
136
A
ASN
137
n
153
ASN
137
A
ALA
138
n
154
ALA
138
A
ARG
139
n
155
ARG
139
A
ALA
140
n
156
ALA
140
A
LEU
141
n
157
LEU
141
A
HIS
142
n
158
HIS
142
A
VAL
143
n
159
VAL
143
A
GLY
144
n
160
GLY
144
A
GLU
145
n
161
GLU
145
A
ALA
146
n
162
ALA
146
A
PRO
147
n
163
PRO
147
A
ASN
148
n
164
ASN
148
A
MET
149
n
165
MET
149
A
VAL
150
n
166
VAL
150
A
VAL
151
n
167
VAL
151
A
CYS
152
n
168
CYS
152
A
TRP
153
n
169
TRP
153
A
GLY
154
n
170
GLY
154
A
GLY
155
n
171
GLY
155
A
HIS
156
n
172
HIS
156
A
SER
157
n
173
SER
157
A
ILE
158
n
174
ILE
158
A
ASN
159
n
175
ASN
159
A
GLU
160
n
176
GLU
160
A
ASN
161
n
177
ASN
161
A
GLU
162
n
178
GLU
162
A
TYR
163
n
179
TYR
163
A
LEU
164
n
180
LEU
164
A
TYR
165
n
181
TYR
165
A
ALA
166
n
182
ALA
166
A
ARG
167
n
183
ARG
167
A
ARG
168
n
184
ARG
168
A
VAL
169
n
185
VAL
169
A
GLY
170
n
186
GLY
170
A
ASN
171
n
187
ASN
171
A
GLN
172
n
188
GLN
172
A
LEU
173
n
189
LEU
173
A
GLY
174
n
190
GLY
174
A
LEU
175
n
191
LEU
175
A
ARG
176
n
192
ARG
176
A
GLU
177
n
193
GLU
177
A
LEU
178
n
194
LEU
178
A
ASN
179
n
195
ASN
179
A
ILE
180
n
196
ILE
180
A
CYS
181
n
197
CYS
181
A
THR
182
n
198
THR
182
A
GLY
183
n
199
GLY
183
A
CYS
184
n
200
CYS
184
A
GLY
185
n
201
GLY
185
A
PRO
186
n
202
PRO
186
A
GLY
187
n
203
GLY
187
A
ALA
188
n
204
ALA
188
A
MET
189
n
205
MET
189
A
GLU
190
n
206
GLU
190
A
ALA
191
n
207
ALA
191
A
PRO
192
n
208
PRO
192
A
MET
193
n
209
MET
193
A
LYS
194
n
210
LYS
194
A
GLY
195
n
211
GLY
195
A
ALA
196
n
212
ALA
196
A
ALA
197
n
213
ALA
197
A
VAL
198
n
214
VAL
198
A
GLY
199
n
215
GLY
199
A
HIS
200
n
216
HIS
200
A
ALA
201
n
217
ALA
201
A
GLN
202
n
218
GLN
202
A
GLN
203
n
219
GLN
203
A
ARG
204
n
220
ARG
204
A
TYR
205
n
221
TYR
205
A
LYS
206
n
222
LYS
206
A
ASP
207
n
223
ASP
207
A
SER
208
n
224
SER
208
A
ARG
209
n
225
ARG
209
A
PHE
210
n
226
PHE
210
A
ILE
211
n
227
ILE
211
A
GLY
212
n
228
GLY
212
A
MET
213
n
229
MET
213
A
THR
214
n
230
THR
214
A
GLU
215
n
231
GLU
215
A
PRO
216
n
232
PRO
216
A
SER
217
n
233
SER
217
A
ILE
218
n
234
ILE
218
A
ILE
219
n
235
ILE
219
A
ALA
220
n
236
ALA
220
A
ALA
221
n
237
ALA
221
A
GLU
222
n
238
GLU
222
A
PRO
223
n
239
PRO
223
A
PRO
224
n
240
PRO
224
A
ASN
225
n
241
ASN
225
A
PRO
226
n
242
PRO
226
A
LEU
227
n
243
LEU
227
A
VAL
228
n
244
VAL
228
A
ASN
229
n
245
ASN
229
A
GLU
230
n
246
GLU
230
A
LEU
231
n
247
LEU
231
A
ILE
232
n
248
ILE
232
