0.021235
0.000000
0.000000
0.000000
0.021235
0.000000
0.000000
0.000000
0.008871
0.00000
0.00000
0.00000
Ahmad, S.
Muthukumar, S.
Sankaranarayanan, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
47.091
47.091
112.729
C14 H21 N7 O5
367.360
3'-deoxy-3'-(L-threonylamino)adenosine
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
Cl -1
35.453
CHLORIDE ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
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
C
N
2
N
N
N
3
N
O
Y
4
N
N
Y
5
N
C
Y
6
N
N
Y
7
N
C
Y
8
N
C
Y
9
N
C
N
10
N
N
Y
11
N
N
Y
12
N
C
N
13
N
N
Y
14
N
N
N
15
S
C
N
16
R
C
N
17
N
O
N
18
R
C
N
19
R
C
N
20
N
O
N
21
S
C
N
22
S
C
N
23
N
O
N
24
N
C
N
25
N
O
N
26
N
C
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
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
N
N
49
S
C
N
50
N
C
N
51
N
O
N
52
N
C
N
53
N
O
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
N
N
62
S
C
N
63
N
C
N
64
N
O
N
65
N
C
N
66
N
C
N
67
N
C
N
68
N
N
N
69
N
C
N
70
N
N
N
71
N
N
N
72
N
O
N
73
N
H
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
O
N
95
N
N
N
96
N
O
N
97
N
H
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
N
N
106
S
C
N
107
N
C
N
108
N
O
N
109
N
C
N
110
N
C
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
H
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
CL
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
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
Y
5
N
doub
Y
6
N
sing
Y
7
N
sing
Y
8
N
doub
Y
9
N
sing
Y
10
N
sing
Y
11
N
doub
Y
12
N
sing
N
13
N
sing
Y
14
N
doub
Y
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
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
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
doub
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
sing
N
68
N
doub
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
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
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
sing
N
94
N
doub
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
N
126
N
sing
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
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
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
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
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
doub
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
Y
189
N
sing
Y
190
N
doub
Y
191
N
doub
N
192
N
sing
Y
193
N
sing
N
194
N
sing
Y
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
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
doub
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
doub
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
doub
