0.014304
0.000000
0.000000
0.000000
0.011075
0.000000
0.000000
0.000000
0.029429
0.00000
0.00000
0.00000
Arni, R.K.
Watanabe, L.
Ward, R.J.
Kreitman, R.J.
Kumar, K.
Walz Jr., F.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
69.910
90.290
33.980
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA 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
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
C10 H15 N2 O9 P
338.208
n
URIDINE 5'-MONOMETHYLPHOSPHATE
RNA linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
O
N
89
N
P
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
C
N
94
R
C
N
95
N
O
N
96
S
C
N
97
N
O
N
98
R
C
N
99
N
O
N
100
R
C
Y
101
N
N
Y
102
N
C
Y
103
N
N
Y
104
N
C
N
105
N
C
N
106
N
O
N
107
N
N
N
108
N
C
N
109
N
N
N
110
N
N
Y
111
N
C
N
112
N
H
N
113
N
H
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
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
N
N
127
S
C
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
O
N
134
N
N
N
135
N
O
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
N
N
147
S
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
O
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
N
N
166
N
C
N
167
N
C
N
168
N
O
N
169
N
O
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
S
C
N
177
N
C
N
178
N
O
N
179
N
C
Y
180
N
C
Y
181
N
N
Y
182
N
C
Y
183
N
C
Y
184
N
N
N
185
N
O
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
O
N
197
N
H
N
198
N
H
N
199
N
N
N
200
S
C
N
201
N
C
N
202
N
O
N
203
S
C
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
O
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
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
S
C
N
223
N
C
N
224
N
O
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
C
N
229
N
O
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
H
N
242
N
H
N
243
N
N
N
244
S
C
N
245
N
C
N
246
N
O
N
247
N
C
N
248
N
C
N
249
N
C
N
250
N
C
N
251
N
N
N
252
N
O
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
Y
278
N
C
N
279
N
O
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
O
N
314
N
O
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
R
C
N
327
N
O
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
Y
344
N
C
Y
345
N
C
Y
346
N
C
Y
347
N
N
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
N
353
N
O
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
N
N
367
S
C
N
368
N
C
N
369
N
O
N
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
N
377
N
O
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
H
N
389
N
H
N
390
N
O
N
391
N
O
N
392
N
P
N
393
N
O
N
394
N
O
N
395
N
C
N
396
R
C
N
397
N
O
N
398
S
C
N
399
N
O
N
400
R
C
N
401
N
O
N
402
R
C
N
403
N
N
N
404
N
C
N
405
N
O
N
406
N
N
N
407
N
C
N
408
N
O
N
409
N
C
N
410
S
C
N
411
N
C
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
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
N
N
428
S
C
N
429
N
C
N
430
N
O
N
431
N
C
N
432
N
C
N
433
N
C
N
434
N
O
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
doub
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
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
Y
107
N
sing
Y
108
N
sing
Y
109
N
doub
N
110
N
sing
Y
111
N
sing
N
112
N
sing
Y
113
N
doub
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
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
doub
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
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
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
Y
180
N
sing
Y
181
N
doub
Y
182
N
doub
N
183
N
sing
Y
184
N
sing
N
185
N
sing
Y
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
doub
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
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
doub
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
Y
269
N
doub
Y
270
N
sing
Y
271
N
sing
N
272
N
sing
Y
273
N
doub
N
274
N
sing
Y
275
N
doub
N
276
N
sing
Y
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
doub
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
doub
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
doub
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
Y
338
N
doub
Y
339
N
sing
Y
340
N
sing
N
341
N
sing
Y
342
N
doub
Y
343
N
sing
Y
344
N
sing
N
345
N
sing
Y
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
doub
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
Y
366
N
doub
Y
367
N
sing
Y
368
N
sing
N
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
372
N
doub
N
373
N
sing
Y
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
sing
N
381
N
sing
N
382
N
sing
N
383
N
doub
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
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
doub
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
doub
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
doub
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
38
2452
2461
10.1021/bi982612q
10029539
Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.
1999
US
Biochemistry
BICHAW
0033
0006-2960
31
3126
3135
Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites
1992
US
Biochemistry
BICHAW
0033
0006-2960
28
7592
Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
1989
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
263
15358
Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
1988
DK
Acta Crystallogr.,Sect.B
ASBSDK
0622
0108-7681
43
548
Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
1987
GW
Fresenius Z.Anal.Chem.