A
ILE
233
n
249
ILE
233
A
MET
234
n
250
MET
234
A
PRO
235
n
251
PRO
235
A
ASP
236
n
252
ASP
236
A
ILE
237
n
253
ILE
237
A
GLU
238
n
254
GLU
238
A
LYS
239
n
255
LYS
239
A
ARG
240
n
256
ARG
240
A
LEU
241
n
257
LEU
241
A
GLU
242
n
258
GLU
242
A
ALA
243
n
259
ALA
243
A
PHE
244
n
260
PHE
244
A
VAL
245
n
261
VAL
245
A
ARG
246
n
262
ARG
246
A
ILE
247
n
263
ILE
247
A
ALA
248
n
264
ALA
248
A
HIS
249
n
265
HIS
249
A
GLY
250
n
266
GLY
250
A
ILE
251
n
267
ILE
251
A
ILE
252
n
268
ILE
252
A
ILE
253
n
269
ILE
253
A
PHE
254
n
270
PHE
254
A
PRO
255
n
271
PRO
255
A
GLY
256
n
272
GLY
256
A
GLY
257
n
273
GLY
257
A
VAL
258
n
274
VAL
258
A
GLY
259
n
275
GLY
259
A
THR
260
n
276
THR
260
A
ALA
261
n
277
ALA
261
A
GLU
262
n
278
GLU
262
A
GLU
263
n
279
GLU
263
A
LEU
264
n
280
LEU
264
A
LEU
265
n
281
LEU
265
A
TYR
266
n
282
TYR
266
A
LEU
267
n
283
LEU
267
A
LEU
268
n
284
LEU
268
A
GLY
269
n
285
GLY
269
A
ILE
270
n
286
ILE
270
A
LEU
271
n
287
LEU
271
A
MET
272
n
288
MET
272
A
ASN
273
n
289
ASN
273
A
PRO
274
n
290
PRO
274
A
ALA
275
n
291
ALA
275
A
ASN
276
n
292
ASN
276
A
LYS
277
n
293
LYS
277
A
ASP
278
n
294
ASP
278
A
GLN
279
n
295
GLN
279
A
VAL
280
n
296
VAL
280
A
LEU
281
n
297
LEU
281
A
PRO
282
n
298
PRO
282
A
LEU
283
n
299
LEU
283
A
ILE
284
n
300
ILE
284
A
LEU
285
n
301
LEU
285
A
THR
286
n
302
THR
286
A
GLY
287
n
303
GLY
287
A
PRO
288
n
304
PRO
288
A
LYS
289
n
305
LYS
289
A
GLU
290
n
306
GLU
290
A
SER
291
n
307
SER
291
A
ALA
292
n
308
ALA
292
A
ASP
293
n
309
ASP
293
A
TYR
294
n
310
TYR
294
A
PHE
295
n
311
PHE
295
A
ARG
296
n
312
ARG
296
A
VAL
297
n
313
VAL
297
A
LEU
298
n
314
LEU
298
A
ASP
299
n
315
ASP
299
A
GLU
300
n
316
GLU
300
A
PHE
301
n
317
PHE
301
A
VAL
302
n
318
VAL
302
A
VAL
303
n
319
VAL
303
A
HIS
304
n
320
HIS
304
A
THR
305
n
321
THR
305
A
LEU
306
n
322
LEU
306
A
GLY
307
n
323
GLY
307
A
GLU
308
n
324
GLU
308
A
ASN
309
n
325
ASN
309
A
ALA
310
n
326
ALA
310
A
ARG
311
n
327
ARG
311
A
ARG
312
n
328
ARG
312
A
HIS
313
n
329
HIS
313
A
TYR
314
n
330
TYR
314
A
ARG
315
n
331
ARG
315
A
ILE
316
n
332
ILE
316
A
ILE
317
n
333
ILE
317
A
ILE
318
n
334
ILE
318
A
ASP
319
n
335
ASP
319
A
ASP
320
n
336
ASP
320
A
ALA
321
n
337
ALA
321
A
ALA
322
n
338
ALA
322
A
GLU
323
n
339
GLU
323
A
VAL
324
n
340
VAL
324
A
ALA
325
n
341
ALA
325
A
ARG
326
n
342
ARG
326
A
GLN
327
n
343
GLN
327
A
MET
328
n
344
MET
328
A
LYS