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
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
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
Y
297
N
doub
Y
298
N
sing
Y
299
N
sing
N
300
N
sing
Y
301
N
doub
N
302
N
sing
Y
303
N
doub
N
304
N
sing
Y
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
doub
N
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
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
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
sing
N
344
N
sing
N
345
N
doub
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
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
doub
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
Y
366
N
doub
Y
367
N
sing
Y
368
N
sing
N
369
N
sing
Y
370
N
doub
Y
371
N
sing
Y
372
N
sing
N
373
N
sing
Y
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
377
N
doub
N
378
N
sing
Y
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
doub
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
Y
394
N
doub
Y
395
N
sing
Y
396
N
sing
N
397
N
sing
Y
398
N
doub
N
399
N
sing
Y
400
N
doub
N
401
N
sing
Y
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
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
doub
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
sing
UK
Nat Commun
2041-1723
6
7552
7552
10.1038/ncomms8552
26113036
Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
2015
10.2210/pdb4rrm/pdb
pdb_00004rrm
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
2013-03-16
RIGAKU RAXIS IV++
Mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU FR-E+ SUPERBRIGHT
15077.378
Probable threonine--tRNA ligase 2
6.1.1.3
UNP residues 1-136
E129A
1
man
polymer
367.360
3'-deoxy-3'-(L-threonylamino)adenosine
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
146
nat
water
Threonyl-tRNA synthetase 2, ThrRS 2
no
no
MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS
RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYKSFSIACKGHPLAALSRSFTE
MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS
RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYKSFSIACKGHPLAALSRSFTE
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
ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
sample
thrS2, APE_0117.1
272557
Aeropyrum pernix K1
562
Escherichia coli
1
2.07
40.65
VAPOR DIFFUSION, HANGING DROP
8.5
0.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Data collection
Database references
Derived calculations
1
0
2015-07-15
1
1
2017-11-22
1
2
2024-02-28
_software.classification
_software.name
_software.version
_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.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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2014-11-06