ZACFAU
0596
0016-1152
327
67
Structure and Function of the Enzyme Ribonuclease T1
1987
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
136
95
Crystallization of Ribonuclease T1
1980
10.2210/pdb1b2m/pdb
pdb_00001b2m
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
287.00
1
IMAGE PLATE
RIGAKU
NI FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
620.441
5'-R(*GP*(U34))-3'
3
syn
polymer
RNASE T1 COMPLEXED WITH 5'-R(*GP*(CH2)U)-3
11093.644
RIBONUCLEASE T1
3.1.27.3
GLN 25 VARIANT
2
nat
polymer
18.015
water
92
nat
water
no
yes
G(U34)
GU
C,D,E
polyribonucleotide
no
no
ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF
NENNQLAGVITHTGASGNNFVECT
ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF
NENNQLAGVITHTGASGNNFVECT
A,B
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
Aspergillus
sample
5062
Aspergillus oryzae
1
2.23
44.82
4.10
pH 4.10
SODIUM ACETATE
1
TRIS
1
MGCL2
1
PEG 4000
1
PEG 4000
2
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Structure summary
Data collection
Database references
Derived calculations
Refinement description
1
0
1999-03-25
1
1
2008-04-26
1
2
2011-07-13
1
3
2017-02-01
1
4
2023-08-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
BNL
Y
RCSB
1998-11-27
REL
HOH
water
1RNT
PDB
experimental model
HOH
137
3
HOH
HOH
137
C
HOH
188
3
HOH
HOH
188
D
HOH
195
3
HOH
HOH
195
D
HOH
107
3
HOH
HOH
107
A
HOH
108
3
HOH
HOH
108
A
HOH
110
3
HOH
HOH
110
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
113
3
HOH
HOH
113
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
117
3
HOH
HOH
117
A
HOH
118
3
HOH
HOH
118
A
HOH
119
3
HOH
HOH
119
A
HOH
120
3
HOH
HOH
120
A
HOH
127
3
HOH
HOH
127
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
HOH
135
3
HOH
HOH
135
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
141
3
HOH
HOH
141
A
HOH
142
3
HOH
HOH
142
A
HOH
144
3
HOH
HOH
144
A
HOH
145
3
HOH
HOH
145
A
HOH
146
3
HOH
HOH
146
A
HOH
147
3
HOH
HOH
147
A
HOH
148
3
HOH
HOH
148
A
HOH
149
3
HOH
HOH
149
A
HOH
155
3
HOH
HOH
155
A
HOH
156
3
HOH
HOH
156
A
HOH
157
3
HOH
HOH
157
A
HOH
169
3
HOH
HOH
169
A
HOH
170
3
HOH
HOH
170
A
HOH
171
3
HOH
HOH
171
A
HOH
177
3
HOH
HOH
177
A
HOH
178
3
HOH
HOH
178
A
HOH
179
3
HOH
HOH
179
A
HOH
180
3
HOH
HOH
180
A
HOH
181
3
HOH
HOH
181
A
HOH
182
3
HOH
HOH
182
A
HOH
183
3
HOH
HOH
