0.009550
0.005514
0.000000
0.000000
0.011028
0.000000
0.000000
0.000000
0.014174
0.00000
0.00000
0.00000
Yanagisawa, 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
104.710
104.710
70.550
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
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
C11 H22 N2 O4
246.303
n
N~6~-(tert-butoxycarbonyl)-L-lysine
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
C
N
137
N
O
N
138
N
C
N
139
N
O
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
C
N
242
N
C
N
243
N
C
N
244
N
C
N
245
N
O
N
246
N
C
N
247
N
O
N
248
N
N
N
249
N
C
N
250
N
C
N
251
N
C
N
252
N
C
N
253
S
C
N
254
N
C
N
255
N
O
N
256
N
O
N
257
N
N
N
258
N
H
N
259
N
H
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
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
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
C
N
288
N
O
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
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
N
N
303
S
C
N
304
N
C
N
305
N
O
N
306
N
C
N
307
N
C
N
308
N
C
N
309
N
C
N
310
N
N
N
311
N
O
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
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
N
332
N
C
N
333
N
S
N
334
N
C
N
335
N
O
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
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
MG
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
H
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
H
N
371
N
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
N
376
N
C
N
377
N
C
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
N
N
389
S
C
N
390
N
C
N
391
N
O
N
392
N
C
N
393
N
O
N
394
N
O
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
R
C
N
407
N
O
N
408
N
C
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
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
N
Y
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
C
Y
432
N
C
N
433
N
O
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
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
N
N
447
S
C
N
448
N
C
N
449
N
O
N
450
N
C
Y
451
N
C
Y
452
N
C
Y
453
N
C
Y
454
N
C
Y
455
N
C
Y
456
N
C
N
457
N
O
N
458
N
O
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
N
N
471
S
C
N
472
N
C
N
473
N
O
N
474
N
C
N
475
N
C
N
476
N
C
N
477
N
O
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
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
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
doub
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
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
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
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
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
doub
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
Y
199
N
sing
Y
200
N
doub
Y
201
N
doub
N
202
N
sing
Y
203
N
sing
N
204
N
sing
Y
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
doub
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
doub
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
doub
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
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
doub
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
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
doub
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
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
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
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
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
doub
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
sing
N
379
N
sing
N
380
N
doub
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
sing
N
392
N
sing
N
393
N
doub
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
sing
N
408
N
sing
N
409
N
doub
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
Y
414
N
doub
Y
415
N
sing
Y
416
N
sing
N
417
N
sing
Y
418
N
doub
Y
419
N
sing
Y
420
N
sing
N
421
N
sing
Y
422
N
sing
Y
423
N
doub
N
424
N
sing
Y
425
N
doub
N
426
N
sing
Y
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
N
436
N
sing
N
437
N
doub
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
Y
442
N
doub
Y
443
N
sing
Y
444
N
sing
N
445
N
sing
Y
446
N
doub
N
447
N
sing
Y
448
N
doub
N
449
N
sing
Y
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
sing
N
460
N
sing
N
461
N
doub
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
N
471
N
sing
N
472
N
sing
UK
Chem.Biol.
CBOLE2
2050
1074-5521
15
1187
1197
10.1016/j.chembiol.2008.10.004
19022179
Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification
2008
10.2210/pdb2zin/pdb
pdb_00002zin
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
2004-12-15
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL41XU
SPring-8
1.0000
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
33344.164
Pyrrolysyl-tRNA synthetase
6.1.1.26
1
man
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
506.196
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
1
syn
non-polymer
246.303
N~6~-(tert-butoxycarbonyl)-L-lysine
1
syn
non-polymer
62.068
1,2-ETHANEDIOL
1
syn
non-polymer
18.015
water
217
nat
water
Pyrrolysine--tRNA ligase, PylRS
no
no
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
A
trt001000322.2
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
63.27
VAPOR DIFFUSION, HANGING DROP
7.0
Na/Cacodylate, MgCl2, PEG3350, pH 7.0, 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_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2008-12-02
1
1
2011-07-13
1
2
2023-11-01
_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.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The ligand-free form
The AMPPNP-bound form
The pyrrolysine/AMPPNP-bound form
Y
PDBJ
Y
PDBJ
2008-02-19
REL
REL
MG
MAGNESIUM ION
ANP
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
LBY
N~6~-(tert-butoxycarbonyl)-L-lysine
EDO
1,2-ETHANEDIOL
HOH
water
THIS CONFLICT IS DUE TO THE STRAIN DIFFERENCE
(JCM9314 AND GOE1).
