0.026399
0.000000
0.012305
0.000000
0.025133
0.000000
0.000000
0.000000
0.030746
0.00000
0.00000
0.00000
Noguchi, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
114.99
90.00
37.880
39.789
35.884
C10 H14 N5 O7 P
347.221
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate
3'-AMP
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
Ca 2
40.078
CALCIUM 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
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
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
R
C
N
7
S
C
N
8
N
O
N
9
R
C
N
10
N
O
N
11
R
C
N
12
N
C
N
13
N
O
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
Y
23
N
N
N
24
N
H
N
25
N
H
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
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
CA
N
112
N
N
N
113
R
C
N
114
N
C
N
115
N
O
N
116
N
C
N
117
N
S
N
118
N
O
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
Y
248
N
C
Y
249
N
C
Y
250
N
C
Y
251
N
C
Y
252
N
C
Y
253
N
C
N
254
N
O
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
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
N
271
N
C
N
272
N
C
N
273
N
O
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
O
N
289
N
O
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
N
N
298
S
C
N
299
N
C
N
300
N
O
N
301
R
C
N
302
N
O
N
303
N
C
N
304
N
O
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
N
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
Y
327
N
C
N
328
N
O
N
329
N
H
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
H
N
340
N
H
N
341
N
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
N
352
N
O
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
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
Y
15
N
sing
Y
16
N
sing
Y
17
N
doub
Y
18
N
sing
Y
19
N
doub
Y
20
N
sing
N
21
N
sing
Y
22
N
sing
Y
23
N
doub
Y
24
N
sing
Y
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
doub
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
doub
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
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
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
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
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
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
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
doub
N
156
N
sing
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
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
doub
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
sing
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
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
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
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
Y
244
N
doub
Y
245
N
sing
Y
246
N
sing
N
247
N
sing
Y
248
N
doub
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
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
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
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
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
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
Y
313
N
doub
Y
314
N
sing
Y
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
sing
Y
322
N
doub
N
323
N
sing
Y
324
N
doub
N
325
N
sing
Y