183
A
HOH
184
3
HOH
HOH
184
A
HOH
185
3
HOH
HOH
185
A
HOH
186
3
HOH
HOH
186
A
HOH
187
3
HOH
HOH
187
A
HOH
189
3
HOH
HOH
189
A
HOH
190
3
HOH
HOH
190
A
HOH
191
3
HOH
HOH
191
A
HOH
194
3
HOH
HOH
194
A
HOH
109
3
HOH
HOH
109
B
HOH
121
3
HOH
HOH
121
B
HOH
122
3
HOH
HOH
122
B
HOH
123
3
HOH
HOH
123
B
HOH
124
3
HOH
HOH
124
B
HOH
125
3
HOH
HOH
125
B
HOH
126
3
HOH
HOH
126
B
HOH
128
3
HOH
HOH
128
B
HOH
129
3
HOH
HOH
129
B
HOH
130
3
HOH
HOH
130
B
HOH
131
3
HOH
HOH
131
B
HOH
132
3
HOH
HOH
132
B
HOH
136
3
HOH
HOH
136
B
HOH
138
3
HOH
HOH
138
B
HOH
143
3
HOH
HOH
143
B
HOH
150
3
HOH
HOH
150
B
HOH
151
3
HOH
HOH
151
B
HOH
152
3
HOH
HOH
152
B
HOH
153
3
HOH
HOH
153
B
HOH
154
3
HOH
HOH
154
B
HOH
158
3
HOH
HOH
158
B
HOH
159
3
HOH
HOH
159
B
HOH
160
3
HOH
HOH
160
B
HOH
161
3
HOH
HOH
161
B
HOH
162
3
HOH
HOH
162
B
HOH
163
3
HOH
HOH
163
B
HOH
164
3
HOH
HOH
164
B
HOH
165
3
HOH
HOH
165
B
HOH
166
3
HOH
HOH
166
B
HOH
167
3
HOH
HOH
167
B
HOH
168
3
HOH
HOH
168
B
HOH
172
3
HOH
HOH
172
B
HOH
173
3
HOH
HOH
173
B
HOH
174
3
HOH
HOH
174
B
HOH
175
3
HOH
HOH
175
B
HOH
176
3
HOH
HOH
176
B
HOH
192
3
HOH
HOH
192
B
HOH
193
3
HOH
HOH
193
B
HOH
196
3
HOH
HOH
196
B
HOH
197
3
HOH
HOH
197
B
HOH
198
3
HOH
HOH
198
B
G
105
n
1
G
105
C
+U
106
n
2
U34
106
C
G
105
n
1
G
105
D
+U
106
n
2
U34
106
D
G
105
n
1
G
105
E
+U
106
n
2
U34
106
E
ALA
1
n
1
ALA
1
A
CYS
2
n
2
CYS
2
A
ASP
3
n
3
ASP
3
A
TYR
4
n
4
TYR
4
A
THR
5
n
5
THR
5
A
CYS
6
n
6
CYS
6
A
GLY
7
n
7
GLY
7
A
SER
8
n
8
SER
8
A
ASN
9
n
9
ASN
9
A
CYS
10
n
10
CYS
10
A
TYR
11
n
11
TYR
11
A
SER
12
n
12
SER
12
A
SER
13
n
13
SER
13
A
SER
14
n
14
SER
14
A
ASP
15
n
15
ASP
15
A
VAL
16
n
16
VAL
16
A
SER
17
n
17
SER
17
A
THR
18
n
18
THR
18
A
ALA
19
n
19
ALA
19
A
GLN
20
n
20
GLN
20
A
ALA
21
n
21
ALA
21
A
ALA
22
n
22
ALA
22
A
GLY
23
n
23
GLY
23
A
TYR
24
n
24
TYR
24
A
GLN
25
n
25
GLN
25
A
LEU
26
n
26
LEU
26
A
HIS
27
n
27
HIS
27
A
GLU
28
n
28
GLU
28
A
ASP
29
n
29
ASP
29
A
GLY
30
n
30
GLY
30
A
GLU
31
n
31
GLU
31
A
THR
32
n
32
THR
32
A
VAL
33
n
33
VAL
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
ASN
36
n
36
ASN
36
A
SER
37
n
37
SER
37
A
TYR
38
n
38
TYR
38
A
PRO
39
n
39
PRO
39
A
HIS
40
n
40
HIS
40
A
LYS
41
n
41
LYS
41
A
TYR
42
n
42
TYR
42
A
ASN
43
n
43
ASN
43
A
ASN
44
n
44
ASN
44
A
TYR
45
n
45
TYR
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
