0.009535
0.005505
0.000000
0.000000
0.011010
0.000000
0.000000
0.000000
0.014198
0.00000
0.00000
0.00000
Yanagisawa, T.
Sumida, T.
Ishii, R.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
104.876
104.876
70.433
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C10 H17 N6 O12 P3
506.196
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
non-polymer
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
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
P
N
15
N
O
N
16
N
O
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
N
N
22
N
P
N
23
N
O
N
24
N
O
N
25
N
O
N
26
N
O
N
27
N
C
N
28
R
C
N
29
N
O
N
30
S
C
N
31
N
O
N
32
R
C
N
33
N
O
N
34
R
C
Y
35
N
N
Y
36
N
C
Y
37
N
N
Y
38
N
C
Y
39
N
C
N
40
N
N
Y
41
N
N
Y
42
N
C
Y
43
N
N
Y
44
N
C
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
H
N
60
N
H
N
61
N
H
N
62
N
N
N
63
S
C
N
64
N
C
N
65
N
O
N
66
N
C
N
67
N
C
N
68
N
C
N
69
N
N
N
70
N
C
N
71
N
N
N
72
N
N
N
73
N
O
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
N
N
107
S
C
N
108
N
C
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
N
N
123
R
C
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
S
N
128
N
O
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
N
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
H
N
156
N
N
N
157
S
C
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
C
N
162
N
C
N
163
N
O
N
164
N
O
N
165
N
O
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
N
N
176
N
C
N
177
N
C
N
178
N
O
N
179
N
O
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
S
C
N
187
N
C
N
188
N
O
N
189
N
C
Y
190
N
C
Y
191
N
N
Y
192
N
C
Y
193
N
C
Y
194
N
N
N
195
N
O
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
H
N
205
N
H
N
206
N
O
N
207
N
H
N
208
N
H
N
209
N
N
N
210
S
C
N
211
N
C
N
212
N
O
N
213
S
C
N
214
N
C
N
215
N
C
N
216
N
C
N
217
N
O
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
C
N
239
N
O
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
H
N
252
N
H
N
253
N
N
N
254
S
C
N
255
N
C
N
256
N
O
N
257
N
C
N
258
N
C
N
259
N
C
N
260
N
C
N
261
N
N
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
N
N
279
S
C
N
280
N
C
N
281
N
O
N
282
N
C
N
283
N
C
N
284
N
S
N
285
N
C
N
286
N
O
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
MG
N
299
N
N
N
300
S
C
N
301
N
C
N
302
N
O
N
303
N
C
Y
304
N
C
Y
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
N
310
N
O
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
N
327
N
C
N
328
N
C
N
329
N
O
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
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
N
C
N
344
N
O
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
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
R
C
N
358
N
O
N
359
N
C
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
N
N
371
S
C
N
372
N
C
N
373
N
O
N
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
N
Y
379
N
C
Y
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
N
384
N
O
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
N
N
398
S
C
N
399
N
C
N
400
N
O
N
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
N
408
N
O
N
409
N
O
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
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
N
N
422
S
C
N
423
N
C
N
424
N
O
N
425
N
C
N
426
N
C
N
427
N
C
N
428
N
O
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
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
doub
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
doub
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
sing
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
sing
N
46
N
sing
N
47
N
sing
Y
48
N
sing
Y
49
N
sing
Y
50
N
doub
N
51
N
sing
Y
52
N
sing
Y
53
N
sing
Y
54
N
doub
N
55
N
sing
Y
56
N
doub
N
57
N
sing
N
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
doub
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
doub
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
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
doub
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
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
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
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
sing
N
158
N
doub
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
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
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
Y
190
N
sing
Y
191
N
doub
Y
192
N
doub
N
193
N
sing
Y
194
N
sing
N
195
N
sing
Y
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
doub
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
doub
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
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
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
doub
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
Y
298
N
doub
Y
299
N
sing
Y
300
N
sing
N
301
N
sing
Y
302
N
doub
N
303
N
sing
Y
304
N
doub
N
305
N
sing
Y
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
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
doub
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
doub
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
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
doub
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
Y
367
N
doub
Y
368
N
sing
Y
369
N
sing
N
370
N
sing
Y
371
N
doub
Y
372
N
sing
Y
373
N
sing
N
374
N
sing
Y
375
N
sing
Y
376
N
doub
N
377
N
sing
Y
378
N
doub
N
379
N
sing
Y
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
doub
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
Y
395
N
doub
Y
396
N
sing
Y
397
N
sing
N
398
N
sing
Y
399
N
doub
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
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
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
doub
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
sing
N
425
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
69
5
15
10.1107/S0907444912039881
23275158
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
2013
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
378
634
652
10.1016/j.jmb.2008.02.045
18387634
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
2008
10.2210/pdb3vqv/pdb
pdb_00003vqv
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
CCD
2005-02-19
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
AR-NW12A
Photon Factory
1.0000
SYNCHROTRON
PHOTON FACTORY BEAMLINE AR-NW12A
33344.164
Pyrrolysine--tRNA ligase
6.1.1.26
E444G
1
man
polymer
506.196
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
1
syn
non-polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
246
nat
water
Pyrrolysyl-tRNA synthetase, PylRS
no
no
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
A
RSGI-trt001000322.1
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
JCM9314
sample
pylS
2209
Methanosarcina mazei
562
Escherichia coli
BL21(DE3) codon plus
plasmid
pET28c
1
3.35
63.32
VAPOR DIFFUSION, HANGING DROP
6.8
Na/Cacodylate, MgCl2, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-01-02
1
1
2013-09-04
1
2
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
2013-01-02
SPRSDE
Y
PDBJ
Y
PDBJ
2012-04-01
REL
REL
ANP
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
MG
MAGNESIUM ION
HOH
water
A SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSARCINA MAZEI JCM9314)
DOES NOT CURRENTLY EXIST.