1WK3
PDB
experimental model
MG
701
2
MG
MG
701
A
MG
702
2
MG
MG
702
A
ACP
501
3
ANP
ANP
501
A
DRG
601
4
LBY
LBY
601
A
EDO
2011
5
EDO
EDO
2011
A
TIP
1
6
HOH
HOH
2012
A
TIP
2
6
HOH
HOH
2013
A
TIP
3
6
HOH
HOH
2014
A
TIP
4
6
HOH
HOH
2015
A
TIP
5
6
HOH
HOH
2016
A
TIP
6
6
HOH
HOH
2017
A
TIP
7
6
HOH
HOH
2018
A
TIP
8
6
HOH
HOH
2019
A
TIP
9
6
HOH
HOH
2020
A
TIP
10
6
HOH
HOH
2021
A
TIP
11
6
HOH
HOH
2022
A
TIP
12
6
HOH
HOH
2023
A
TIP
13
6
HOH
HOH
2024
A
TIP
14
6
HOH
HOH
2025
A
TIP
16
6
HOH
HOH
2026
A
TIP
17
6
HOH
HOH
2027
A
TIP
18
6
HOH
HOH
2028
A
TIP
19
6
HOH
HOH
2029
A
TIP
20
6
HOH
HOH
2030
A
TIP
21
6
HOH
HOH
2031
A
TIP
22
6
HOH
HOH
2032
A
TIP
23
6
HOH
HOH
2033
A
TIP
24
6
HOH
HOH
2034
A
TIP
25
6
HOH
HOH
2035
A
TIP
26
6
HOH
HOH
2036
A
TIP
27
6
HOH
HOH
2037
A
TIP
28
6
HOH
HOH
2038
A
TIP
29
6
HOH
HOH
2039
A
TIP
30
6
HOH
HOH
2040
A
TIP
31
6
HOH
HOH
2041
A
TIP
33
6
HOH
HOH
2042
A
TIP
34
6
HOH
HOH
2043
A
TIP
35
6
HOH
HOH
2044
A
TIP
36
6
HOH
HOH
2045
A
TIP
37
6
HOH
HOH
2046
A
TIP
38
6
HOH
HOH
2047
A
TIP
40
6
HOH
HOH
2048
A
TIP
42
6
HOH
HOH
2049
A
TIP
43
6
HOH
HOH
2050
A
TIP
44
6
HOH
HOH
2051
A
TIP
45
6
HOH
HOH
2052
A
TIP
46
6
HOH
HOH
2053
A
TIP
48
6
HOH
HOH
2054
A
TIP
49
6
HOH
HOH
2055
A
TIP
50
6
HOH
HOH
2056
A
TIP
52
6
HOH
HOH
2057
A
TIP
54
6
HOH
HOH
2058
A
TIP
55
6
HOH
HOH
2059
A
TIP
56
6
HOH
HOH
2060
A
TIP
57
6
HOH
HOH
2061
A
TIP
59
6
HOH
HOH
2062
A
TIP
60
6
HOH
HOH
2063
A
TIP
61
6
HOH
HOH
2064
A
TIP
62
6
HOH
HOH
2065
A
TIP
64
6
HOH
HOH
2066
A
TIP
65
6
HOH
HOH
2067
A
TIP
66
6
HOH
HOH
2068
A
TIP
67
6
HOH
HOH
2069
A
TIP
68
6
HOH
HOH
2070
A
TIP
69
6
HOH
HOH
2071
A
TIP
70
6
HOH
HOH
2072
A
TIP
71
6
HOH
HOH
2073
A
TIP
72
6
HOH
HOH
2074
A
TIP
73
6
HOH
HOH
2075
A
TIP
74
6
HOH
HOH
2076
A
TIP
75
6
HOH
HOH
2077
A
TIP
76
6
HOH
HOH
2078
A
TIP
77
6
HOH
HOH
2079
A
TIP
78
6
HOH
HOH
2080
A
TIP
79
6
HOH
HOH
2081
A
TIP
80
6
HOH
HOH
2082
A
TIP
81
6
HOH
HOH
2083
A
TIP
82
6
HOH
HOH
2084
A
TIP
83
6
HOH
HOH
2085
A
TIP
84
6
HOH
HOH
2086
A
TIP
85
6
HOH
HOH
2087
A
TIP
88
6
HOH
HOH
2088
A
TIP
89
6
HOH
HOH
2089
A
TIP
91
6
HOH
HOH
2090
A
TIP
92
6
HOH
HOH
2091
A
TIP
93
6
HOH
HOH
2092
A
TIP
94
6
HOH
HOH
2093
A
TIP
98
6
HOH
HOH
2094
A
TIP
99
6
HOH
HOH
2095
A
TIP
100
6
HOH
HOH
2096
A
TIP
102
6
HOH
HOH
2097
A
TIP
103
6
HOH
HOH
2098
A