329
n
345
LYS
329
A
LYS
330
n
346
LYS
330
A
SER
331
n
347
SER
331
A
MET
332
n
348
MET
332
A
PRO
333
n
349
PRO
333
A
LEU
334
n
350
LEU
334
A
VAL
335
n
351
VAL
335
A
LYS
336
n
352
LYS
336
A
GLU
337
n
353
GLU
337
A
ASN
338
n
354
ASN
338
A
ARG
339
n
355
ARG
339
A
ARG
340
n
356
ARG
340
A
ASP
341
n
357
ASP
341
A
THR
342
n
358
THR
342
A
GLY
343
n
359
GLY
343
A
ASP
344
n
360
ASP
344
A
ALA
345
n
361
ALA
345
A
TYR
346
n
362
TYR
346
A
SER
347
n
363
SER
347
A
PHE
348
n
364
PHE
348
A
ASN
349
n
365
ASN
349
A
TRP
350
n
366
TRP
350
A
SER
351
n
367
SER
351
A
MET
352
n
368
MET
352
A
ARG
353
n
369
ARG
353
A
ILE
354
n
370
ILE
354
A
ALA
355
n
371
ALA
355
A
PRO
356
n
372
PRO
356
A
ASP
357
n
373
ASP
357
A
LEU
358
n
374
LEU
358
A
GLN
359
n
375
GLN
359
A
MET
360
n
376
MET
360
A
PRO
361
n
377
PRO
361
A
PHE
362
n
378
PHE
362
A
GLU
363
n
379
GLU
363
A
PRO
364
n
380
PRO
364
A
SER
365
n
381
SER
365
A
HIS
366
n
382
HIS
366
A
GLU
367
n
383
GLU
367
A
ASN
368
n
384
ASN
368
A
MET
369
n
385
MET
369
A
ALA
370
n
386
ALA
370
A
ASN
371
n
387
ASN
371
A
LEU
372
n
388
LEU
372
A
LYS
373
n
389
LYS
373
A
LEU
374
n
390
LEU
374
A
TYR
375
n
391
TYR
375
A
PRO
376
n
392
PRO
376
A
ASP
377
n
393
ASP
377
A
GLN
378
n
394
GLN
378
A
PRO
379
n
395
PRO
379
A
VAL
380
n
396
VAL
380
A
GLU
381
n
397
GLU
381
A
VAL
382
n
398
VAL
382
A
LEU
383
n
399
LEU
383
A
ALA
384
n
400
ALA
384
A
ALA
385
n
401
ALA
385
A
ASP
386
n
402
ASP
386
A
LEU
387
n
403
LEU
387
A
ARG
388
n
404
ARG
388
A
ARG
389
n
405
ARG
389
A
ALA
390
n
406
ALA
390
A
PHE
391
n
407
PHE
391
A
SER
392
n
408
SER
392
A
GLY
393
n
409
GLY
393
A
ILE
394
n
410
ILE
394
A
VAL
395
n
411
VAL
395
A
ALA
396
n
412
ALA
396
A
GLY
397
n
413
GLY
397
A
ASN
398
n
414
ASN
398
A
VAL
399
n
415
VAL
399
A
LYS
400
n
416
LYS
400
A
GLU
401
n
417
GLU
401
A
VAL
402
n
418
VAL
402
A
GLY
403
n
419
GLY
403
A
ILE
404
n
420
ILE
404
A
ARG
405
n
421
ARG
405
A
ALA
406
n
422
ALA
406
A
ILE
407
n
423
ILE
407
A
GLU
408
n
424
GLU
408
A
GLU
409
n
425
GLU
409
A
PHE
410
n
426
PHE
410
A
GLY
411
n
427
GLY
411
A
PRO
412
n
428
PRO
412
A
TYR
413
n
429
TYR
413
A
LYS
414
n
430
LYS
414
A
ILE
415
n
431
ILE
415
A
ASN
416
n
432
ASN
416
A
GLY
417
n
433
GLY
417
A
ASP
418
n
434
ASP
418
A
LYS
419
n
435
LYS
419
A
GLU
420
n
436
GLU
420
A
ILE
421
n
437
ILE
421
A
MET
422
n
438
MET
422
A
ARG
423
n
439
ARG
423
A
ARG
424
n
440
ARG
424
A
MET
425
n