THIS SEQUENCE CONTAINS 21 A.A. N-TERMINAL TAGS
AND C-TERMINAL DOMAIN(RESIDUES 185-454) OF PYLRS. AND THIS PROTEIN IS E444G MUTANT.
3VQW
PDB
experimental model
ACP
301
2
ANP
ANP
501
A
MG
5401
3
MG
MG
502
A
MG
5402
3
MG
MG
503
A
HOH
2
4
HOH
HOH
601
A
HOH
3
4
HOH
HOH
602
A
HOH
5
4
HOH
HOH
603
A
HOH
6
4
HOH
HOH
604
A
HOH
7
4
HOH
HOH
605
A
HOH
8
4
HOH
HOH
606
A
HOH
9
4
HOH
HOH
607
A
HOH
10
4
HOH
HOH
608
A
HOH
11
4
HOH
HOH
609
A
HOH
12
4
HOH
HOH
610
A
HOH
13
4
HOH
HOH
611
A
HOH
14
4
HOH
HOH
612
A
HOH
15
4
HOH
HOH
613
A
HOH
16
4
HOH
HOH
614
A
HOH
17
4
HOH
HOH
615
A
HOH
18
4
HOH
HOH
616
A
HOH
19
4
HOH
HOH
617
A
HOH
20
4
HOH
HOH
618
A
HOH
21
4
HOH
HOH
619
A
HOH
22
4
HOH
HOH
620
A
HOH
23
4
HOH
HOH
621
A
HOH
24
4
HOH
HOH
622
A
HOH
25
4
HOH
HOH
623
A
HOH
26
4
HOH
HOH
624
A
HOH
27
4
HOH
HOH
625
A
HOH
28
4
HOH
HOH
626
A
HOH
29
4
HOH
HOH
627
A
HOH
30
4
HOH
HOH
628
A
HOH
31
4
HOH
HOH
629
A
HOH
32
4
HOH
HOH
630
A
HOH
34
4
HOH
HOH
631
A
HOH
35
4
HOH
HOH
632
A
HOH
36
4
HOH
HOH
633
A
HOH
37
4
HOH
HOH
634
A
HOH
38
4
HOH
HOH
635
A
HOH
39
4
HOH
HOH
636
A
HOH
41
4
HOH
HOH
637
A
HOH
42
4
HOH
HOH
638
A
HOH
43
4
HOH
HOH
639
A
HOH
44
4
HOH
HOH
640
A
HOH
45
4
HOH
HOH
641
A
HOH
46
4
HOH
HOH
642
A
HOH
47
4
HOH
HOH
643
A
HOH
48
4
HOH
HOH
644
A
HOH
49
4
HOH
HOH
645
A
HOH
50
4
HOH
HOH
646
A
HOH
51
4
HOH
HOH
647
A
HOH
52
4
HOH
HOH
648
A
HOH
53
4
HOH
HOH
649
A
HOH
54
4
HOH
HOH
650
A
HOH
55
4
HOH
HOH
651
A
HOH
56
4
HOH
HOH
652
A
HOH
57
4
HOH
HOH
653
A
HOH
58
4
HOH
HOH
654
A
HOH
59
4
HOH
HOH
655
A
HOH
60
4
HOH
HOH
656
A
HOH
61
4
HOH
HOH
657
A
HOH
62
4
HOH
HOH
658
A
HOH
63
4
HOH
HOH
659
A
HOH
64
4
HOH
HOH
660
A
HOH
65
4
HOH
HOH
661
A
HOH
66
4
HOH
HOH
662
A
HOH
67
4
HOH
HOH
663
A
HOH
69
4
HOH
HOH
664
A
HOH
70
4
HOH
HOH
665
A
HOH
71
4
HOH
HOH
666
A
HOH
72
4
HOH
HOH
667
A
HOH
73
4
HOH
HOH
668
A
HOH
74
4
HOH
HOH
669
A
HOH
75
4
HOH
HOH
670
A
HOH
76
4
HOH
HOH
671
A
HOH
77
4
HOH
HOH
672
A
HOH
78
4
HOH
HOH
673
A
HOH
79
4
HOH
HOH
674
A
HOH
80
4
HOH
HOH
675
A
HOH
81
4
HOH
HOH
676
A
HOH
82
4
HOH
HOH
677
A
HOH
83
4
HOH
HOH
678
A
HOH
84
4
HOH
HOH
679
A
HOH
85
4
HOH
HOH
680
A
HOH
86
4
HOH
HOH
681
A
HOH
87
4
HOH
HOH
682
A
HOH
88
4
HOH
HOH
683
A
HOH
89
4
HOH
HOH
684
A
HOH
90
4
HOH
HOH
685
A
HOH
91
4
HOH
HOH
686
A
HOH
92
4
HOH
HOH
687
A
HOH
93
4
HOH
HOH
688
A
HOH
94
4
HOH
HOH
689
A
HOH
95
4
HOH
HOH
690
A
HOH
96
4
HOH
HOH
691
A
HOH
97
4
HOH
HOH
692
A
HOH
98
4
HOH
HOH
693
A
HOH
99
4
HOH
HOH
694
A
HOH
100
4
HOH
HOH
695
A
HOH
101
4
HOH
HOH
696
A
HOH
102
4
HOH
HOH
697
A
HOH
103
4
HOH
HOH
698
A
HOH
104
4
HOH
HOH
699
A
HOH
105
4
HOH
HOH
700
A
HOH
107
4
HOH
HOH
701
A
HOH
108
4
HOH
HOH
702
A
HOH
110
4
HOH
HOH
703
A
HOH
111
4
HOH
HOH
704
A
HOH
112
4
HOH
HOH
705
A
HOH
113
4
HOH
HOH
706
A
HOH
114
4
HOH
HOH
707
A
HOH
115
4
HOH
HOH
708
A
HOH
116
4
HOH
HOH
709
A
HOH
117
4
HOH
HOH
710
A
HOH
118
4
HOH
HOH
711
A
HOH
120
4
HOH
HOH
712
A
HOH
121
4
HOH
HOH
713
A
HOH
123
4
HOH
HOH
714
A
HOH
124
4
HOH
HOH
715
A
HOH
125
4
HOH
HOH
716
A
HOH
126
4
HOH
HOH
717
A
HOH
127
4
HOH
HOH
718
A
HOH
128
4
HOH
HOH
719
A
HOH
129
4
HOH
HOH
720
A
HOH
130
4