TIP
104
6
HOH
HOH
2099
A
TIP
105
6
HOH
HOH
2100
A
TIP
106
6
HOH
HOH
2101
A
TIP
109
6
HOH
HOH
2102
A
TIP
112
6
HOH
HOH
2103
A
TIP
113
6
HOH
HOH
2104
A
TIP
114
6
HOH
HOH
2105
A
TIP
115
6
HOH
HOH
2106
A
TIP
116
6
HOH
HOH
2107
A
TIP
117
6
HOH
HOH
2108
A
TIP
118
6
HOH
HOH
2109
A
TIP
119
6
HOH
HOH
2110
A
TIP
120
6
HOH
HOH
2111
A
TIP
121
6
HOH
HOH
2112
A
TIP
122
6
HOH
HOH
2113
A
TIP
123
6
HOH
HOH
2114
A
TIP
124
6
HOH
HOH
2115
A
TIP
126
6
HOH
HOH
2116
A
TIP
127
6
HOH
HOH
2117
A
TIP
131
6
HOH
HOH
2118
A
TIP
132
6
HOH
HOH
2119
A
TIP
133
6
HOH
HOH
2120
A
TIP
134
6
HOH
HOH
2121
A
TIP
135
6
HOH
HOH
2122
A
TIP
136
6
HOH
HOH
2123
A
TIP
137
6
HOH
HOH
2124
A
TIP
138
6
HOH
HOH
2125
A
TIP
139
6
HOH
HOH
2126
A
TIP
140
6
HOH
HOH
2127
A
TIP
141
6
HOH
HOH
2128
A
TIP
142
6
HOH
HOH
2129
A
TIP
144
6
HOH
HOH
2130
A
TIP
146
6
HOH
HOH
2131
A
TIP
147
6
HOH
HOH
2132
A
TIP
148
6
HOH
HOH
2133
A
TIP
149
6
HOH
HOH
2134
A
TIP
151
6
HOH
HOH
2135
A
TIP
155
6
HOH
HOH
2136
A
TIP
156
6
HOH
HOH
2137
A
TIP
157
6
HOH
HOH
2138
A
TIP
159
6
HOH
HOH
2139
A
TIP
160
6
HOH
HOH
2140
A
TIP
161
6
HOH
HOH
2141
A
TIP
162
6
HOH
HOH
2142
A
TIP
164
6
HOH
HOH
2143
A
TIP
165
6
HOH
HOH
2144
A
TIP
167
6
HOH
HOH
2145
A
TIP
168
6
HOH
HOH
2146
A
TIP
170
6
HOH
HOH
2147
A
TIP
171
6
HOH
HOH
2148
A
TIP
172
6
HOH
HOH
2149
A
TIP
173
6
HOH
HOH
2150
A
TIP
174
6
HOH
HOH
2151
A
TIP
175
6
HOH
HOH
2152
A
TIP
176
6
HOH
HOH
2153
A
TIP
177
6
HOH
HOH
2154
A
TIP
181
6
HOH
HOH
2155
A
TIP
182
6
HOH
HOH
2156
A
TIP
183
6
HOH
HOH
2157
A
TIP
184
6
HOH
HOH
2158
A
TIP
185
6
HOH
HOH
2159
A
TIP
187
6
HOH
HOH
2160
A
TIP
188
6
HOH
HOH
2161
A
TIP
189
6
HOH
HOH
2162
A
TIP
190
6
HOH
HOH
2163
A
TIP
192
6
HOH
HOH
2164
A
TIP
193
6
HOH
HOH
2165
A
TIP
194
6
HOH
HOH
2166
A
TIP
195
6
HOH
HOH
2167
A
TIP
196
6
HOH
HOH
2168
A
TIP
197
6
HOH
HOH
2169
A
TIP
198
6
HOH
HOH
2170
A
TIP
205
6
HOH
HOH
2171
A
TIP
206
6
HOH
HOH
2172
A
TIP
207
6
HOH
HOH
2173
A
TIP
208
6
HOH
HOH
2174
A
TIP
209
6
HOH
HOH
2175
A
TIP
210
6
HOH
HOH
2176
A
TIP
211
6
HOH
HOH
2177
A
TIP
212
6
HOH
HOH
2178
A
TIP
213
6
HOH
HOH
2179
A
TIP
214
6
HOH
HOH
2180
A
TIP
215
6
HOH
HOH
2181
A
TIP
216
6
HOH
HOH
2182
A
TIP
217
6
HOH
HOH
2183
A
TIP
218
6
HOH
HOH
2184
A
TIP
219
6
HOH
HOH
2185
A
TIP
220
6
HOH
HOH
2186
A
TIP
221
6
HOH
HOH
2187
A
