0.016181
0.000000
0.000000
0.000000
0.016181
0.000000
0.000000
0.000000
0.015161
0.00000
0.00000
0.00000
Tsai, C.-J.
Liu, J.-H.
Liao, Y.-D.
Chen, L.-y.
Cheng, P.-T.
Sun, Y.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
61.800
61.800
65.960
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
C19 H25 N8 O12 P
588.422
CYTIDYL-2'-5'-PHOSPHO-GUANOSINE
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
C5 H7 N O3
129.114
n
PYROGLUTAMIC ACID
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
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
N
C
N
76
N
N
N
77
N
N
Y
78
N
C
Y
79
N
C
N
80
N
C
N
81
N
O
Y
82
N
N
Y
83
N
C
Y
84
N
N
N
85
R
C
N
86
R
C
N
87
N
O
N
88
S
C
N
89
N
O
N
90
R
C
N
91
N
O
N
92
N
C
N
93
N
O
N
94
R
P
N
95
N
O
N
96
N
O
N
97
N
O
N
98
N
C
N
99
R
C
N
100
N
O
N
101
R
C
N
102
N
O
N
103
R
C
N
104
N
O
N
105
R
C
N
106
N
N
N
107
N
C
N
108
N
O
N
109
N
N
N
110
N
C
N
111
N
C
N
112
N
C
N
113
N
N
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
H
N
127
N
H
N
128
N
H
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
H
N
137
N
H
N
138
N
H
N
139
N
N
N
140
R
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
S
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
N
N
154
S
C
N
155
N
C
N
156
N
O
N
157
N
C
N
158
N
C
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
O
N
163
N
H
N
164
N
H
N
165
N
H
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
N
N
174
S
C
N
175
N
C
N
176
N
O
N
177
N
C
N
178
N
C
N
179
N
C
N
180
N
O
N
181
N
O
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
H
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
N
N
193
N
C
N
194
N
C
N
195
N
O
N
196
N
O
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
Y
207
N
C
Y
208
N
N
Y
209
N
C
Y
210
N
C
Y
211
N
N
N
212
N
O
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
H
N
222
N
H
N
223
N
O
N
224
N
H
N
225
N
H
N
226
N
N
N
227
S
C
N
228
N
C
N
229
N
O
N
230
S
C
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
O
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
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
C
N
255
N
C
N
256
N
O
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
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
N
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
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
N
N
296
S
C
N
297
N
C
N
298
N
O
N
299
N
C
N
300
N
C
N
301
N
S
N
302
N
C
N
303
N
O
N
304
N
H
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
H
N
315
N
N
N
316
S
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
O
N
321
N
C
N
322
N
O
N
323
N
O
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
N
342
N
O
N
343
N
H
N
344
N
H
N
345
N
H
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
H
N
354
N
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
N
359
N
C
N
360
N
C
N
361
N
O
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
O
N
377
N
O
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
384
N
H
N
385
N
S
N
386
N
O
N
387
N
O
N
388
N
O
N
389
N
O
N
390
N
N
N
391
S
C
N
392
N
C
N
393
N
O
N
394
R
C
N
395
N
O
N
396
N
C
N
397
N
O
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
N
C
Y
412
N
C
Y
413
N
C
Y
414
N
C
Y
415
N
N
Y
416
N
C
Y
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
N
421
N
O
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