HOH
HOH
721
A
HOH
131
4
HOH
HOH
722
A
HOH
132
4
HOH
HOH
723
A
HOH
133
4
HOH
HOH
724
A
HOH
134
4
HOH
HOH
725
A
HOH
135
4
HOH
HOH
726
A
HOH
136
4
HOH
HOH
727
A
HOH
137
4
HOH
HOH
728
A
HOH
138
4
HOH
HOH
729
A
HOH
139
4
HOH
HOH
730
A
HOH
141
4
HOH
HOH
731
A
HOH
142
4
HOH
HOH
732
A
HOH
147
4
HOH
HOH
733
A
HOH
148
4
HOH
HOH
734
A
HOH
150
4
HOH
HOH
735
A
HOH
152
4
HOH
HOH
736
A
HOH
153
4
HOH
HOH
737
A
HOH
155
4
HOH
HOH
738
A
HOH
156
4
HOH
HOH
739
A
HOH
159
4
HOH
HOH
740
A
HOH
160
4
HOH
HOH
741
A
HOH
163
4
HOH
HOH
742
A
HOH
164
4
HOH
HOH
743
A
HOH
165
4
HOH
HOH
744
A
HOH
167
4
HOH
HOH
745
A
HOH
168
4
HOH
HOH
746
A
HOH
171
4
HOH
HOH
747
A
HOH
172
4
HOH
HOH
748
A
HOH
174
4
HOH
HOH
749
A
HOH
175
4
HOH
HOH
750
A
HOH
176
4
HOH
HOH
751
A
HOH
177
4
HOH
HOH
752
A
HOH
178
4
HOH
HOH
753
A
HOH
179
4
HOH
HOH
754
A
HOH
182
4
HOH
HOH
755
A
HOH
185
4
HOH
HOH
756
A
HOH
188
4
HOH
HOH
757
A
HOH
190
4
HOH
HOH
758
A
HOH
192
4
HOH
HOH
759
A
HOH
193
4
HOH
HOH
760
A
HOH
199
4
HOH
HOH
761
A
HOH
200
4
HOH
HOH
762
A
HOH
203
4
HOH
HOH
763
A
HOH
205
4
HOH
HOH
764
A
HOH
209
4
HOH
HOH
765
A
HOH
213
4
HOH
HOH
766
A
HOH
214
4
HOH
HOH
767
A
HOH
215
4
HOH
HOH
768
A
HOH
217
4
HOH
HOH
769
A
HOH
222
4
HOH
HOH
770
A
HOH
223
4
HOH
HOH
771
A
HOH
233
4
HOH
HOH
772
A
HOH
237
4
HOH
HOH
773
A
HOH
238
4
HOH
HOH
774
A
HOH
239
4
HOH
HOH
775
A
HOH
241
4
HOH
HOH
776
A
HOH
243
4
HOH
HOH
777
A
HOH
246
4
HOH
HOH
778
A
HOH
247
4
HOH
HOH
779
A
HOH
250
4
HOH
HOH
780
A
HOH
251
4
HOH
HOH
781
A
HOH
252
4
HOH
HOH
782
A
HOH
253
4
HOH
HOH
783
A
HOH
254
4
HOH
HOH
784
A
HOH
255
4
HOH
HOH
785
A
HOH
256
4
HOH
HOH
786
A
HOH
257
4
HOH
HOH
787
A
HOH
258
4
HOH
HOH
788
A
HOH
259
4
HOH
HOH
789
A
HOH
260
4
HOH
HOH
790
A
HOH
261
4
HOH
HOH
791
A
HOH
262
4
HOH
HOH
792
A
HOH
263
4
HOH
HOH
793
A
HOH
264
4
HOH
HOH
794
A
HOH
265
4
HOH
HOH
795
A
HOH
266
4
HOH
HOH
796
A
HOH
267
4
HOH
HOH
797
A
HOH
268
4
HOH
HOH
798
A
HOH
269
4
HOH
HOH
799
A
HOH
270
4
HOH
HOH
800
A
HOH
272
4
HOH
HOH
801
A
HOH
273
4
HOH
HOH
802
A
HOH
274
4
HOH
HOH
803
A
HOH
275
4
HOH
HOH
804
A
HOH
276
4
HOH
HOH
805
A
HOH
277
4
HOH
HOH
806
A
HOH
278
4
HOH
HOH
807
A
HOH
280
4
HOH
HOH
808
A
HOH
282
4
HOH
HOH
809
A
HOH
283
4
HOH
HOH
810
A
HOH
284
4
HOH
HOH
811
A
HOH
285
4
HOH
HOH
812
A
HOH
286
4
HOH
HOH
813
A
HOH
288
4
HOH
HOH
814
A
HOH
289
4
HOH
HOH
815
A
HOH
290
4
HOH
HOH
816
A
HOH
292
4
HOH
HOH
817
A
HOH
293
4
HOH
HOH
818
A
HOH
294
4
HOH
HOH
819
A
HOH
295
4
HOH
HOH
820
A
HOH
296
4
HOH
HOH
821
A
HOH
298
4
HOH
HOH
822
A
HOH
300
4
HOH
HOH
823
A
HOH
304
4
HOH
HOH
824
A
HOH
305
4
HOH
HOH
825
A
HOH
310
4
HOH
HOH
826
A
HOH
312
4
HOH
HOH
827
A
HOH
317
4
HOH
HOH
828
A
HOH
318
4
HOH
HOH
829
A
HOH
319
4
HOH
HOH
830
A
HOH
324
4
HOH
HOH
831
A
HOH
331
4
HOH
HOH
832
A
HOH
333
4
HOH
HOH
833
A
HOH
334
4
HOH
HOH
834
A
HOH
335
4
HOH
HOH
835
A
HOH
337
4
HOH
HOH
836
A
HOH
343
4
HOH
HOH
837
A
HOH
344
4
HOH
HOH
838
A
HOH
348
4
HOH
HOH
839
A
HOH
349
4
HOH
HOH
840
A
HOH
355
4
HOH
HOH
841
A
HOH
358
4
HOH
HOH
842
A
HOH
359
4
HOH
HOH
843
A
HOH
362
4
HOH
HOH
844
A
HOH
367
4
HOH
HOH
845
A
HOH
372
4
HOH
HOH
846
A
n
1