REL
REL
A3T
3'-deoxy-3'-(L-threonylamino)adenosine
MG
MAGNESIUM ION
CL
CHLORIDE ION
HOH
water
A3T
501
2
A3T
A3T
501
A
MG
1
3
MG
MG
502
A
CL
2
4
CL
CL
503
A
HOH
1
5
HOH
HOH
601
A
HOH
2
5
HOH
HOH
602
A
HOH
3
5
HOH
HOH
603
A
HOH
4
5
HOH
HOH
604
A
HOH
6
5
HOH
HOH
605
A
HOH
7
5
HOH
HOH
606
A
HOH
9
5
HOH
HOH
607
A
HOH
10
5
HOH
HOH
608
A
HOH
11
5
HOH
HOH
609
A
HOH
12
5
HOH
HOH
610
A
HOH
13
5
HOH
HOH
611
A
HOH
14
5
HOH
HOH
612
A
HOH
15
5
HOH
HOH
613
A
HOH
16
5
HOH
HOH
614
A
HOH
17
5
HOH
HOH
615
A
HOH
18
5
HOH
HOH
616
A
HOH
19
5
HOH
HOH
617
A
HOH
20
5
HOH
HOH
618
A
HOH
22
5
HOH
HOH
619
A
HOH
23
5
HOH
HOH
620
A
HOH
24
5
HOH
HOH
621
A
HOH
25
5
HOH
HOH
622
A
HOH
26
5
HOH
HOH
623
A
HOH
27
5
HOH
HOH
624
A
HOH
29
5
HOH
HOH
625
A
HOH
30
5
HOH
HOH
626
A
HOH
31
5
HOH
HOH
627
A
HOH
32
5
HOH
HOH
628
A
HOH
33
5
HOH
HOH
629
A
HOH
34
5
HOH
HOH
630
A
HOH
35
5
HOH
HOH
631
A
HOH
36
5
HOH
HOH
632
A
HOH
37
5
HOH
HOH
633
A
HOH
38
5
HOH
HOH
634
A
HOH
39
5
HOH
HOH
635
A
HOH
40
5
HOH
HOH
636
A
HOH
41
5
HOH
HOH
637
A
HOH
42
5
HOH
HOH
638
A
HOH
43
5
HOH
HOH
639
A
HOH
44
5
HOH
HOH
640
A
HOH
45
5
HOH
HOH
641
A
HOH
46
5
HOH
HOH
642
A
HOH
47
5
HOH
HOH
643
A
HOH
48
5
HOH
HOH
644
A
HOH
49
5
HOH
HOH
645
A
HOH
50
5
HOH
HOH
646
A
HOH
51
5
HOH
HOH
647
A
HOH
53
5
HOH
HOH
648
A
HOH
54
5
HOH
HOH
649
A
HOH
55
5
HOH
HOH
650
A
HOH
56
5
HOH
HOH
651
A
HOH
59
5
HOH
HOH
652
A
HOH
60
5
HOH
HOH
653
A
HOH
62
5
HOH
HOH
654
A
HOH
64
5
HOH
HOH
655
A
HOH
65
5
HOH
HOH
656
A
HOH
66
5
HOH
HOH
657
A
HOH
67
5
HOH
HOH
658
A
HOH
68
5
HOH
HOH
659
A
HOH
69
5
HOH
HOH
660
A
HOH
70
5
HOH
HOH
661
A
HOH
72
5
HOH
HOH
662
A
HOH
73
5
HOH
HOH
663
A
HOH
75
5
HOH
HOH
664
A
HOH
76
5
HOH
HOH
665
A
HOH
78
5
HOH
HOH
666
A
HOH
80
5
HOH
HOH
667
A
HOH
81
5
HOH
HOH
668
A
HOH
82
5
HOH
HOH
669
A
HOH
83
5
HOH
HOH
670
A
HOH
84
5
HOH
HOH
671
A
HOH
85
5
HOH
HOH
672
A
HOH
86
5
HOH
HOH
673
A
HOH
87
5
HOH
HOH
674
A
HOH
88
5
HOH
HOH
675
A
HOH
89
5
HOH
HOH
676
A
HOH
90
5
HOH
HOH
677
A
HOH
96
5
HOH
HOH
678
A
HOH
99
5
HOH
HOH
679
A
HOH
100
5
HOH
HOH
680
A
HOH
101
5
HOH
HOH
681
A
HOH
102
5
HOH
HOH
682
A
HOH
103
5
HOH
HOH
683
A
HOH
104
5
HOH
HOH
684
A
HOH
105
5
HOH
HOH
685
A
HOH
108
5
HOH
HOH
686
A
HOH
109
5
HOH
HOH
687
A
HOH
111
5
HOH
HOH
688
A
HOH
112
5
HOH
HOH
689
A
HOH
113
5
HOH
HOH
690
A
HOH
114
5
HOH
HOH
691
A
HOH
116
5
HOH
HOH
692
A
HOH
118
5
HOH
HOH
693
A
HOH
119
5
HOH
HOH
694
A
HOH
121
5
HOH
HOH
695
A
HOH
122
5
HOH
HOH
696
A
HOH
123
5
HOH
HOH
697
A
HOH
124
5
HOH
HOH
698
A
HOH
125
5
HOH
HOH
699
A
HOH
126
5
HOH
HOH
700
A
HOH
127
5
HOH
HOH
701
A
HOH
128
5
HOH
HOH
702
A
HOH
129
5
HOH
HOH
703
A
HOH
130
5
HOH
HOH
704
A
HOH
131
5
HOH
HOH
705
A
HOH
132
5
HOH
HOH
706
A
HOH
133
5
HOH
HOH
707
A
HOH
134
5
HOH