C
Y
444
N
C
N
445
N
O
N
446
N
O
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
N
N
459
S
C
N
460
N
C
N
461
N
O
N
462
N
C
N
463
N
C
N
464
N
C
N
465
N
O
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
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
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
Y
78
N
doub
Y
79
N
sing
N
80
N
sing
Y
81
N
sing
N
82
N
doub
Y
83
N
doub
Y
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
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
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
sing
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
sing
N
129
N
doub
N
130
N
sing
N
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
doub
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
doub
N
146
N
sing
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
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
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
sing
N
195
N
doub
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
doub
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
Y
209
N
sing
Y
210
N
doub
Y
211
N
doub
N
212
N
sing
Y
213
N
sing
N
214
N
sing
Y
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
doub
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
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
doub
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
doub
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
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
doub
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
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
doub
N
319
N
doub
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
doub
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
doub
N
340
N
sing
Y
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
doub
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
doub
N
376
N
doub
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
sing
N
384
N
sing
N
385
N
doub
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
doub
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
Y
406
N
doub
Y
407
N
sing
Y
408
N
sing
N
409
N
sing
Y
410
N
doub
Y
411
N
sing
Y
412
N
sing
N
413
N
sing
Y
414
N
sing
Y
415
N
doub
N
416
N
sing
Y
417
N
doub
N
418
N
sing
Y
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
doub
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
Y
434
N
doub
Y
435
N
sing
Y
436
N
sing
N
437
N
sing
Y
438
N
doub
N
439
N
sing
Y
440
N
doub
N
441
N
sing
Y
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
doub
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
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
To be Published
0353
Nonproductive and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with C(2,5 Cpg) and D(Apcpgpa)
10.2210/pdb1oj1/pdb
pdb_00001oj1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
110.0
1
MIRRIE
IMAGE PLATE
RIGAKU IMAGE PLATE
NI
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU RU300
12185.388
RC-RNASE6 RIBONUCLEASE
1
nat
polymer
588.422
CYTIDYL-2'-5'-PHOSPHO-GUANOSINE
1
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
107
nat
water
no
yes
(PCA)DWDTFQKKHLTDTKKVKCDVEMKKALFDCKKTNTFIFARPPRVQALCKNIKNNTNVLSRDVFYLPQCNRKKLPCH
YRLDGSTNTICLTCMKELPIHFAGVGKCP