164
A
n
2
165
A
n
3
166
A
n
4
167
A
n
5
168
A
n
6
169
A
n
7
170
A
n
8
171
A
n
9
172
A
n
10
173
A
n
11
174
A
n
12
175
A
n
13
176
A
n
14
177
A
n
15
178
A
n
16
179
A
n
17
180
A
n
18
181
A
n
19
182
A
n
20
183
A
n
21
184
A
n
22
185
A
n
23
186
A
n
24
187
A
PRO
188
n
25
PRO
188
A
ALA
189
n
26
ALA
189
A
LEU
190
n
27
LEU
190
A
THR
191
n
28
THR
191
A
LYS
192
n
29
LYS
192
A
SER
193
n
30
SER
193
A
GLN
194
n
31
GLN
194
A
THR
195
n
32
THR
195
A
ASP
196
n
33
ASP
196
A
ARG
197
n
34
ARG
197
A
LEU
198
n
35
LEU
198
A
GLU
199
n
36
GLU
199
A
VAL
200
n
37
VAL
200
A
LEU
201
n
38
LEU
201
A
LEU
202
n
39
LEU
202
A
ASN
203
n
40
ASN
203
A
PRO
204
n
41
PRO
204
A
LYS
205
n
42
LYS
205
A
ASP
206
n
43
ASP
206
A
GLU
207
n
44
GLU
207
A
n
45
208
A
n
46
209
A
n
47
210
A
n
48
211
A
SER
212
n
49
SER
212
A
GLY
213
n
50
GLY
213
A
LYS
214
n
51
LYS
214
A
PRO
215
n
52
PRO
215
A
PHE
216
n
53
PHE
216
A
ARG
217
n
54
ARG
217
A
GLU
218
n
55
GLU
218
A
LEU
219
n
56
LEU
219
A
GLU
220
n
57
GLU
220
A
SER
221
n
58
SER
221
A
GLU
222
n
59
GLU
222
A
LEU
223
n
60
LEU
223
A
LEU
224
n
61
LEU
224
A
SER
225
n
62
SER
225
A
ARG
226
n
63
ARG
226
A
ARG
227
n
64
ARG
227
A
LYS
228
n
65
LYS
228
A
LYS
229
n
66
LYS
229
A
ASP
230
n
67
ASP
230
A
LEU
231
n
68
LEU
231
A
GLN
232
n
69
GLN
232
A
GLN
233
n
70
GLN
233
A
ILE
234
n
71
ILE
234
A
TYR
235
n
72
TYR
235
A
ALA
236
n
73
ALA
236
A
GLU
237
n
74
GLU
237
A
GLU
238
n
75
GLU
238
A
ARG
239
n
76
ARG
239
A
GLU
240
n
77
GLU
240
A
ASN
241
n
78
ASN
241
A
TYR
242
n
79
TYR
242
A
LEU
243
n
80
LEU
243
A
GLY
244
n
81
GLY
244
A
LYS
245
n
82
LYS
245
A
LEU
246
n
83
LEU
246
A
GLU
247
n
84
GLU
247
A
ARG
248
n
85
ARG
248
A
GLU
249
n
86
GLU
249
A
ILE
250
n
87
ILE
250
A
THR
251
n
88
THR
251
A
ARG
252
n
89
ARG
252
A
PHE
253
n
90
PHE
253
A
PHE
254
n
91
PHE
254
A
VAL
255
n
92
VAL
255
A
ASP
256
n
93
ASP
256
A
ARG
257
n
94
ARG
257
A
GLY
258
n
95
GLY
258
A
PHE
259
n
96
PHE
259
A
LEU
260
n
97
LEU
260
A
GLU
261
n
98
GLU
261
A
ILE
262
n
99
ILE
262
A
LYS
263
n
100
LYS
263
A
SER
264
n
101
SER
264
A
PRO
265
n
102
PRO
265
A
ILE
266
n
103
ILE
266
A
LEU
267
n
104
LEU
267
A
ILE
268
n
105
ILE
268
A
PRO
269
n
106
PRO
269
A
LEU
270
n
107
LEU
270
A
GLU
271
n
108
GLU
271
A
TYR
272
n
109
TYR
272
A
ILE
273
n
110
ILE
273
A
GLU
274
n
111
GLU
274
A
ARG
275
n
112
ARG
275
A
MET
276
n
113
MET
276
A
GLY
277
n
114
GLY
277
A
ILE
278
n
115
ILE
278
A
ASP
279
n
116
ASP
279
A
ASN
280
n
117
ASN
280
A
ASP
281
n
118
ASP
281
A
THR
282
n
119
THR
282
A
GLU
283
n
120
GLU
283
A
LEU
284
n
121
LEU
284
A
SER
285
n
122
SER
285
A
LYS
286
n
123
LYS
286
A
GLN
287
n
124
GLN
287
A
ILE
288
n
125
ILE
288
A
PHE
289
n
126
PHE
289
A
ARG
290
n
127
ARG
290
A
VAL
291
n
128
VAL
291
A
ASP
292
n
129
ASP
292
A
LYS
293
n
130
LYS
293
A
ASN
294
n
131
ASN
294
A
PHE
295
n
132
PHE
295
A
CYS
296
n
133
CYS
296
A
LEU
297
n
134
LEU
297
A
ARG
298
n
135
ARG
298
A
PRO
299
n
136
PRO
299
A
MET
300
n
137
MET
300
A
LEU
301
n
138
LEU
301
A
ALA
302
n
139
ALA
302
A
PRO
303
n
140
PRO
303
A
ASN
304
n
141
ASN
304
A
LEU
305
n
142
LEU
305
A
TYR
306
n
143
TYR
306
A
ASN
307
n
144
ASN
307
A
TYR
308
n