HOH
708
A
HOH
135
5
HOH
HOH
709
A
HOH
136
5
HOH
HOH
710
A
HOH
137
5
HOH
HOH
711
A
HOH
141
5
HOH
HOH
712
A
HOH
142
5
HOH
HOH
713
A
HOH
143
5
HOH
HOH
714
A
HOH
144
5
HOH
HOH
715
A
HOH
151
5
HOH
HOH
716
A
HOH
152
5
HOH
HOH
717
A
HOH
153
5
HOH
HOH
718
A
HOH
154
5
HOH
HOH
719
A
HOH
155
5
HOH
HOH
720
A
HOH
156
5
HOH
HOH
721
A
HOH
157
5
HOH
HOH
722
A
HOH
158
5
HOH
HOH
723
A
HOH
159
5
HOH
HOH
724
A
HOH
161
5
HOH
HOH
725
A
HOH
162
5
HOH
HOH
726
A
HOH
163
5
HOH
HOH
727
A
HOH
164
5
HOH
HOH
728
A
HOH
165
5
HOH
HOH
729
A
HOH
166
5
HOH
HOH
730
A
HOH
167
5
HOH
HOH
731
A
HOH
168
5
HOH
HOH
732
A
HOH
169
5
HOH
HOH
733
A
HOH
170
5
HOH
HOH
734
A
HOH
171
5
HOH
HOH
735
A
HOH
172
5
HOH
HOH
736
A
HOH
173
5
HOH
HOH
737
A
HOH
174
5
HOH
HOH
738
A
HOH
175
5
HOH
HOH
739
A
HOH
176
5
HOH
HOH
740
A
HOH
177
5
HOH
HOH
741
A
HOH
178
5
HOH
HOH
742
A
HOH
179
5
HOH
HOH
743
A
HOH
180
5
HOH
HOH
744
A
HOH
181
5
HOH
HOH
745
A
HOH
182
5
HOH
HOH
746
A
MET
1
n
1
MET
1
A
ARG
2
n
2
ARG
2
A
LEU
3
n
3
LEU
3
A
LEU
4
n
4
LEU
4
A
TYR
5
n
5
TYR
5
A
LEU
6
n
6
LEU
6
A
HIS
7
n
7
HIS
7
A
ALA
8
n
8
ALA
8
A
ASP
9
n
9
ASP
9
A
ARG
10
n
10
ARG
10
A
PHE
11
n
11
PHE
11
A
GLU
12
n
12
GLU
12
A
TYR
13
n
13
TYR
13
A
LYS
14
n
14
LYS
14
A
THR
15
n
15
THR
15
A
VAL
16
n
16
VAL
16
A
LYS
17
n
17
LYS
17
A
PRO
18
n
18
PRO
18
A
ALA
19
n
19
ALA
19
A
LEU
20
n
20
LEU
20
A
LYS
21
n
21
LYS
21
A
ASN
22
n
22
ASN
22
A
PRO
23
n
23
PRO
23
A
PRO
24
n
24
PRO
24
A
ASP
25
n
25
ASP
25
A
PRO
26
n
26
PRO
26
A
PRO
27
n
27
PRO
27
A
GLY
28
n
28
GLY
28
A
GLU
29
n
29
GLU
29
A
ALA
30
n
30
ALA
30
A
SER
31
n
31
SER
31
A
PHE
32
n
32
PHE
32
A
GLY
33
n
33
GLY
33
A
GLU
34
n
34
GLU
34
A
ALA
35
n
35
ALA
35
A
LEU
36
n
36
LEU
36
A
VAL
37
n
37
VAL
37
A
VAL
38
n
38
VAL
38
A
PHE
39
n
39
PHE
39
A
THR
40
n
40
THR
40
A
THR
41
n
41
THR
41
A
VAL
42
n
42
VAL
42
A
GLU
43
n
43
GLU
43
A
ASP
44
n
44
ASP
44
A
GLY
45
n
45
GLY
45
A
ASP
46
n
46
ASP
46
A
GLY
47
n
47
GLY
47
A
PRO
48
n
48
PRO
48
A
GLN
49
n
49
GLN
49
A
THR
50
n
50
THR
50
A
VAL
51
n
51
VAL
51
A
MET
52
n
52
MET
52
A
TYR
53
n
53
TYR
53
A
ALA
54
n
54
ALA
54
A
ALA
55
n
55
ALA
55
A
SER
56
n
56
SER
56
A
ASP
57
n
57
ASP
57
A
ILE
58
n
58
ILE
58
A
ALA
59
n
59
ALA
59
A
SER
60
n
60
SER
60
A
HIS
61
n
61
HIS
61
A
SER
62
n
62
SER
62
A
SER
63
n
63
SER
63
A
ARG
64
n
64
ARG
64
A
LEU
65
n
65
LEU
65
A
LYS
66
n
66
LYS
66
A
VAL
67
n
67
VAL
67
A
THR
68
n
68
THR
68
A
THR
69
n
69
THR
69
A
VAL
70
n
70
VAL
70
A
ILE
71
n
71
ILE
71
A
LEU
72
n
72
LEU
72
A
TYR
73
n
73
TYR
73
A
PRO
74
n
74
PRO
74
A
TYR
75
n
75
TYR
75
A
ALA
76
n
76
ALA
76
A
HIS
77
n
77
HIS
77
A
LEU
78
n
78
LEU
78
A
SER
79
n
79
SER
79
A
SER
80
n
80
SER
80
A
ARG
81
n
81
ARG
81
A
LEU
82
n
82
LEU
82
A
ALA
83
n
83
ALA
83
A
LYS
84
n
84
LYS
84
A
PRO
85
n
85