QDWDTFQKKHLTDTKKVKCDVEMKKALFDCKKTNTFIFARPPRVQALCKNIKNNTNVLSRDVFYLPQCNRKKLPCHYRLD
GSTNTICLTCMKELPIHFAGVGKCP
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
BULL FROG
sample
8400
OOCYTES
RANA CATESBEIANA
1
2.59
53
7.00
pH 7.00
diffrn_source
refine
struct_conn
entity_poly
pdbx_database_status
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Data collection
Derived calculations
Refinement description
Other
Polymer sequence
Data collection
Database references
Refinement description
1
0
2004-07-15
1
1
2011-05-08
1
2
2011-07-13
1
3
2017-06-28
1
4
2019-05-22
2
0
2020-03-11
2
1
2023-12-13
_diffrn_source.type
_refine.pdbx_ls_cross_valid_method
_struct_conn.pdbx_leaving_atom_flag
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_database_status.status_code_sf
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RETRO AND NOVEL BINDING MODES IN CYTOTOXIC RIBONUCLEASES FROM RANA CATESBEIANA OF TWO CRYSTAL STRUCTURES COMPLEXED WITH (2',5'CPG) AND D(APCPGPA)
PDBE
Y
PDBE
2003-06-28
REL
REL
1
A
O
HOH
2004
9.22
1
A
O
HOH
2013
6.62
1
A
O
HOH
2014
7.26
1
A
O
HOH
2029
6.47
CG2
CYTIDYL-2'-5'-PHOSPHO-GUANOSINE
SO4
SULFATE ION
HOH
water
1ONC
PDB ENTRY 1ONC
PDB
experimental model
CG2
1106
2
CG2
CG2
1106
A
SO4
1107
3
SO4
SO4
1107
A
HOH
2001
4
HOH
HOH
2001
A
HOH
2002
4
HOH
HOH
2002
A
HOH
2003
4
HOH
HOH
2003
A
HOH
2004
4
HOH
HOH
2004
A
HOH
2005
4
HOH
HOH
2005
A
HOH
2006
4
HOH
HOH
2006
A
HOH
2007
4
HOH
HOH
2007
A
HOH
2008
4
HOH
HOH
2008
A
HOH
2009
4
HOH
HOH
2009
A
HOH
2010
4
HOH
HOH
2010
A
HOH
2011
4
HOH
HOH
2011
A
HOH
2012
4
HOH
HOH
2012
A
HOH
2013
4
HOH
HOH
2013
A
HOH
2014
4
HOH
HOH
2014
A
HOH
2015
4
HOH
HOH
2015
A
HOH
2016
4
HOH
HOH
2016
A
HOH
2017
4
HOH
HOH
2017
A
HOH
2018
4
HOH
HOH
2018
A
HOH
2019
4
HOH
HOH
2019
A
HOH
2020
4
HOH
HOH
2020
A
HOH
2021
4
HOH
HOH
2021
A
HOH
2022
4
HOH
HOH
2022
A
HOH
2023
4
HOH
HOH
2023
A
HOH
2024
4
HOH
HOH
2024
A
HOH
2025
4
HOH
HOH
2025
A
HOH
2026
4
HOH
HOH
2026
A
HOH
2027
4
HOH
HOH
2027
A
HOH
2028
4
HOH
HOH
2028
A
HOH
2029
4
HOH
HOH
2029
A
HOH
2030
4
HOH
HOH
2030
A
HOH
2031
4
HOH
HOH
2031
A
HOH
2032
4
HOH
HOH
2032
A
HOH
2033
4
HOH
HOH
2033
A
HOH
2034
4
HOH
HOH
2034
A
HOH
2035
4
HOH
HOH
2035
A
HOH
2036
4
HOH
HOH
2036
A
HOH
2037
4
HOH
HOH
2037
A
HOH
2038
4
HOH
HOH
2038
A
HOH
2039
4
HOH
HOH
2039
A
HOH
2040
4
HOH
HOH
2040
A
HOH
2041
4
HOH
HOH
2041
A
HOH
2042
4
HOH
HOH
2042
A
HOH
2043
4
HOH
HOH
2043
A
HOH
2044
4
HOH
HOH
2044
A
HOH
2045
4
HOH
HOH
2045
A
HOH
2046
4
HOH
HOH
2046
A
HOH
2047
4
HOH
HOH
2047
A
HOH
2048
4
HOH
HOH
2048
A
HOH
2049
4
HOH
HOH
2049
A
HOH
2050
4
HOH
HOH
2050
A
HOH
2051
4
HOH
HOH
2051
A
HOH
2052
4
HOH
HOH
2052
A
HOH
2053
4
HOH
HOH
2053
A
HOH
2054
4
HOH
HOH
2054
A
HOH
2055
4
HOH
HOH
2055
A
HOH
2056
4
HOH
HOH
2056
A
HOH
2057
4
HOH
HOH
2057
A
HOH
2058
4
HOH
HOH
2058
A
HOH
2059
4
HOH
HOH
2059
A
HOH
2060
4
HOH
HOH
2060
A
HOH
2061
4
HOH
HOH
2061
A
HOH
2062
4
HOH
HOH
2062
A
HOH
2063
4
HOH
HOH
2063
A
HOH
2064
4
HOH
HOH
2064
A
HOH
2065
4
HOH
HOH
2065
A
HOH
2066
4
HOH
HOH
2066
A
HOH
2067
4
HOH
HOH
2067
A
HOH
2068
4
HOH
HOH
2068
A
HOH
2069
4
HOH
HOH
2069
A
HOH
2070
4
HOH
HOH
2070
A
HOH
2071
4
HOH
HOH
2071
A
HOH
2072
4
HOH
HOH
2072
A
HOH
2073
4
HOH
HOH
2073
A
HOH
2074
4
HOH
HOH
2074
A
HOH
2075
4
HOH
HOH
2075
A
HOH
2076
4
HOH
HOH
2076
A
HOH
2077
4
HOH
HOH
2077
A
HOH
2078
4
HOH