145
TYR
308
A
LEU
309
n
146
LEU
309
A
ARG
310
n
147
ARG
310
A
LYS
311
n
148
LYS
311
A
LEU
312
n
149
LEU
312
A
ASP
313
n
150
ASP
313
A
ARG
314
n
151
ARG
314
A
ALA
315
n
152
ALA
315
A
LEU
316
n
153
LEU
316
A
PRO
317
n
154
PRO
317
A
ASP
318
n
155
ASP
318
A
PRO
319
n
156
PRO
319
A
ILE
320
n
157
ILE
320
A
LYS
321
n
158
LYS
321
A
ILE
322
n
159
ILE
322
A
PHE
323
n
160
PHE
323
A
GLU
324
n
161
GLU
324
A
ILE
325
n
162
ILE
325
A
GLY
326
n
163
GLY
326
A
PRO
327
n
164
PRO
327
A
CYS
328
n
165
CYS
328
A
TYR
329
n
166
TYR
329
A
ARG
330
n
167
ARG
330
A
LYS
331
n
168
LYS
331
A
GLU
332
n
169
GLU
332
A
SER
333
n
170
SER
333
A
ASP
334
n
171
ASP
334
A
GLY
335
n
172
GLY
335
A
LYS
336
n
173
LYS
336
A
GLU
337
n
174
GLU
337
A
HIS
338
n
175
HIS
338
A
LEU
339
n
176
LEU
339
A
GLU
340
n
177
GLU
340
A
GLU
341
n
178
GLU
341
A
PHE
342
n
179
PHE
342
A
THR
343
n
180
THR
343
A
MET
344
n
181
MET
344
A
LEU
345
n
182
LEU
345
A
ASN
346
n
183
ASN
346
A
PHE
347
n
184
PHE
347
A
CYS
348
n
185
CYS
348
A
GLN
349
n
186
GLN
349
A
MET
350
n
187
MET
350
A
GLY
351
n
188
GLY
351
A
SER
352
n
189
SER
352
A
GLY
353
n
190
GLY
353
A
CYS
354
n
191
CYS
354
A
THR
355
n
192
THR
355
A
ARG
356
n
193
ARG
356
A
GLU
357
n
194
GLU
357
A
ASN
358
n
195
ASN
358
A
LEU
359
n
196
LEU
359
A
GLU
360
n
197
GLU
360
A
SER
361
n
198
SER
361
A
ILE
362
n
199
ILE
362
A
ILE
363
n
200
ILE
363
A
THR
364
n
201
THR
364
A
ASP
365
n
202
ASP
365
A
PHE
366
n
203
PHE
366
A
LEU
367
n
204
LEU
367
A
ASN
368
n
205
ASN
368
A
HIS
369
n
206
HIS
369
A
LEU
370
n
207
LEU
370
A
GLY
371
n
208
GLY
371
A
ILE
372
n
209
ILE
372
A
ASP
373
n
210
ASP
373
A
PHE
374
n
211
PHE
374
A
LYS
375
n
212
LYS
375
A
ILE
376
n
213
ILE
376
A
VAL
377
n
214
VAL
377
A
GLY
378
n
215
GLY
378
A
ASP
379
n
216
ASP
379
A
n
217
380
A
n
218
381
A
n
219
382
A
n
220
383
A
n
221
384
A
GLY
385
n
222
GLY
385
A
ASP
386
n
223
ASP
386
A
THR
387
n
224
THR
387
A
LEU
388
n
225
LEU
388
A
ASP
389
n
226
ASP
389
A
VAL
390
n
227
VAL
390
A
MET
391
n
228
MET
391
A
HIS
392
n
229
HIS
392
A
GLY
393
n
230
GLY
393
A
ASP
394
n
231
ASP
394
A
LEU
395
n
232
LEU
395
A
GLU
396
n
233
GLU
396
A
LEU
397
n
234
LEU
397
A
SER
398
n
235
SER
398
A
SER
399
n
236
SER
399
A
ALA
400
n
237
ALA
400
A
VAL
401
n
238
VAL
401
A
VAL
402
n
239
VAL
402
A
GLY
403
n
240
GLY
403
A
PRO
404
n
241
PRO
404
A
ILE
405
n
242
ILE
405
A
PRO
406
n
243
PRO
406
A
LEU
407
n
244
LEU
407
A
ASP
408
n
245
ASP
408
A
ARG
409
n
246
ARG
409
A
GLU
410
n
247
GLU
410
A
TRP
411
n
248
TRP
411
A
GLY
412
n
249
GLY
412
A
ILE
413
n
250
ILE
413
A
ASP
414
n
251
ASP
414
A
LYS
415
n
252
LYS
415
A
PRO
416
n
253
PRO
416
A
TRP
417
n
254
TRP
417
A
ILE
418
n
255
ILE
418
A
GLY
419
n
256
GLY
419
A
ALA
420
n
257
ALA
420
A
GLY
421
n
258
GLY
421
A
PHE
422
n
259
PHE
422
A
GLY
423
n
260
GLY
423
A
LEU
424
n
261
LEU
424
A
GLU
425
n
262
GLU
425
A
ARG
426
n
263
ARG
426
A
LEU
427
n
264
LEU
427
A
LEU
428
n
265
LEU
428
A
LYS
429
n
266
LYS
429
A
VAL
430
n
267
VAL
430
A
LYS
431
n
268
LYS
431
A
HIS
432
n
269
HIS
432
A
ASP
433
n
270
ASP
433
A
PHE
434
n
271
PHE
434
A
LYS
435
n
272
LYS
435
A
ASN
436
n
273
ASN