PRO
85
A
MET
86
n
86
MET
86
A
ALA
87
n
87
ALA
87
A
ALA
88
n
88
ALA
88
A
HIS
89
n
89
HIS
89
A
LYS
90
n
90
LYS
90
A
ARG
91
n
91
ARG
91
A
LEU
92
n
92
LEU
92
A
ILE
93
n
93
ILE
93
A
GLU
94
n
94
GLU
94
A
LEU
95
n
95
LEU
95
A
GLU
96
n
96
GLU
96
A
GLY
97
n
97
GLY
97
A
ALA
98
n
98
ALA
98
A
LEU
99
n
99
LEU
99
A
ARG
100
n
100
ARG
100
A
THR
101
n
101
THR
101
A
LYS
102
n
102
LYS
102
A
PHE
103
n
103
PHE
103
A
PRO
104
n
104
PRO
104
A
GLY
105
n
105
GLY
105
A
HIS
106
n
106
HIS
106
A
VAL
107
n
107
VAL
107
A
HIS
108
n
108
HIS
108
A
ARG
109
n
109
ARG
109
A
ALA
110
n
110
ALA
110
A
PRO
111
n
111
PRO
111
A
PHE
112
n
112
PHE
112
A
GLY
113
n
113
GLY
113
A
TRP
114
n
114
TRP
114
A
TYR
115
n
115
TYR
115
A
LYS
116
n
116
LYS
116
A
SER
117
n
117
SER
117
A
PHE
118
n
118
PHE
118
A
SER
119
n
119
SER
119
A
ILE
120
n
120
ILE
120
A
ALA
121
n
121
ALA
121
A
CYS
122
n
122
CYS
122
A
LYS
123
n
123
LYS
123
A
GLY
124
n
124
GLY
124
A
HIS
125
n
125
HIS
125
A
PRO
126
n
126
PRO
126
A
LEU
127
n
127
LEU
127
A
ALA
128
n
128
ALA
128
A
ALA
129
n
129
ALA
129
A
LEU
130
n
130
LEU
130
A
SER
131
n
131
SER
131
A
ARG
132
n
132
ARG
132
A
SER
133
n
133
SER
133
A
PHE
134
n
134
PHE
134
A
THR
135
n
135
THR
135
A
GLU
136
n
136
GLU
136
A
author_and_software_defined_assembly
PISA
2
dimeric
1920
-7
11900
A
GLU
29
A
OE2
GLU
29
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
602
E
O
HOH
1_555
89.8
A
GLU
29
A
OE2
GLU
29
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
658
E
O
HOH
1_555
175.0
A
HOH
602
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
658
E
O
HOH
1_555
86.4
A
GLU
29
A
OE2
GLU
29
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
703
E
O
HOH
1_555
98.5
A
HOH
602
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
703
E
O
HOH
1_555
170.7
A
HOH
658
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
703
E
O
HOH
1_555
85.6
A
GLU
29
A
OE2
GLU
29
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
731
E
O
HOH
1_555
95.0
A
HOH
602
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
731
E
O
HOH
1_555
84.5
A
HOH
658
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
731
E
O
HOH
1_555
87.9
A
HOH
703
E
O
HOH
1_555
A
MG
502
C
MG
MG
1_555
A
HOH
731
E
O
HOH
1_555
90.4
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
PHE
32
A
O
PHE
32
A
N
PHE
11
A
N
PHE
11
A
N
VAL
16
A
N
VAL
16
A
O
TYR
115
A
O
TYR
115
A
O
HIS
108
A
O
HIS
108
A
N
LEU
72
A
N
LEU
72
A
O
ILE
71
A
O
ILE
71
A
N
VAL
38
A
N
VAL
38
A
O
VAL
37
A
O
VAL
37
A
N
LEU
6
A
N
LEU
6
A
N
TYR
5
A
N
TYR
5
A
O
LEU
130
A
O
LEU
130
1
A
VAL
16
-114.05
-117.11
1
A
ARG
81
-144.52
55.31
20.957
0.01
0.00
0.00
0.01
0.00
-0.02
0.957
0.930
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.25880
0.18807
0.19152
1.55
25.00