441
MET
425
A
ASP
426
n
442
ASP
426
A
ASP
427
n
443
ASP
427
A
LEU
428
n
444
LEU
428
A
LEU
429
n
445
LEU
429
A
GLN
430
n
446
GLN
430
A
GLY
431
n
447
GLY
431
A
PHE
432
n
448
PHE
432
A
VAL
433
n
449
VAL
433
A
ALA
434
n
450
ALA
434
A
GLN
435
n
451
GLN
435
A
HIS
436
n
452
HIS
436
A
ARG
437
n
453
ARG
437
A
n
454
438
A
n
455
439
A
n
456
440
A
n
457
441
A
n
458
442
A
n
459
443
A
n
460
444
A
n
461
445
A
n
462
446
A
n
463
447
A
n
464
448
A
n
465
449
A
n
466
450
A
n
467
451
A
n
468
452
A
n
469
453
A
n
470
454
A
n
471
455
A
n
472
456
A
n
473
457
A
n
474
458
A
author_and_software_defined_assembly
PISA
1
monomeric
gel filtration
0
0
21010
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
A
N
ILE
4
A
N
ILE
20
A
O
LEU
73
A
O
LEU
89
A
O
LYS
72
A
O
LYS
88
A
N
LEU
65
A
N
LEU
81
A
N
VAL
84
A
N
VAL
100
A
O
ARG
87
A
O
ARG
103
A
O
ILE
232
A
O
ILE
248
A
N
THR
214
A
N
THR
230
A
O
MET
213
A
O
MET
229
A
N
THR
182
A
N
THR
198
A
O
CYS
181
A
O
CYS
197
A
N
CYS
152
A
N
CYS
168
A
N
VAL
151
A
N
VAL
167
A
O
GLY
250
A
O
GLY
266
A
N
ILE
251
A
N
ILE
267
A
O
ILE
284
A
O
ILE
300
A
N
LEU
285
A
N
LEU
301
A
O
ARG
315
A
O
ARG
331
1
A
HOH
658
C
HOH
1
A
ARG
-16
A
ARG
1
1
Y
1
A
GLY
-15
A
GLY
2
1
Y
1
A
SER
-14
A
SER
3
1
Y
1
A
HIS
-13
A
HIS
4
1
Y
1
A
HIS
-12
A
HIS
5
1
Y
1
A
HIS
-11
A
HIS
6
1
Y
1
A
HIS
-10
A
HIS
7
1
Y
1
A
HIS
-9
A
HIS
8
1
Y
1
A
HIS
-8
A
HIS
9
1
Y
1
A
THR
-7
A
THR
10
1
Y
1
A
ASP
-6
A
ASP
11
1
Y
1
A
PRO
-5
A
PRO
12
1
Y
1
A
ALA
-4
A
ALA
13
1
Y
1
A
MET
438
A
MET
454
1
Y
1
A
LYS
439
A
LYS
455
1
Y
1
A
LEU
440
A
LEU
456
1
Y
1
A
PRO
441
A
PRO
457
1
Y
1
A
GLY
442
A
GLY
458
1
Y
1
A
SER
443
A
SER
459
1
Y
1
A
ALA
444
A
ALA
460
1
Y
1
A
TYR
445
A
TYR
461
1
Y
1
A
ILE
446
A
ILE
462
1
Y
1
A
PRO
447
A
PRO
463
1
Y
1
A
CYS
448
A
CYS
464
1
Y
1
A
TYR
449
A
TYR
465
1
Y
1
A
GLU
450
A
GLU
466
1
Y
1
A
ILE
451
A
ILE
467
1
Y
1
A
CYS
452
A
CYS
468
1
Y
1
A
THR
453
A
THR
469
1
Y
1
A
GLY
454
A
GLY
470
1
Y
1
A
LEU
455
A
LEU
471
1
Y
1
A
CYS
456
A
CYS
472
1
Y
1
A
GLY
457
A
GLY
473
1
Y
1
A
ARG
458
A
ARG
474
1
Y
1
A
A
OG
OE1
SER
GLN
124
359
2.14
1
A
PHE
57
-113.32
72.50
1
A
GLU
81
-57.41
-8.64
1
A
ASN
112
-54.41
102.56
1
A
ASN
118
-54.55
105.00
1
A
ASN
120
-65.55
87.78
1
A
ASN
148
-146.41
14.98
1
A
ASN
371
-92.17
34.39
1
A
ALA
396
-81.77
30.99
1
A
LYS
414
45.10
75.26
0.2319
0.1813
2.77
34.7
19329
99.74
1
FREE R-VALUE
MOLECULAR REPLACEMENT