436
A
ILE
437
n
274
ILE
437
A
LYS
438
n
275
LYS
438
A
ARG
439
n
276
ARG
439
A
ALA
440
n
277
ALA
440
A
ALA
441
n
278
ALA
441
A
ARG
442
n
279
ARG
442
A
SER
443
n
280
SER
443
A
GLY
444
n
281
GLY
444
A
SER
445
n
282
SER
445
A
TYR
446
n
283
TYR
446
A
TYR
447
n
284
TYR
447
A
ASN
448
n
285
ASN
448
A
GLY
449
n
286
GLY
449
A
ILE
450
n
287
ILE
450
A
SER
451
n
288
SER
451
A
THR
452
n
289
THR
452
A
ASN
453
n
290
ASN
453
A
LEU
454
n
291
LEU
454
A
author_and_software_defined_assembly
PISA
2
dimeric
6890
-55
23290
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
GLU
396
A
OE1
GLU
233
1_555
48.6
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
SER
399
A
OG
SER
236
1_555
90.0
A
GLU
396
A
OE1
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
SER
399
A
OG
SER
236
1_555
91.3
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1B
ANP
1_555
99.7
A
GLU
396
A
OE1
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1B
ANP
1_555
104.1
A
SER
399
A
OG
SER
236
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1B
ANP
1_555
164.6
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1A
ANP
1_555
96.1
A
GLU
396
A
OE1
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1A
ANP
1_555
144.7
A
SER
399
A
OG
SER
236
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1A
ANP
1_555
86.7
A
ANP
501
B
O1B
ANP
1_555
A
MG
503
D
MG
MG
1_555
A
ANP
501
B
O1A
ANP
1_555
80.5
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
131.7
A
GLU
396
A
OE1
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
91.1
A
SER
399
A
OG
SER
236
1_555
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
120.6
A
ANP
501
B
O1B
ANP
1_555
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
60.6
A
ANP
501
B
O1A
ANP
1_555
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
120.0
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
ANP
501
B
O2G
ANP
1_555
82.3
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
752
E
O
HOH
1_555
86.3
A
ANP
501
B
O2G
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
752
E
O
HOH
1_555
168.3
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
768
E
O
HOH
1_555
88.2
A
ANP
501
B
O2G
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
768
E
O
HOH
1_555
91.2
A
HOH
752
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
768
E
O
HOH
1_555
90.8
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
772
E
O
HOH
1_555
174.1
A
ANP
501
B
O2G
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
772
E
O
HOH
1_555
94.2
A
HOH
752
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
772
E
O
HOH
1_555
97.4
A
HOH
768
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
772
E
O
HOH
1_555
87.2
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
91.0
A
ANP
501
B
O2G
ANP
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
81.8
A
HOH
752
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
96.1
A
HOH
768
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
173.0
A
HOH
772
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
93.1
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