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
doub
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
Y
341
N
doub
Y
342
N
sing
Y
343
N
sing
N
344
N
sing
Y
345
N
doub
N
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
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
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
66
843
849
10.1107/S0907444910019621
20606265
Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate
2010
10.2210/pdb3agn/pdb
pdb_00003agn
95
1
CCD
2010-01-25
ADSC QUANTUM 4r
TRIANGULAR Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.978
1.0
BL-6A
Photon Factory
0.978
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-6A
12392.090
Ribonuclease U2
3.1.27.4
1
nat
polymer
347.221
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate
1
syn
non-polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
166
nat
water
RNase U2
no
no
CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS
PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS
CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS
PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS
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
Smut fungus
sample
5271
Ustilago sphaerogena
1
1.98
37.81
VAPOR DIFFUSION, HANGING DROP
3.75
12.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2010-07-07
1
1
2011-07-13
1
2
2012-04-04
1
3
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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The same protein, Asp45 of which is isomerized to isoaspartate
Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate
PDBJ
Y
PDBJ
2010-04-03
REL
REL
3AM
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate
CA
CALCIUM ION
HOH
water
1RTU
PDB ENTRY 1RTU
PDB
experimental model
3AM
115
2
3AM
3AM
115
A
CA
116
3
CA
CA
116
A
HOH
117
4
HOH
HOH
117
A
HOH
118
4
HOH
HOH
118
A
HOH
119
4
HOH
HOH
119
A
HOH
120
4
HOH
HOH
120
A
HOH
121
4
HOH
HOH
121
A
HOH
122
4
HOH
HOH
122
A
HOH
123
4
HOH
HOH
123
A
HOH
124
4
HOH
HOH
124
A
HOH
125
4
HOH
HOH
125
A
HOH
126
4
HOH
HOH
126
A
HOH
127
4
HOH
HOH
127
A
HOH
128
4
HOH
HOH
128
A
HOH
129
4
HOH
HOH
129
A
HOH
130
4
HOH
HOH
130
A
HOH
131
4
HOH
HOH
131
A
HOH
132
4
HOH
HOH
132
A
HOH
133
4
HOH
HOH
133
A
HOH
134
4
HOH
HOH
134
A
HOH
135
4
HOH
HOH
135
A
HOH
136
4
HOH
HOH
136
A
HOH
137
4
HOH
HOH
137
A
HOH
138
4
HOH
HOH
138
A
HOH
139
4
HOH
HOH
139
A
HOH
140
4
HOH
HOH
140
A
HOH
141
4
HOH
HOH
141
A
HOH
142
4
HOH
HOH
142
A
HOH
143
4
HOH
HOH
143
A
HOH
144
4
HOH
HOH
144
A
HOH
145
4
HOH
HOH
145
A
HOH
146
4
HOH
HOH
146
A
HOH
147
4
HOH
HOH
147
A
HOH
148
4
HOH
HOH
148
A
HOH
149
4
HOH
HOH
149
A
HOH
150
4
HOH
HOH
150
A
HOH
151
4
HOH
HOH
151
A
HOH
152
4
HOH
HOH
152
A
HOH
153
4
HOH
HOH
153
A
HOH
154
4
HOH
HOH
154
A
HOH
155
4
HOH
HOH
155
A
HOH
156
4
HOH
HOH
156
A
HOH
157
4
HOH
HOH
157
A
HOH
158
4
HOH
HOH
158
A
HOH
159
4
HOH
HOH
159
A
HOH
160
4
HOH
HOH
160
A
HOH
161
4
HOH
HOH
161
A
HOH
162
4
HOH
HOH
162
A
HOH
163
4
HOH
HOH
163
A
HOH
164
4
HOH
HOH
164
A
HOH
165
4
HOH
HOH
165
A
HOH
166
4
HOH
HOH
166
A
HOH
167
4
HOH
HOH
167
A
HOH
168
4
HOH
HOH
168
A
HOH
169
4
HOH
HOH
169
A
HOH
170
4
HOH
HOH
170
A
HOH
171
4
HOH
HOH
171
A
HOH
172
4
HOH
HOH
172
A
HOH
173
4
HOH
HOH
173
A
HOH
174
4
HOH
HOH
174
A
HOH
175
4
HOH
HOH
175
A
HOH
176
4
HOH
HOH
176
A
HOH
177
4
HOH
HOH
177
A
HOH
178
4
HOH
HOH
178
A
HOH