TIP
222
6
HOH
HOH
2188
A
TIP
223
6
HOH
HOH
2189
A
TIP
224
6
HOH
HOH
2190
A
TIP
225
6
HOH
HOH
2191
A
TIP
226
6
HOH
HOH
2192
A
TIP
227
6
HOH
HOH
2193
A
TIP
228
6
HOH
HOH
2194
A
TIP
229
6
HOH
HOH
2195
A
TIP
230
6
HOH
HOH
2196
A
TIP
232
6
HOH
HOH
2197
A
TIP
233
6
HOH
HOH
2198
A
TIP
234
6
HOH
HOH
2199
A
TIP
235
6
HOH
HOH
2200
A
TIP
236
6
HOH
HOH
2201
A
TIP
237
6
HOH
HOH
2202
A
TIP
238
6
HOH
HOH
2203
A
TIP
239
6
HOH
HOH
2204
A
TIP
240
6
HOH
HOH
2205
A
TIP
241
6
HOH
HOH
2206
A
TIP
242
6
HOH
HOH
2207
A
TIP
243
6
HOH
HOH
2208
A
TIP
244
6
HOH
HOH
2209
A
TIP
245
6
HOH
HOH
2210
A
TIP
246
6
HOH
HOH
2211
A
TIP
247
6
HOH
HOH
2212
A
TIP
248
6
HOH
HOH
2213
A
TIP
249
6
HOH
HOH
2214
A
TIP
250
6
HOH
HOH
2215
A
TIP
251
6
HOH
HOH
2216
A
TIP
252
6
HOH
HOH
2217
A
TIP
253
6
HOH
HOH
2218
A
TIP
254
6
HOH
HOH
2219
A
TIP
255
6
HOH
HOH
2220
A
TIP
258
6
HOH
HOH
2221
A
TIP
259
6
HOH
HOH
2222
A
TIP
261
6
HOH
HOH
2223
A
TIP
262
6
HOH
HOH
2224
A
TIP
263
6
HOH
HOH
2225
A
TIP
265
6
HOH
HOH
2226
A
TIP
266
6
HOH
HOH
2227
A
TIP
267
6
HOH
HOH
2228
A
n
1
-21
A
n
2
-20
A
n
3
-19
A
n
4
-18
A
n
5
-17
A
n
6
-16
A
n
7
-15
A
n
8
-14
A
n
9
-13
A
n
10
-12
A
n
11
-11
A
n
12
-10
A
n
13
-9
A
n
14
-8
A
n
15
-7
A
n
16
-6
A
n
17
-5
A
n
18
-4
A
n
19
-3
A
n
20
-2
A
n
21
-1
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
7280
-49.0
22940
A
SER
399
A
OG
SER
236
1_555
A
MG
702
C
MG
MG
1_555
A
ANP
501
D
O2B
ANP
1_555
173.2
A
SER
399
A
OG
SER
236
1_555
A
MG
702
C
MG
MG
1_555
A
ANP
501
D
O1A
ANP
1_555
93.7
A
ANP
501
D
O2B
ANP
1_555
A
MG
702
C
MG
MG
1_555
A
ANP
501
D
O1A
ANP
1_555
80.0
A
SER
399
A
OG
SER
236
1_555
A
MG
702
C
MG
MG
1_555
A
HOH
2060
G
O
HOH
1_555
100.3
A
ANP
501
D
O2B
ANP
1_555
A
MG
702
C
MG
MG
1_555
A
HOH
2060
G
O
HOH
1_555
84.5
A
ANP
501
D
O1A
ANP
1_555
A
MG
702
C
MG
MG
1_555
A
HOH
2060
G
O
HOH
1_555
154.0
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
ANP
501
D
O1B
ANP
1_555
87.5
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2141
G
O
HOH
1_555
94.7
A
ANP
501
D
O1B
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2141
G
O
HOH
1_555
171.3
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2161
G
O
HOH
1_555
89.4
A
ANP
501
D
O1B
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2161
G
O
HOH
1_555
86.5
A
HOH