4_665
-x+1,-y+1,z
crystal symmetry operation
52.4380000000
90.8252802473
0.0000000000
A
N
LEU
260
A
N
LEU
97
A
O
LYS
321
A
O
LYS
158
A
N
CYS
328
A
N
CYS
165
A
O
PHE
342
A
O
PHE
179
A
N
LEU
345
A
N
LEU
182
A
O
PHE
422
A
O
PHE
259
A
O
GLY
419
A
O
GLY
256
A
N
VAL
401
A
N
VAL
238
A
O
LEU
395
A
O
LEU
232
A
N
HIS
392
A
N
HIS
229
A
O
MET
391
A
O
MET
228
A
N
LYS
375
A
N
LYS
212
A
N
ILE
268
A
N
ILE
105
A
O
CYS
296
A
O
CYS
133
A
O
PHE
295
A
O
PHE
132
A
N
VAL
291
A
N
VAL
128
A
N
TYR
447
A
N
TYR
284
A
O
ILE
450
A
O
ILE
287
1
A
MET
164
A
MET
1
1
Y
1
A
GLY
165
A
GLY
2
1
Y
1
A
SER
166
A
SER
3
1
Y
1
A
SER
167
A
SER
4
1
Y
1
A
HIS
168
A
HIS
5
1
Y
1
A
HIS
169
A
HIS
6
1
Y
1
A
HIS
170
A
HIS
7
1
Y
1
A
HIS
171
A
HIS
8
1
Y
1
A
HIS
172
A
HIS
9
1
Y
1
A
HIS
173
A
HIS
10
1
Y
1
A
SER
174
A
SER
11
1
Y
1
A
SER
175
A
SER
12
1
Y
1
A
GLY
176
A
GLY
13
1
Y
1
A
LEU
177
A
LEU
14
1
Y
1
A
VAL
178
A
VAL
15
1
Y
1
A
PRO
179
A
PRO
16
1
Y
1
A
ARG
180
A
ARG
17
1
Y
1
A
GLY
181
A
GLY
18
1
Y
1
A
SER
182
A
SER
19
1
Y
1
A
HIS
183
A
HIS
20
1
Y
1
A
MET
184
A
MET
21
1
Y
1
A
ALA
185
A
ALA
22
1
Y
1
A
SER
186
A
SER
23
1
Y
1
A
ALA
187
A
ALA
24
1
Y
1
A
ILE
208
A
ILE
45
1
Y
1
A
SER
209
A
SER
46
1
Y
1
A
LEU
210
A
LEU
47
1
Y
1
A
ASN
211
A
ASN
48
1
Y
1
A
SER
380
A
SER
217
1
Y
1
A
CYS
381
A
CYS
218
1
Y
1
A
MET
382
A
MET
219
1
Y
1
A
VAL
383
A
VAL
220
1
Y
1
A
TYR
384
A
TYR
221
1
Y
1
A
A
N
O
ASP
HOH
414
845
1.77
1
A
A
O
O
HOH
HOH
638
709
1.98
1
A
A
O
O
HOH
HOH
608
771
1.99
1
A
A
O
O
HOH
HOH
750
814
2.04
1
A
A
O
O
ILE
HOH
413
709
2.09
1
A
A
O
O
HOH
HOH
628
704
2.10
1
-4.25
0.50
120.30
116.05
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
227
227
227
N
1
5.49
0.50
120.30
125.79
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
298
298
298
N
1
-4.31
0.50
120.30
115.99
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
298
298
298
N
1
A
GLU
237
-109.54
-84.45
1
A
ASN
280
-67.73
5.65
1
A
ASP
292
59.63
-158.96
1
A
ILE
413
-84.51
-74.12
1
A
SER
443
-171.06
149.40
38.945
-0.70
-0.35
0.00
-0.70
0.00
1.05
0.967
0.949
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.21910
0.18657
0.18820
1.90
42.07
1750
33041
5.0
100.00
3.400
0.095
RANDOM
1
THROUGHOUT
0
MOLECULAR REPLACEMENT
0.115
0.114
0.80
0.80
1.20
3VQW
MAXIMUM LIKELIHOOD
MASK
1.90
42.07
246
2374
33
0
2095
0.017
0.022
2170
1.706
2.010
2924
6.095
5.000
255
33.637
23.925
107
17.916
15.000
406
20.486
15.000
19
0.120
0.200
316
0.007
0.020
1621
0.225
0.200
945
0.315
0.200
1468
0.225
0.200
184
0.228
0.200
44
0.256
0.200
17
1.186
1.500
1322
2.080
2.000
2074
2.925
3.000
953
4.783
4.500
850
0.358
0.307
1.949
124
2449
20
100.00
1.9
50
3VQV
34806
0.089
1
8
99.8
1.9
1.93
0.45
1
4.9
99.5
data collection
HKL-2000
phasing
MOLREP
refinement
REFMAC
5.2.0019
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AMPPNP (re-refined)
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
A
THR
191
A
THR
28
HELX_P
A
LEU
202
A
LEU
39
1
1
12
A
PRO
215
A
PRO
52
HELX_P
A
GLU
237
A
GLU
74
1
2
23
A
ASN
241
A
ASN
78
HELX_P
A
ARG
257
A
ARG
94
1
3
17
A
LEU
270
A
LEU
107
HELX_P
A
MET
276
A
MET
113
1
4