6GFL
2.77
34.7
99
3610
40
0
3471
84.07
2.77
34.7
6GFM
19332
0.99
0.1421
0.029
0.1451
1
17.45
24.8
99.77
2.704
2.77
2.869
1.35
1907
0.58
0.6416
2.781
1
18.2
99.74
refinement
PHENIX
data reduction
XDS
data scaling
XSCALE
phasing
PHENIX
98
tetragonal
I 41 2 2
I 4bw 2bw
x,y,z
-y+1/2,x,z+3/4
y+1/2,-x,z+3/4
x+1/2,-y,-z+3/4
-x+1/2,y,-z+3/4
-x,-y,z
y,x,-z
-y,-x,-z
x+1/2,y+1/2,z+1/2
-y+1,x+1/2,z+5/4
y+1,-x+1/2,z+5/4
x+1,-y+1/2,-z+5/4
-x+1,y+1/2,-z+5/4
-x+1/2,-y+1/2,z+1/2
y+1/2,x+1/2,-z+1/2
-y+1/2,-x+1/2,-z+1/2
N
Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form)
1
N
N
2
N
N
3
N
N
A
SER
14
A
SER
30
HELX_P
A
ALA
25
A
ALA
41
1
AA1
12
A
SER
26
A
SER
42
HELX_P
A
ASP
28
A
ASP
44
5
AA2
3
A
LEU
29
A
LEU
45
HELX_P
A
LEU
41
A
LEU
57
1
AA3
13
A
ASN
49
A
ASN
65
HELX_P
A
ARG
56
A
ARG
72
1
AA4
8
A
PRO
79
A
PRO
95
HELX_P
A
GLU
81
A
GLU
97
5
AA5
3
A
ILE
89
A
ILE
105
HELX_P
A
LEU
104
A
LEU
120
1
AA6
16
A
VAL
106
A
VAL
122
HELX_P
A
ASN
112
A
ASN
128
1
AA7
7
A
ASN
123
A
ASN
139
HELX_P
A
ALA
138
A
ALA
154
1
AA8
16
A
ASN
159
A
ASN
175
HELX_P
A
LEU
175
A
LEU
191
1
AA9
17
A
PRO
186
A
PRO
202
HELX_P
A
MET
189
A
MET
205
5
AB1
4
A
GLU
190
A
GLU
206
HELX_P
A
GLN
203
A
GLN
219
1
AB2
14
A
GLU
215
A
GLU
231
HELX_P
A
ALA
220
A
ALA
236
1
AB3
6
A
ASP
236
A
ASP
252
HELX_P
A
ALA
248
A
ALA
264
1
AB4
13
A
VAL
258
A
VAL
274
HELX_P
A
MET
272
A
MET
288
1
AB5
15
A
ASN
273
A
ASN
289
HELX_P
A
LYS
277
A
LYS
293
5
AB6
5
A
PRO
288
A
PRO
304
HELX_P
A
GLU
290
A
GLU
306
5
AB7
3
A
SER
291
A
SER
307
HELX_P
A
GLY
307
A
GLY
323
1
AB8
17
A
GLU
308
A
GLU
324
HELX_P
A
TYR
314
A
TYR
330
5
AB9
7
A
ASP
320
A
ASP
336
HELX_P
A
GLY
343
A
GLY
359
1
AC1
24
A
ALA
355
A
ALA
371
HELX_P
A
MET
360
A
MET
376
5
AC2
6
A
SER
365
A
SER
381
HELX_P
A
ASN
371
A
ASN
387
1
AC3
7
A
PRO
379
A
PRO
395
HELX_P
A
ALA
396
A
ALA
412
1
AC4
18
A
GLY
403
A
GLY
419
HELX_P
A
GLU
408
A
GLU
424
1
AC5
6
A
ASP
418
A
ASP
434
HELX_P
A
ALA
434
A
ALA
450
1
AC6
17
HYDROLASE
YgdH, PpnN, allosteric enzyme, nucleotide metabolism, stringent response, antibiotic tolerance, persistence, fluoroquinolone, hydrolase
PPNN_ECOLI
UNP
1
2
P0ADR8
ITHISPLGSMDMLSQLEVDMLKRTASSDLYQLFRNCSLAVLNSGSLTDNSKELLSRFENFDINVLRRERGVKLELINPPE
EAFVDGRIIRALQANLFAVLRDILFVYGQIHNTVRFPNLNLDNSVHITNLVFSILRNARALHVGEAPNMVVCWGGHSINE
NEYLYARRVGNQLGLRELNICTGCGPGAMEAPMKGAAVGHAQQRYKDSRFIGMTEPSIIAAEPPNPLVNELIIMPDIEKR