985
18248
18120
5.2
99.39
4.680
0.076
RANDOM
1
THROUGHOUT
2
MOLECULAR REPLACEMENT
0.125
0.107
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.55
25.00
146
1238
28
0
1064
0.015
0.020
1124
1.744
1.998
1529
6.447
5.000
135
40.000
21.395
43
14.938
15.000
176
15.779
15.000
8
0.111
0.200
168
0.011
0.022
849
4.495
3.000
1124
26.345
5.000
56
14.256
5.000
1182
0.465
0.370
1.590
86
1095
20
95.09
1.55
25
4RRM
18248
18120
2
2
1
99.3
data collection
CrystalClear
phasing
MOLREP
phasing
PHASER
refinement
REFMAC
5.6.0117
data reduction
HKL-2000
data scaling
HKL-2000
E129A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
GLY
47
A
GLY
47
HELX_P
A
LYS
66
A
LYS
66
1
1
20
A
LYS
84
A
LYS
84
HELX_P
A
THR
101
A
THR
101
1
2
18
metalc
2.408
A
GLU
29
A
OE2
GLU
29
1_555
A
MG
502
C
MG
MG
1_555
metalc
2.007
A
MG
502
C
MG
MG
1_555
A
HOH
602
E
O
HOH
1_555
metalc
2.186
A
MG
502
C
MG
MG
1_555
A
HOH
658
E
O
HOH
1_555
metalc
2.044
A
MG
502
C
MG
MG
1_555
A
HOH
703
E
O
HOH
1_555
metalc
2.308
A
MG
502
C
MG
MG
1_555
A
HOH
731
E
O
HOH
1_555
LIGASE
DTD-like fold, Proofreading, LIGASE
SYT2_AERPE
UNP
1
1
Q9YFY3
MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS
RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYKSFSIACKGHPLAELSRSFTE
1
136
4RRM
1
136
Q9YFY3
A
1
1
136
1
GLU
engineered mutation
ALA
129
4RRM
A
Q9YFY3
UNP
129
129
3
5
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
A
GLU
29
A
GLU
29
A
PHE
32
A
PHE
32
A
ARG
2
A
ARG
2
A
PRO
18
A
PRO
18
A
TRP
114
A
TRP
114
A
CYS
122
A
CYS
122
A
HIS
106
A
HIS
106
A
ARG
109
A
ARG
109
A
THR
69
A
THR
69
A
PRO
74
A
PRO
74
A
ALA
35
A
ALA
35
A
THR
41
A
THR
41
A
ARG
2
A
ARG
2
A
PRO
18
A
PRO
18
A
ALA
129
A
ALA
129
A
SER
133
A
SER
133
BINDING SITE FOR RESIDUE A3T A 501
A
A3T
501
Software
19
BINDING SITE FOR RESIDUE MG A 502
A
MG
502
Software
6
BINDING SITE FOR RESIDUE CL A 503
A
CL
503
Software
6
A
ALA
19
A
ALA
19
19
1_555
A
THR
40
A
THR
40
19
1_555
A
VAL
42
A
VAL
42
19
1_555
A
TYR
75
A
TYR
75
19
1_555
A
ALA
76
A
ALA
76
19
1_555
A
LEU
82
A
LEU
82
19
1_555
A
ALA
83
A
ALA
83
19
1_555
A
ALA
88
A
ALA
88
19
1_555
A
PHE
112
A
PHE
112
19
1_555
A
GLY
113
A
GLY
113
19
1_555
A
TRP
114
A
TRP
114
19
1_555
A
TYR
115
A
TYR
115
19
1_555
A
LYS
116
A
LYS
116
19
1_555
A
HOH
616
E
HOH
19
1_555
A
HOH
618
E
HOH
19
1_555
A
HOH
638
E
HOH
19
1_555
A
HOH
644
E
HOH
19
1_555
A
HOH
664
E
HOH
19
1_555
A
HOH
722
E
HOH
19
1_555
A
GLU
29
A
GLU
29
6
1_555
A
HOH
602
E
HOH
6
1_555
A
HOH
627
E
HOH
6
7_545
A
HOH
658
E
HOH
6
1_555
A
HOH
703
E
HOH
6
1_555
A
HOH
731
E
HOH
6
1_555
A
ARG
100
A
ARG
100
6
5_555
A
HIS
106
A
HIS
106
6
5_555
A
VAL
107
A
VAL
107
6
5_555
A
SER
133
A
SER
133
6
1_555
A
PHE
134
A
PHE
134
6
1_555
A
HOH
604
E
HOH
6
5_555
92
P 41 21 2