2141
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2161
G
O
HOH
1_555
85.1
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2188
G
O
HOH
1_555
173.0
A
ANP
501
D
O1B
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2188
G
O
HOH
1_555
86.5
A
HOH
2141
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2188
G
O
HOH
1_555
91.8
A
HOH
2161
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2188
G
O
HOH
1_555
93.9
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
83.0
A
ANP
501
D
O1B
ANP
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
94.6
A
HOH
2141
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
94.0
A
HOH
2161
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
172.3
A
HOH
2188
G
O
HOH
1_555
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
93.8
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_565
-x,-y+1,z
crystal symmetry operation
-52.3550000000
90.6815200303
0.0000000000
A
N
LEU
260
A
N
LEU
97
A
O
LYS
321
A
O
LYS
158
A
N
GLY
326
A
N
GLY
163
A
O
MET
344
A
O
MET
181
A
N
LEU
345
A
N
LEU
182
A
O
PHE
422
A
O
PHE
259
A
O
GLY
421
A
O
GLY
258
A
N
SER
399
A
N
SER
236
A
O
ALA
400
A
O
ALA
237
A
N
LEU
388
A
N
LEU
225
A
O
ASP
389
A
O
ASP
226
A
N
VAL
377
A
N
VAL
214
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
-21
A
MET
1
1
Y
1
A
GLY
-20
A
GLY
2
1
Y
1
A
SER
-19
A
SER
3
1
Y
1
A
SER
-18
A
SER
4
1
Y
1
A
HIS
-17
A
HIS
5
1
Y
1
A
HIS
-16
A
HIS
6
1
Y
1
A
HIS
-15
A
HIS
7
1
Y
1
A
HIS
-14
A
HIS
8
1
Y
1
A
HIS
-13
A
HIS
9
1
Y
1
A
HIS
-12
A
HIS
10
1
Y
1
A
SER
-11
A
SER
11
1
Y
1
A
SER
-10
A
SER
12
1
Y
1
A
GLY
-9
A
GLY
13
1
Y
1
A
LEU
-8
A
LEU
14
1
Y
1
A
VAL
-7
A
VAL
15
1
Y
1
A
PRO
-6
A
PRO
16
1
Y
1
A
ARG
-5
A
ARG
17
1
Y
1
A
GLY
-4
A
GLY
18
1
Y
1
A
SER
-3
A
SER
19
1
Y
1
A
HIS
-2
A
HIS
20
1
Y
1
A
MET
-1
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
2071
1.86
1
4.23
0.50
120.30
124.53
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
298
298
298
N
1
-3.91
0.50
120.30
116.39
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
298
298
298
N
1
A
GLU
237
-107.77
-90.97
1
A
ASN
280
-47.24
-0.68
1
A
ASP
292
59.13
-157.70
1
A
ILE
413
-85.06
-74.91
protein_rep.param
protein.top
water_rep.param
water.top
ion.param
ion.top
ligand2.param
ligand2.top
46.1
-3.80