LEAFVRIAHGIIIFPGGVGTAEELLYLLGILMNPANKDQVLPLILTGPKESADYFRVLDEFVVHTLGENARRHYRIIIDD
AAEVARQMKKSMPLVKENRRDTGDAYSFNWSMRIAPDLQMPFEPSHENMANLKLYPDQPVEVLAADLRRAFSGIVAGNVK
EVGIRAIEEFGPYKINGDKEIMRRMDDLLQGFVAQHRMKLPGSAYIPCYEICT
2
454
6GFM
1
453
P0ADR8
A
1
17
469
1
expression tag
ARG
-16
6GFM
A
P0ADR8
UNP
1
1
expression tag
GLY
-15
6GFM
A
P0ADR8
UNP
2
1
expression tag
SER
-14
6GFM
A
P0ADR8
UNP
3
1
expression tag
HIS
-13
6GFM
A
P0ADR8
UNP
4
1
expression tag
HIS
-12
6GFM
A
P0ADR8
UNP
5
1
expression tag
HIS
-11
6GFM
A
P0ADR8
UNP
6
1
expression tag
HIS
-10
6GFM
A
P0ADR8
UNP
7
1
expression tag
HIS
-9
6GFM
A
P0ADR8
UNP
8
1
expression tag
HIS
-8
6GFM
A
P0ADR8
UNP
9
1
expression tag
THR
-7
6GFM
A
P0ADR8
UNP
10
1
expression tag
ASP
-6
6GFM
A
P0ADR8
UNP
11
1
expression tag
PRO
-5
6GFM
A
P0ADR8
UNP
12
1
expression tag
ALA
-4
6GFM
A
P0ADR8
UNP
13
1
expression tag
LEU
-3
6GFM
A
P0ADR8
UNP
14
1
expression tag
ARG
-2
6GFM
A
P0ADR8
UNP
15
1
expression tag
ALA
-1
6GFM
A
P0ADR8
UNP
16
1
expression tag
GLY
454
6GFM
A
P0ADR8
UNP
470
1
expression tag
LEU
455
6GFM
A
P0ADR8
UNP
471
1
expression tag
CYS
456
6GFM
A
P0ADR8
UNP
472
1
expression tag
GLY
457
6GFM
A
P0ADR8
UNP
473
1
expression tag
ARG
458
6GFM
A
P0ADR8
UNP
474
3
2
7
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
parallel
parallel
parallel
parallel
A
ILE
1
A
ILE
17
A
ILE
4
A
ILE
20
A
VAL
71
A
VAL
87
A
ILE
76
A
ILE
92
A
ASP
61
A
ASP
77
A
ARG
66
A
ARG
82
A
PHE
83
A
PHE
99
A
VAL
84
A
VAL
100
A
ARG
87
A
ARG
103
A
ILE
88
A
ILE
104
A
GLU
230
A
GLU
246
A
ILE
233
A
ILE
249
A
PHE
210
A
PHE
226
A
THR
214
A
THR
230
A
ASN
179
A
ASN
195
A
THR
182
A
THR
198
A
MET
149
A
MET
165
A
TRP
153
A
TRP
169
A
GLY
250
A
GLY
266
A
ILE
253
A
ILE
269
A
LEU
283
A
LEU
299
A
GLY
287
A
GLY
303
A
ARG
315
A
ARG
331
A
ILE
318
A
ILE
334
binding site for residue 0O2 A 501
A
0O2
501
Software
17
A
ARG
67
A
ARG
83
17
15_554
A
ARG
69
A
ARG
85
17
15_554
A
LYS
72
A
LYS
88
17
15_554
A
GLY
144
A
GLY
160
17
1_555
A
ARG
339
A
ARG
355
17
1_555
A
ARG
340
A
ARG
356
17
1_555
A
GLY
343
A
GLY
359
17
1_555
A
ASP
344
A
ASP
360
17
1_555
A
ALA
345
A
ALA
361
17
1_555
A
TYR
346
A
TYR
362
17
1_555
A
HOH
601
C
HOH
17
1_555
A
HOH
609
C
HOH
17
1_555
A
HOH
616
C
HOH
17
1_555
A
HOH
628
C
HOH
17
1_555
A
HOH
636
C
HOH
17
1_555
A
HOH
639
C
HOH
17
1_555
A
HOH
654
C
HOH
17
1_555
98
I 41 2 2
I 4bw 2bw