PHE
48
n
48
PHE
48
A
ASP
49
n
49
ASP
49
A
PHE
50
n
50
PHE
50
A
SER
51
n
51
SER
51
A
VAL
52
n
52
VAL
52
A
SER
53
n
53
SER
53
A
SER
54
n
54
SER
54
A
PRO
55
n
55
PRO
55
A
TYR
56
n
56
TYR
56
A
TYR
57
n
57
TYR
57
A
GLU
58
n
58
GLU
58
A
TRP
59
n
59
TRP
59
A
PRO
60
n
60
PRO
60
A
ILE
61
n
61
ILE
61
A
LEU
62
n
62
LEU
62
A
SER
63
n
63
SER
63
A
SER
64
n
64
SER
64
A
GLY
65
n
65
GLY
65
A
ASP
66
n
66
ASP
66
A
VAL
67
n
67
VAL
67
A
TYR
68
n
68
TYR
68
A
SER
69
n
69
SER
69
A
GLY
70
n
70
GLY
70
A
GLY
71
n
71
GLY
71
A
SER
72
n
72
SER
72
A
PRO
73
n
73
PRO
73
A
GLY
74
n
74
GLY
74
A
ALA
75
n
75
ALA
75
A
ASP
76
n
76
ASP
76
A
ARG
77
n
77
ARG
77
A
VAL
78
n
78
VAL
78
A
VAL
79
n
79
VAL
79
A
PHE
80
n
80
PHE
80
A
ASN
81
n
81
ASN
81
A
GLU
82
n
82
GLU
82
A
ASN
83
n
83
ASN
83
A
ASN
84
n
84
ASN
84
A
GLN
85
n
85
GLN
85
A
LEU
86
n
86
LEU
86
A
ALA
87
n
87
ALA
87
A
GLY
88
n
88
GLY
88
A
VAL
89
n
89
VAL
89
A
ILE
90
n
90
ILE
90
A
THR
91
n
91
THR
91
A
HIS
92
n
92
HIS
92
A
THR
93
n
93
THR
93
A
GLY
94
n
94
GLY
94
A
ALA
95
n
95
ALA
95
A
SER
96
n
96
SER
96
A
GLY
97
n
97
GLY
97
A
ASN
98
n
98
ASN
98
A
ASN
99
n
99
ASN
99
A
PHE
100
n
100
PHE
100
A
VAL
101
n
101
VAL
101
A
GLU
102
n
102
GLU
102
A
CYS
103
n
103
CYS
103
A
THR
104
n
104
THR
104
A
ALA
1
n
1
ALA
1
B
CYS
2
n
2
CYS
2
B
ASP
3
n
3
ASP
3
B
TYR
4
n
4
TYR
4
B
THR
5
n
5
THR
5
B
CYS
6
n
6
CYS
6
B
GLY
7
n
7
GLY
7
B
SER
8
n
8
SER
8
B
ASN
9
n
9
ASN
9
B
CYS
10
n
10
CYS
10
B
TYR
11
n
11
TYR
11
B
SER
12
n
12
SER
12
B
SER
13
n
13
SER
13
B
SER
14
n
14
SER
14
B
ASP
15
n
15
ASP
15
B
VAL
16
n
16
VAL
16
B
SER
17
n
17
SER
17
B
THR
18
n
18
THR
18
B
ALA
19
n
19
ALA
19
B
GLN
20
n
20
GLN
20
B
ALA
21
n
21
ALA
21
B
ALA
22
n
22
ALA
22
B
GLY
23
n
23
GLY
23
B
TYR
24
n
24
TYR
24
B
GLN
25
n
25
GLN
25
B
LEU
26
n
26
LEU
26
B
HIS
27
n
27
HIS
27
B
GLU
28
n
28
GLU
28
B
ASP
29
n
29
ASP
29
B
GLY
30
n
30
GLY
30
B
GLU
31
n
31
GLU
31
B
THR
32
n
32
THR
32
B
VAL
33
n
33
VAL
33
B
GLY
34
n
34
GLY
34
B
SER
35
n
35
SER
35
B
ASN
36
n
36
ASN
36
B
SER
37
n
37
SER
37
B
TYR
38
n
38
TYR
38
B
PRO
39
n
39
PRO
39
B
HIS
40
n
40
HIS
40
B
LYS
41
n
41
LYS
41
B
TYR
42
n
42
TYR
42
B
ASN
43
n
43
ASN
43
B
ASN
44
n
44
ASN
44
B
TYR
45
n
45
TYR
45
B
GLU
46
n
46
GLU
46
B
GLY
47
n
47
GLY
47
B
PHE
48
n
48
PHE
48
B
ASP
49
n
49
ASP
49
B
PHE
50
n
50
PHE
50
B
SER
51
n
51
SER
51
B
VAL
52
n
52
VAL