1.13
0.00
-3.80
0.00
7.59
0.222
0.003
0.19
0.19
1.79
34.28
4162
41325
10.1
99.3
RANDOM
1595795.85
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
1WK3
FLAT MODEL
69.0378
0.3467
0.25
0.21
5.00
0.39
0.36
1.79
34.28
217
2366
54
0
2095
0.010
1.6
23.4
1.86
4.08
1.50
5.20
2.00
6.33
2.00
8.20
2.50
0.372
0.014
0.355
1.90
690
6058
6
10.2
98.0
29.6
1.79
50
2ZIN
41338
0.063
1
99.3
1.79
1.82
0.486
96
refinement
CNS
1.1
data collection
HKL-2000
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
MOLREP
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
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
ASP
313
A
ASP
150
1
6
13
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
HIS
432
A
HIS
269
1
9
9
A
ASN
436
A
ASN
273
HELX_P
A
ALA
441
A
ALA
278
5
10
6
metalc
2.263
A
SER
399
A
OG
SER
236
1_555
A
MG
702
C
MG
MG
1_555
metalc
2.097
A
ANP
501
D
O1G
ANP
1_555
A
MG
701
B
MG
MG
1_555
metalc
2.188
A
ANP
501
D
O1B
ANP
1_555
A
MG
701
B
MG
MG
1_555
metalc
2.249
A
ANP
501
D
O2B
ANP
1_555
A
MG
702
C
MG
MG
1_555
metalc
2.436
A
ANP
501
D
O1A
ANP
1_555
A
MG
702
C
MG
MG
1_555
metalc
2.280
A
MG
701
B
MG
MG
1_555
A
HOH
2141
G
O
HOH
1_555
metalc
2.223
A
MG
701
B
MG
MG
1_555
A
HOH
2161
G
O
HOH
1_555
metalc
2.272
A
MG
701
B
MG
MG
1_555
A
HOH
2188
G
O
HOH
1_555
metalc
2.345
A
MG
701
B
MG
MG
1_555
A
HOH
2193
G
O
HOH
1_555
metalc
2.329
A
MG
702
C
MG
MG
1_555
A
HOH
2060
G
O
HOH
1_555
LIGASE
aminoacyl-tRNA synthetase, pyrrolysyl-tRNA synthetase, pyrrolysine, tRNA, ATP analogue, non-natural amino acid, unnatural amino acid, ATP-binding, Cytoplasm, Ligase, Nucleotide-binding, Protein biosynthesis, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI
A
ASP
318
A
ASP
155
1
A
PRO
319
A
PRO
156
-0.12
A
GLY
403
A
GLY
240
1
A
PRO
404
A
PRO
241
0.19
PYLS_METMA
UNP
1
185
Q8PWY1
ASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKS
PILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTM
LNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGL
ERLLKVKHDFKNIKRAARSESYYNGISTNL
185
454
2ZIN
185
454
Q8PWY1
A
1
22
291
1
expression tag
MET
-21
2ZIN
A
Q8PWY1
UNP
1
1
expression tag
GLY
-20
2ZIN
A
Q8PWY1
UNP
2
1
expression tag
SER
-19
2ZIN
A
Q8PWY1
UNP
3
1
expression tag
SER
-18
2ZIN
A
Q8PWY1
UNP
4
1
expression tag
HIS
-17