7
A
GLU
283
A
GLU
120
HELX_P
A
ILE
288
A
ILE
125
5
5
6
A
LEU
301
A
LEU
138
HELX_P
A
ARG
314
A
ARG
151
1
6
14
A
THR
355
A
THR
192
HELX_P
A
GLY
371
A
GLY
208
1
7
17
A
ILE
405
A
ILE
242
HELX_P
A
GLY
412
A
GLY
249
5
8
8
A
LEU
424
A
LEU
261
HELX_P
A
ASP
433
A
ASP
270
1
9
10
A
ASN
436
A
ASN
273
HELX_P
A
ALA
441
A
ALA
278
5
10
6
metalc
2.429
A
GLU
396
A
OE2
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
metalc
2.773
A
GLU
396
A
OE1
GLU
233
1_555
A
MG
503
D
MG
MG
1_555
metalc
2.220
A
SER
399
A
OG
SER
236
1_555
A
MG
503
D
MG
MG
1_555
metalc
2.064
A
ANP
501
B
O2B
ANP
1_555
A
MG
502
C
MG
MG
1_555
metalc
2.108
A
ANP
501
B
O2G
ANP
1_555
A
MG
502
C
MG
MG
1_555
metalc
2.308
A
ANP
501
B
O1B
ANP
1_555
A
MG
503
D
MG
MG
1_555
metalc
2.359
A
ANP
501
B
O1A
ANP
1_555
A
MG
503
D
MG
MG
1_555
metalc
2.104
A
MG
502
C
MG
MG
1_555
A
HOH
752
E
O
HOH
1_555
metalc
2.155
A
MG
502
C
MG
MG
1_555
A
HOH
768
E
O
HOH
1_555
metalc
2.020
A
MG
502
C
MG
MG
1_555
A
HOH
772
E
O
HOH
1_555
metalc
2.181
A
MG
502
C
MG
MG
1_555
A
HOH
779
E
O
HOH
1_555
metalc
2.539
A
MG
503
D
MG
MG
1_555
A
HOH
813
E
O
HOH
1_555
LIGASE
Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, aminoacyl-tRNA synthetase, pyrrolysyl-tRNA synthetase, AMPPNP, LIGASE
A
ASP
318
A
ASP
155
1
A
PRO
319
A
PRO
156
-1.22
A
GLY
403
A
GLY
240
1
A
PRO
404
A
PRO
241
1.56
3VQV
PDB
1
3VQV
164
454
3VQV
164
454
3VQV
A
1
1
291
7
3
2
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
260
A
LEU
97
A
ILE
262
A
ILE
99
A
ILE
320
A
ILE
157
A
TYR
329
A
TYR
166
A
GLU
341
A
GLU
178
A
MET
350
A
MET
187
A
TRP
417
A
TRP
254
A
GLY
423
A
GLY
260
A
LEU
395
A
LEU
232
A
VAL
402
A
VAL
239
A
THR
387
A
THR
224
A
HIS
392
A
HIS
229
A
LYS
375
A
LYS
212
A
VAL
377
A
VAL
214
A
LEU
267
A
LEU
104
A
PRO
269
A
PRO
106
A
PHE
295
A
PHE
132
A
LEU
297
A
LEU
134
A
ARG
290
A
ARG
127
A
VAL
291
A
VAL
128
A
TYR
446
A
TYR
283
A
TYR
447
A
TYR
284
A
ILE
450
A
ILE
287
A
SER
451
A
SER
288
BINDING SITE FOR RESIDUE ANP A 501
A
ANP
501
Software
27
BINDING SITE FOR RESIDUE MG A 502
A
MG
502
Software
5
BINDING SITE FOR RESIDUE MG A 503
A
MG
503
Software
4
A
ARG
330
A
ARG
167
27
1_555
A
GLU
332
A
GLU
169
27
1_555
A
HIS
338
A
HIS
175
27
1_555
A
LEU
339
A
LEU
176
27
1_555
A
PHE
342
A
PHE
179
27
1_555
A
MET
344
A
MET
181
27
1_555
A
GLU
396
A
GLU
233
27
1_555
A
LEU
397
A
LEU
234
27
1_555
A
SER
398
A
SER
235
27
1_555
A
SER
399
A
SER
236
27
1_555
A
GLY
421
A
GLY
258
27
1_555
A
GLY
423
A
GLY
260
27
1_555
A
ARG
426
A
ARG
263
27
1_555
A
MG
502
C
MG
27
1_555
A
MG
503
D
MG
27
1_555
A
HOH
601
E
HOH
27
1_555
A
HOH
602
E
HOH
27
1_555
A
HOH
657
E
HOH
27
1_555
A
HOH
678
E
HOH
27
1_555
A
HOH
752
E
HOH
27
1_555
A
HOH
768
E
HOH
27
1_555
A
HOH
772
E
HOH
27
1_555
A
HOH
779
E
HOH
27
1_555
A
HOH
792
E
HOH
27
1_555
A
HOH
809
E
HOH
27
1_555
A
HOH
813
E
HOH
27
1_555
A
HOH
822
E
HOH
27
1_555
A
ANP
501
B
ANP
5
1_555
A
HOH
752
E
HOH
5
1_555
A
HOH
768
E
HOH
5
1_555
A
HOH
772
E
HOH
5
1_555
A
HOH
779
E
HOH
5
1_555
A
GLU
396
A
GLU
233
4
1_555
A
SER
399
A
SER
236
4
1_555
A
ANP
501
B
ANP
4
1_555
A
HOH
813
E
HOH
4
1_555
172
P 64