52
B
SER
53
n
53
SER
53
B
SER
54
n
54
SER
54
B
PRO
55
n
55
PRO
55
B
TYR
56
n
56
TYR
56
B
TYR
57
n
57
TYR
57
B
GLU
58
n
58
GLU
58
B
TRP
59
n
59
TRP
59
B
PRO
60
n
60
PRO
60
B
ILE
61
n
61
ILE
61
B
LEU
62
n
62
LEU
62
B
SER
63
n
63
SER
63
B
SER
64
n
64
SER
64
B
GLY
65
n
65
GLY
65
B
ASP
66
n
66
ASP
66
B
VAL
67
n
67
VAL
67
B
TYR
68
n
68
TYR
68
B
SER
69
n
69
SER
69
B
GLY
70
n
70
GLY
70
B
GLY
71
n
71
GLY
71
B
SER
72
n
72
SER
72
B
PRO
73
n
73
PRO
73
B
GLY
74
n
74
GLY
74
B
ALA
75
n
75
ALA
75
B
ASP
76
n
76
ASP
76
B
ARG
77
n
77
ARG
77
B
VAL
78
n
78
VAL
78
B
VAL
79
n
79
VAL
79
B
PHE
80
n
80
PHE
80
B
ASN
81
n
81
ASN
81
B
GLU
82
n
82
GLU
82
B
ASN
83
n
83
ASN
83
B
ASN
84
n
84
ASN
84
B
GLN
85
n
85
GLN
85
B
LEU
86
n
86
LEU
86
B
ALA
87
n
87
ALA
87
B
GLY
88
n
88
GLY
88
B
VAL
89
n
89
VAL
89
B
ILE
90
n
90
ILE
90
B
THR
91
n
91
THR
91
B
HIS
92
n
92
HIS
92
B
THR
93
n
93
THR
93
B
GLY
94
n
94
GLY
94
B
ALA
95
n
95
ALA
95
B
SER
96
n
96
SER
96
B
GLY
97
n
97
GLY
97
B
ASN
98
n
98
ASN
98
B
ASN
99
n
99
ASN
99
B
PHE
100
n
100
PHE
100
B
VAL
101
n
101
VAL
101
B
GLU
102
n
102
GLU
102
B
CYS
103
n
103
CYS
103
B
THR
104
n
104
THR
104
B
author_defined_assembly
2
dimeric
author_defined_assembly
3
trimeric
C
U34
106
URIDINE 5'-MONOMETHYLPHOSPHATE
A
U34
2
U
D
U34
106
URIDINE 5'-MONOMETHYLPHOSPHATE
B
U34
2
U
E
U34
106
URIDINE 5'-MONOMETHYLPHOSPHATE
C
U34
2
U
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
TYR
4
D
O
TYR
4
A
N
TYR
11
D
N
TYR
11
A
O
HIS
40
D
O
HIS
40
A
N
GLU
58
D
N
GLU
58
A
O
TYR
57
D
O
TYR
57
A
N
PHE
80
D
N
PHE
80
A
O
ARG
77
D
O
ARG
77
A
N
ILE
90
D
N
ILE
90
B
O
TYR
4
E
O
TYR
4
B
N
TYR
11
E
N
TYR
11
B
O
HIS
40
E
O
HIS
40
B
N
GLU
58
E
N
GLU
58
B
O
TYR
57
E
O
TYR
57
B
N
PHE
80
E
N
PHE
80
B
O
ARG
77
E
O
ARG
77
B
N
ILE
90
E
N
ILE
90
1
C
OXT
U34
106
A
OXT
U34
2
1
Y
1
D
OXT
U34
106
B
OXT
U34
2
1
Y
1
E
OXT
U34
106
C
OXT
U34
2
1
Y
1
-4.72
0.50
104.30
99.58
C
C
C
C5
N7
C8
G
G
G
105
105
105
N
1
6.95
0.50
113.10
120.05
C
C
C
N7
C8
N9
G
G
G
105
105
105
N
1
-3.64
0.40
106.40
102.76
C
C
C
C8
N9
C4
G
G
G
105
105
105
N
1
-3.54
0.50
104.30
100.76
D
D
D
C5
N7
C8
G
G
G
105
105
105
N
1
6.83
0.50
113.10
119.93
D
D
D
N7
C8
N9
G
G
G
105
105
105
N
1
-3.48
0.40
106.40
102.92
D
D
D
C8
N9
C4
G
G
G
105
105
105
N
1
-4.06
0.50
104.30
100.24
E
E
E
C5
N7
C8
G
G
G
105
105
105
N
1
6.82
0.50