179
4
HOH
HOH
179
A
HOH
180
4
HOH
HOH
180
A
HOH
181
4
HOH
HOH
181
A
HOH
182
4
HOH
HOH
182
A
HOH
183
4
HOH
HOH
183
A
HOH
184
4
HOH
HOH
184
A
HOH
185
4
HOH
HOH
185
A
HOH
186
4
HOH
HOH
186
A
HOH
187
4
HOH
HOH
187
A
HOH
188
4
HOH
HOH
188
A
HOH
189
4
HOH
HOH
189
A
HOH
190
4
HOH
HOH
190
A
HOH
191
4
HOH
HOH
191
A
HOH
192
4
HOH
HOH
192
A
HOH
193
4
HOH
HOH
193
A
HOH
194
4
HOH
HOH
194
A
HOH
195
4
HOH
HOH
195
A
HOH
196
4
HOH
HOH
196
A
HOH
197
4
HOH
HOH
197
A
HOH
198
4
HOH
HOH
198
A
HOH
199
4
HOH
HOH
199
A
HOH
200
4
HOH
HOH
200
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
207
4
HOH
HOH
207
A
HOH
208
4
HOH
HOH
208
A
HOH
209
4
HOH
HOH
209
A
HOH
210
4
HOH
HOH
210
A
HOH
211
4
HOH
HOH
211
A
HOH
212
4
HOH
HOH
212
A
HOH
213
4
HOH
HOH
213
A
HOH
214
4
HOH
HOH
214
A
HOH
215
4
HOH
HOH
215
A
HOH
216
4
HOH
HOH
216
A
HOH
217
4
HOH
HOH
217
A
HOH
218
4
HOH
HOH
218
A
HOH
219
4
HOH
HOH
219
A
HOH
220
4
HOH
HOH
220
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
242
4
HOH
HOH
242
A
HOH
243
4
HOH
HOH
243
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
HOH
246
4
HOH
HOH
246
A
HOH
247
4
HOH
HOH
247
A
HOH
248
4
HOH
HOH
248
A
HOH
249
4
HOH
HOH
249
A
HOH
250
4
HOH
HOH
250
A
HOH
251
4
HOH
HOH
251
A
HOH
252
4
HOH
HOH
252
A
HOH
253
4
HOH
HOH
253
A
HOH
254
4
HOH
HOH
254
A
HOH
255
4
HOH
HOH
255
A
HOH
256
4
HOH
HOH
256
A
HOH
257
4
HOH
HOH
257
A
HOH
258
4
HOH
HOH
258
A
HOH
259
4
HOH
HOH
259
A
HOH
260
4
HOH
HOH
260
A
HOH
261
4
HOH
HOH
261
A
HOH
262
4
HOH
HOH
262
A
HOH
263
4
HOH
HOH
263
A
HOH
264
4
HOH
HOH
264
A
HOH
265
4
HOH
HOH
265
A
HOH
266
4
HOH
HOH
266
A
HOH
267
4
HOH
HOH
267
A
HOH
268
4
HOH
HOH
268
A
HOH
269
4
HOH
HOH
269
A
HOH
270
4
HOH
HOH
270
A
HOH
271
4
HOH
HOH
271
A
HOH
272
4
HOH
HOH
272
A
HOH
273
4
HOH
HOH
273
A
HOH
274
4
HOH
HOH
274
A
HOH
275
4
HOH
HOH
275
A
HOH
276
4
HOH
HOH
276
A
HOH
277
4
HOH
HOH
277
A
HOH
278
4
HOH
HOH
278
A
HOH
279
4
HOH
HOH
279
A
HOH
280
4
HOH
HOH
280
A
HOH
281
4
HOH
HOH
281
A
HOH
282
4
HOH
HOH
282
A
CYS
1
n
1
CYS
1
A
ASP
2
n
2
ASP
2
A
ILE
3
n
3
ILE
3
A
PRO
4
n
4
PRO
4
A
GLN
5
n
5
GLN
5
A
SER
6
n
6
SER
6
A
THR
7
n
7
THR
7
A
ASN
8
n
8
ASN
8
A
CYS
9
n
9
CYS
9
A
GLY
10
n
10
GLY
10
A
GLY
11
n
11
GLY
11
A
ASN
12
n
12
ASN
12
A
VAL
13
n
13
VAL
13
A
TYR
14
n
14
TYR
14
A
SER
15
n
15
SER
15
A
ASN
16
n
16
ASN
16
A
ASP
17
n
17
ASP
17
A
ASP
18
n
18
ASP
18
A
ILE
19
n
19
ILE
19
A
ASN
20
n
20
ASN
20
A
THR
21
n
21
THR
21
A
ALA
22
n
22
ALA
22
A
ILE
23
n
23
ILE
23
A
GLN
24
n
24
GLN
24
A
GLY
25
n
25
GLY
25
A
ALA
26
n
26
ALA
26
A
LEU
27
n
27
LEU
27
A
ASP
28
n
28
ASP
28
A
ASP
29
n
29
ASP
29
A
VAL
30
n
30
VAL
30
A
ALA
31
n
31
ALA
31
A
ASN
32
n
32
ASN
32
A
GLY
33
n
33
GLY
33
A
ASP
34
n
34
ASP
34
A
ARG
35
n
35
ARG
35
A
PRO
36
n
36
PRO
36
A
ASP
37
n
37
ASP
37
A
ASN
38
n
38
ASN
38
A
TYR
39
n
39
TYR
39
A
PRO
40
n
40
PRO
40
A
HIS
41
n
41
HIS
41
A
GLN
42
n
42
GLN
42
A
TYR
43
n
43
TYR
43
A
TYR
44
n
44
TYR
44
A
ASP
45
n
45
ASP
45
A
GLU
46
n
46
GLU
46
A
ALA
47
n
47
ALA
47
A
SER
48
n
48
SER
48
A
GLU
49
n
49
GLU
49
A
ASP
50
n
50
ASP
50
A
ILE
51
n
51
ILE
51
A
THR
52
n
52
THR
52
A
LEU
53
n
53
LEU
53
A
CYS
54
n
54
CYS
54
A
CYS
55
n
55
CYS
55
A
GLY
56
n
56
GLY
56
A
SER
57
n
57
SER
57
A
GLY
58
n
58
GLY
58
A
PRO
59
n
59
PRO
59
A
TRP
60
n
60
TRP
60
A
SER
61
n
61
SER
61
A
GLU
62
n
62
GLU
62
A
PHE
63
n
63
PHE
63
A
PRO
64
n
64
PRO
64
A
LEU