2ZIN
A
Q8PWY1
UNP
5
1
expression tag
HIS
-16
2ZIN
A
Q8PWY1
UNP
6
1
expression tag
HIS
-15
2ZIN
A
Q8PWY1
UNP
7
1
expression tag
HIS
-14
2ZIN
A
Q8PWY1
UNP
8
1
expression tag
HIS
-13
2ZIN
A
Q8PWY1
UNP
9
1
expression tag
HIS
-12
2ZIN
A
Q8PWY1
UNP
10
1
expression tag
SER
-11
2ZIN
A
Q8PWY1
UNP
11
1
expression tag
SER
-10
2ZIN
A
Q8PWY1
UNP
12
1
expression tag
GLY
-9
2ZIN
A
Q8PWY1
UNP
13
1
expression tag
LEU
-8
2ZIN
A
Q8PWY1
UNP
14
1
expression tag
VAL
-7
2ZIN
A
Q8PWY1
UNP
15
1
expression tag
PRO
-6
2ZIN
A
Q8PWY1
UNP
16
1
expression tag
ARG
-5
2ZIN
A
Q8PWY1
UNP
17
1
expression tag
GLY
-4
2ZIN
A
Q8PWY1
UNP
18
1
expression tag
SER
-3
2ZIN
A
Q8PWY1
UNP
19
1
expression tag
HIS
-2
2ZIN
A
Q8PWY1
UNP
20
1
expression tag
MET
-1
2ZIN
A
Q8PWY1
UNP
21
1
GLU
SEE REMARK 999
GLY
444
2ZIN
A
Q8PWY1
UNP
444
281
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
ASP
386
A
ASP
223
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 MG A 701
A
MG
701
Software
4
BINDING SITE FOR RESIDUE MG A 702
A
MG
702
Software
3
BINDING SITE FOR RESIDUE ANP A 501
A
ANP
501
Software
20
BINDING SITE FOR RESIDUE LBY A 601
A
LBY
601
Software
8
BINDING SITE FOR RESIDUE EDO A 2011
A
EDO
2011
Software
3
A
HOH
2141
G
HOH
4
1_555
A
HOH
2161
G
HOH
4
1_555
A
HOH
2188
G
HOH
4
1_555
A
HOH
2193
G
HOH
4
1_555
A
GLU
396
A
GLU
233
3
1_555
A
SER
399
A
SER
236
3
1_555
A
HOH
2060
G
HOH
3
1_555
A
ARG
330
A
ARG
167
20
1_555
A
GLU
332
A
GLU
169
20
1_555
A
HIS
338
A
HIS
175
20
1_555
A
LEU
339
A
LEU
176
20
1_555
A
PHE
342
A
PHE
179
20
1_555
A
GLU
396
A
GLU
233
20
1_555
A
LEU
397
A
LEU
234
20
1_555
A
SER
398
A
SER
235
20
1_555
A
SER
399
A
SER
236
20
1_555
A
GLY
421
A
GLY
258
20
1_555
A
GLY
423
A
GLY
260
20
1_555
A
ARG
426
A
ARG
263
20
1_555
A
HOH
2013
G
HOH
20
1_555
A
HOH
2053
G
HOH
20
1_555
A
HOH
2057
G
HOH
20
1_555
A
HOH
2060
G
HOH
20
1_555
A
HOH
2076
G
HOH
20
1_555
A
HOH
2161
G
HOH
20
1_555
A
HOH
2188
G
HOH
20
1_555
A
HOH
2193
G
HOH
20
1_555
A
MET
300
A
MET
137
8
1_555
A
TYR
306
A
TYR
143
8
1_555
A
ASN
346
A
ASN
183
8
1_555
A
CYS
348
A
CYS
185
8
1_555
A
TRP
417
A
TRP
254
8
1_555
A
GLY
419
A
GLY
256
8
1_555
A
ALA
420
A
ALA
257
8
1_555
A
HOH
2012
G
HOH
8
1_555
A
MET
276
A
MET
113
3
1_555
A
TRP
417
A
TRP
254
3
1_555
A
HOH
2221
G
HOH
3
1_555
172
P 64