113.10
119.92
E
E
E
N7
C8
N9
G
G
G
105
105
105
N
1
-3.54
0.40
106.40
102.86
E
E
E
C8
N9
C4
G
G
G
105
105
105
N
1
A
SER
37
50.39
77.79
1
A
ASN
44
73.54
51.45
1
B
SER
37
50.17
76.12
1
B
ASN
44
73.23
41.60
1
B
THR
93
-47.75
107.55
0.254
0.187
0.187
2.000
8.000
9879
10.000
75.000
RANDOM
1
2.000
MOLECULAR REPLACEMENT
1RNT
2.000
8.000
92
1774
0
120
1562
0.011
1.74
1.42
2.000
20.000
1B2M
11298
2.000
0.64
1
75.000
phasing
AMoRE
refinement
X-PLOR
3.1
THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
A
SER
13
D
SER
13
HELX_P
A
GLU
28
D
GLU
28
1
1
16
B
SER
13
E
SER
13
HELX_P
B
ASP
29
E
ASP
29
1
2
17
disulf
2.016
A
CYS
2
D
SG
CYS
2
1_555
A
CYS
10
D
SG
CYS
10
1_555
disulf
2.035
A
CYS
6
D
SG
CYS
6
1_555
A
CYS
103
D
SG
CYS
103
1_555
disulf
2.017
B
CYS
2
E
SG
CYS
2
1_555
B
CYS
10
E
SG
CYS
10
1_555
disulf
2.024
B
CYS
6
E
SG
CYS
6
1_555
B
CYS
103
E
SG
CYS
103
1_555
covale
1.604
both
C
G
105
A
O3'
G
1
1_555
C
U34
106
A
P
U34
2
1_555
covale
1.579
both
D
G
105
B
O3'
G
1
1_555
D
U34
106
B
P
U34
2
1_555
covale
1.599
both
E
G
105
C
O3'
G
1
1_555
E
U34
106
C
P
U34
2
1_555
HYDROLASE/RNA
HYDROLASE, ENDORIBONUCLEASE, HYDROLASE/RNA, HYDROLASE-RNA complex
A
TYR
38
D
TYR
38
1
A
PRO
39
D
PRO
39
-0.07
A
SER
54
D
SER
54
1
A
PRO
55
D
PRO
55
1.24
B
TYR
38
E
TYR
38
1
B
PRO
39
E
PRO
39
1.06
B
SER
54
E
SER
54
1
B
PRO
55
E
PRO
55
-0.08
given
-0.070100
0.967600
-0.242700
-0.524700
0.171100
0.833900
0.848400
0.185800
0.495700
51.29900
4.64900
-14.75900
given
0.541300
0.640400
0.546900
0.040900
0.627200
-0.777800
-0.839800
0.443300
0.313300
-16.61400
43.66600
67.11300
RNT1_ASPOR
UNP
2
P00651
1B2M
PDB
1
1B2M
27
130
1B2M
1
104
P00651
A
1
1
104
27
130
1B2M
1
104
P00651
B
1
1
104
105
106
1B2M
105
106
1B2M
C
2
1
2
105
106
1B2M
105
106
1B2M
D
2
1
2
105
106
1B2M
105
106
1B2M
E
2
1
2
2
4
2
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
4
D
TYR
4
A
CYS
6
D
CYS
6
A
ASN
9
D
ASN
9
A
TYR
11
D
TYR
11
A
HIS
40
D
HIS
40
A
TYR
42
D
TYR
42
A
TYR
56
D
TYR
56
A
PRO
60
D
PRO
60
A
ASP
76
D
ASP
76
A
ASN
81
D
ASN
81
A
LEU
86
D
LEU
86
A
THR
91
D
THR
91
B
TYR
4
E
TYR
4
B
CYS
6
E
CYS
6
B
ASN
9
E
ASN
9
B
TYR
11
E
TYR
11
B
HIS
40
E
HIS
40
B
TYR
42
E
TYR
42
B
TYR
56
E
TYR
56
B
PRO
60
E
PRO
60
B
ASP
76
E
ASP
76
B
ASN
81
E
ASN
81
B
LEU
86
E
LEU
86
B
THR
91
E
THR
91
19
orthorhombic
P 21 21 21