65
n
65
LEU
65
A
VAL
66
n
66
VAL
66
A
TYR
67
n
67
TYR
67
A
ASN
68
n
68
ASN
68
A
GLY
69
n
69
GLY
69
A
PRO
70
n
70
PRO
70
A
TYR
71
n
71
TYR
71
A
TYR
72
n
72
TYR
72
A
SER
73
n
73
SER
73
A
SER
74
n
74
SER
74
A
ARG
75
n
75
ARG
75
A
ASP
76
n
76
ASP
76
A
ASN
77
n
77
ASN
77
A
TYR
78
n
78
TYR
78
A
VAL
79
n
79
VAL
79
A
SER
80
n
80
SER
80
A
PRO
81
n
81
PRO
81
A
GLY
82
n
82
GLY
82
A
PRO
83
n
83
PRO
83
A
ASP
84
n
84
ASP
84
A
ARG
85
n
85
ARG
85
A
VAL
86
n
86
VAL
86
A
ILE
87
n
87
ILE
87
A
TYR
88
n
88
TYR
88
A
GLN
89
n
89
GLN
89
A
THR
90
n
90
THR
90
A
ASN
91
n
91
ASN
91
A
THR
92
n
92
THR
92
A
GLY
93
n
93
GLY
93
A
GLU
94
n
94
GLU
94
A
PHE
95
n
95
PHE
95
A
CYS
96
n
96
CYS
96
A
ALA
97
n
97
ALA
97
A
THR
98
n
98
THR
98
A
VAL
99
n
99
VAL
99
A
THR
100
n
100
THR
100
A
HIS
101
n
101
HIS
101
A
THR
102
n
102
THR
102
A
GLY
103
n
103
GLY
103
A
ALA
104
n
104
ALA
104
A
ALA
105
n
105
ALA
105
A
SER
106
n
106
SER
106
A
TYR
107
n
107
TYR
107
A
ASP
108
n
108
ASP
108
A
GLY
109
n
109
GLY
109
A
PHE
110
n
110
PHE
110
A
THR
111
n
111
THR
111
A
GLN
112
n
112
GLN
112
A
CYS
113
n
113
CYS
113
A
SER
114
n
114
SER
114
A
author_and_software_defined_assembly
PISA
1
monomeric
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
GLN
112
A
OE1
GLN
112
1_555
79.8
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
163
D
O
HOH
1_555
79.4
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
163
D
O
HOH
1_555
111.9
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
164
D
O
HOH
1_555
130.9
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
164
D
O
HOH
1_555
77.9
A
HOH
163
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
164
D
O
HOH
1_555
149.7
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
165
D
O
HOH
1_555
137.7
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
165
D
O
HOH
1_555
78.7
A
HOH
163
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
165
D
O
HOH
1_555
75.6
A
HOH
164
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
165
D
O
HOH
1_555
78.7
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
126.0
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
154.1
A
HOH
163
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
76.1
A
HOH
164
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
83.9
A
HOH
165
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
79.9
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
72.2
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
125.2
A
HOH
163
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
107.9
A
HOH
164
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
86.2
A
HOH
165
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
148.4
A
HOH
166
D
O
HOH
1_555
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
71.0
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
CYS
9
A
N
CYS
9
A
O
ASN
12
A
O
ASN
12
A
N
HIS
41
A
N
HIS
41
A
O
GLU
62
A
O
GLU
62
A
N
SER
61
A
N
SER
61
A
O
TYR
88
A
O
TYR
88
A
N
ILE
87
A
N
ILE
87
A
O
ALA
97
A
O
ALA
97
A
N
THR
100
A
N
THR
100
A
O
THR
111
A
O
THR
111
1
A
ASN
77
-155.87
86.36
48.82
6.480
2.73
0.020
0.000
0.000
0.030
0.000
-0.050
0.978
0.975
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
0.127
0.117
0.118
0.960
31.050
2949
58481
5.000
98.760
0.125
0.116
1.00
0.25
0.954
0.336
0.009
0.018
0.018
RANDOM
1
anisotropic
THROUGHOUT
0.00
0
MOLECULAR REPLACEMENT
0.018
0.018
0.800
0.800
1.400
PDB ENTRY 1RTU
MAXIMUM LIKELIHOOD
MASK
0.018
0.018
0.960
31.050
166
1060
24
0
870
0.012
0.021
982
0.008
0.020
601
2.405
1.972
1358
3.562
3.000
1480
7.071
5.000
122
37.064
25.769
52
12.389
15.000
124
4.071
15.000
3
0.086
0.200
138
0.010
0.021
1143
0.003
0.020
194
1.122
1.500
601
0.287
1.500
241
1.691
2.000
972
2.160
3.000
381
2.803
4.500
385
0.735
3.000
1582
0.252
0.238
0.984
178
3571
3749
3749
20
86.340
8.0
0.96
34.3
3AGN
58543
0
0.052
1
72.2
14.7
98.9
0.295
0.960
0.984
7.43
3749
1
5.0
86.3
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
help@deposit.rcsb.org
Jan. 22, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.100
data collection
HKL-2000
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
MOLREP
Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complexed with adenosine 3'-monophosphate
1
N
N
2
N
N
3
N
N
4
N
N
A
ASN
16
A
ASN
16
HELX_P
A
ASN
32
A
ASN
32
1
1
17
A
ARG
35
A
ARG
35
HELX_P
A
TYR
39
A
TYR
39
5
2
5
A
GLU
46
A
GLU
46
HELX_P
A
ASP
50
A
ASP
50
5
3
5
disulf
2.023
A
A
A
CYS
1
A
SG
CYS
1
1_555
A
CYS
54
A
SG
CYS
54
1_555
disulf
2.059
B
B
A
CYS
1
A
SG
CYS
1
1_555
A
CYS
54
A
SG
CYS
54
1_555
disulf
2.050
A
CYS
9
A
SG
CYS
9
1_555
A
CYS
113
A
SG
CYS
113
1_555
disulf
2.030
A
A
CYS
55
A
SG
CYS
55
1_555
A
CYS
96
A
SG
CYS
96
1_555
disulf
2.041
B
A
CYS
55
A
SG
CYS
55
1_555
A
CYS
96
A
SG
CYS
96
1_555
metalc
2.402
A
ASP
50
A
O
ASP
50
1_555
A
CA
116
C
CA
CA
1_555
metalc
2.666
A
GLN
112
A
OE1
GLN
112
1_555
A
CA
116
C
CA
CA
1_555
metalc
2.312
A
CA
116
C
CA
CA
1_555
A
HOH
163
D
O
HOH
1_555
metalc
2.320
A
CA
116
C
CA
CA
1_555
A
HOH
164
D
O
HOH
1_555
metalc
2.347
A
CA
116
C
CA
CA
1_555
A
HOH
165
D
O
HOH
1_555
metalc
2.373
A
CA
116
C
CA
CA
1_555
A
HOH
166
D
O
HOH
1_555
metalc
2.511
A
CA
116
C
CA
CA
1_555
A
HOH
279
D
O
HOH
1_555
HYDROLASE
purine-specific endo-ribonuclease, HYDROLASE
A
TYR
39
A
TYR
39
1
A
PRO
40
A
PRO
40
8.00
A
GLY
58
A
GLY
58
1
A
PRO
59
A
PRO
59
7.21
A
GLY
58
A
GLY
58
1
A
PRO
59
A
PRO
59
7.13
A
GLY
69
A
GLY
69
1
A
PRO
70
A
PRO
70
5.43
RNU2_USTSP
UNP
1
1
P00654
CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS
PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS
1
114
3AGN
1
114
P00654
A
1
1
114
2
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
6
A
SER
6
A
CYS
9
A
CYS
9
A
ASN
12
A
ASN
12
A
SER
15
A
SER
15
A
HIS
41
A
HIS
41
A
TYR
43
A
TYR
43
A
TRP
60
A
TRP
60
A
PRO
64
A
PRO
64
A
ASP
84
A
ASP
84
A
GLN
89
A
GLN
89
A
PHE
95
A
PHE
95
A
THR
100
A
THR
100
A
THR
111
A
THR
111
A
GLN
112
A
GLN
112
BINDING SITE FOR RESIDUE 3AM A 115
A
3AM
115
Software
17
BINDING SITE FOR RESIDUE CA A 116
A
CA
116
Software
7
A
TYR
39
A
TYR
39
17
1_555
A
HIS
41
A
HIS
41
17
1_555
A
GLN
42
A
GLN
42
17
1_555
A
TYR
43
A
TYR
43
17
1_555
A
TYR
44
A
TYR
44
17
1_555
A
GLU
46
A
GLU
46
17
1_555
A
GLU
49
A
GLU
49
17
1_555
A
GLU
62
A
GLU
62
17
1_555
A
ARG
85
A
ARG
85
17
1_555
A
HIS
101
A
HIS
101
17
1_555
A
ASP
108
A
ASP
108
17
1_555
A
PHE
110
A
PHE
110
17
1_555
A
HOH
180
D
HOH
17
1_555
A
HOH
238
D
HOH
17
1_555
A
HOH
240
D
HOH
17
1_555
A
HOH
246
D
HOH
17
1_555
A
HOH
247
D
HOH
17
1_555
A
ASP
50
A
ASP
50
7
1_555
A
GLN
112
A
GLN
112
7
1_555
A
HOH
163
D
HOH
7
1_555
A
HOH
164
D
HOH
7
1_555
A
HOH
165
D
HOH
7
1_555
A
HOH
166
D
HOH
7
1_555
A
HOH
279
D
HOH
7
1_555
4
P 1 21 1