HOH
2078
A
HOH
2079
4
HOH
HOH
2079
A
HOH
2080
4
HOH
HOH
2080
A
HOH
2081
4
HOH
HOH
2081
A
HOH
2082
4
HOH
HOH
2082
A
HOH
2083
4
HOH
HOH
2083
A
HOH
2084
4
HOH
HOH
2084
A
HOH
2085
4
HOH
HOH
2085
A
HOH
2086
4
HOH
HOH
2086
A
HOH
2087
4
HOH
HOH
2087
A
HOH
2088
4
HOH
HOH
2088
A
HOH
2089
4
HOH
HOH
2089
A
HOH
2090
4
HOH
HOH
2090
A
HOH
2091
4
HOH
HOH
2091
A
HOH
2092
4
HOH
HOH
2092
A
HOH
2093
4
HOH
HOH
2093
A
HOH
2094
4
HOH
HOH
2094
A
HOH
2095
4
HOH
HOH
2095
A
HOH
2096
4
HOH
HOH
2096
A
HOH
2097
4
HOH
HOH
2097
A
HOH
2098
4
HOH
HOH
2098
A
HOH
2099
4
HOH
HOH
2099
A
HOH
2100
4
HOH
HOH
2100
A
HOH
2101
4
HOH
HOH
2101
A
HOH
2102
4
HOH
HOH
2102
A
HOH
2103
4
HOH
HOH
2103
A
HOH
2104
4
HOH
HOH
2104
A
HOH
2105
4
HOH
HOH
2105
A
HOH
2106
4
HOH
HOH
2106
A
HOH
2107
4
HOH
HOH
2107
A
PCA
1
n
1
PCA
1
A
ASP
2
n
2
ASP
2
A
TRP
3
n
3
TRP
3
A
ASP
4
n
4
ASP
4
A
THR
5
n
5
THR
5
A
PHE
6
n
6
PHE
6
A
GLN
7
n
7
GLN
7
A
LYS
8
n
8
LYS
8
A
LYS
9
n
9
LYS
9
A
HIS
10
n
10
HIS
10
A
LEU
11
n
11
LEU
11
A
THR
12
n
12
THR
12
A
ASP
13
n
13
ASP
13
A
THR
14
n
14
THR
14
A
LYS
15
n
15
LYS
15
A
LYS
16
n
16
LYS
16
A
VAL
17
n
17
VAL
17
A
LYS
18
n
18
LYS
18
A
CYS
19
n
19
CYS
19
A
ASP
20
n
20
ASP
20
A
VAL
21
n
21
VAL
21
A
GLU
22
n
22
GLU
22
A
MET
23
n
23
MET
23
A
LYS
24
n
24
LYS
24
A
LYS
25
n
25
LYS
25
A
ALA
26
n
26
ALA
26
A
LEU
27
n
27
LEU
27
A
PHE
28
n
28
PHE
28
A
ASP
29
n
29
ASP
29
A
CYS
30
n
30
CYS
30
A
LYS
31
n
31
LYS
31
A
LYS
32
n
32
LYS
32
A
THR
33
n
33
THR
33
A
ASN
34
n
34
ASN
34
A
THR
35
n
35
THR
35
A
PHE
36
n
36
PHE
36
A
ILE
37
n
37
ILE
37
A
PHE
38
n
38
PHE
38
A
ALA
39
n
39
ALA
39
A
ARG
40
n
40
ARG
40
A
PRO
41
n
41
PRO
41
A
PRO
42
n
42
PRO
42
A
ARG
43
n
43
ARG
43
A
VAL
44
n
44
VAL
44
A
GLN
45
n
45
GLN
45
A
ALA
46
n
46
ALA
46
A
LEU
47
n
47
LEU
47
A
CYS
48
n
48
CYS
48
A
LYS
49
n
49
LYS
49
A
ASN
50
n
50
ASN
50
A
ILE
51
n
51
ILE
51
A
LYS
52
n
52
LYS
52
A
ASN
53
n
53
ASN
53
A
ASN
54
n
54
ASN
54
A
THR
55
n
55
THR
55
A
ASN
56
n
56
ASN
56
A
VAL
57
n
57
VAL
57
A
LEU
58
n
58
LEU
58
A
SER
59
n
59
SER
59
A
ARG
60
n
60
ARG
60
A
ASP
61
n
61
ASP
61
A
VAL
62
n
62
VAL
62
A
PHE
63
n
63
PHE
63
A
TYR
64
n
64
TYR
64
A
LEU
65
n
65
LEU
65
A
PRO
66
n
66
PRO
66
A
GLN
67
n
67
GLN
67
A
CYS
68
n
68
CYS
68
A
ASN
69
n
69
ASN
69
A
ARG
70
n
70
ARG
70
A
LYS
71
n
71
LYS
71
A
LYS
72
n
72
LYS
72
A
LEU
73
n
73
LEU
73
A
PRO
74
n
74
PRO
74
A
CYS
75
n
75
CYS
75
A
HIS
76
n
76
HIS
76
A
TYR
77
n
77
TYR
77
A
ARG
78
n
78
ARG
78
A
LEU
79
n
79
LEU
79
A
ASP
80
n
80
ASP
80
A
GLY
81
n
81
GLY
81
A
SER
82
n
82
SER
82
A
THR
83
n
83
THR
83
A
ASN
84
n
84
ASN
84
A
THR
85
n
85
THR
85
A
ILE
86
n
86
ILE
86
A
CYS
87
n
87
CYS
87
A
LEU
88
n
88
LEU
88
A
THR
89
n
89
THR
89
A
CYS
90
n
90
CYS
90
A
MET
91
n
91
MET
91
A
LYS
92
n
92
LYS
92
A
GLU
93
n
93
GLU
93
A
LEU
94
n
94
LEU
94
A
PRO
95
n
95
PRO
95
A
ILE
96
n
96
ILE
96
A
HIS
97
n
97
HIS
97
A
PHE
98
n
98
PHE
98
A
ALA
99
n
99
ALA
99
A
GLY
100
n
100
GLY
100
A
VAL
101
n
101
VAL
101
A
GLY
102
n
102
GLY
102
A
LYS
103
n
103
LYS
103
A
CYS
104
n
104
CYS
104
A
PRO
105
n
105
PRO
105
A
author_and_software_defined_assembly
PQS
1
monomeric
A
PCA
1
PYROGLUTAMIC ACID
A
PCA
1
GLU
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
THR
12
A
N
THR
12
A
O
ILE
37
A
O
ILE
37
A
N
ASN
34
A
N
ASN
34
A
O
CYS
68
A
O
CYS
68
A
N
LYS
71
A
N
LYS
71
A
O
HIS
76
A
O
HIS
76
A
N
VAL
57
A
N
VAL
57
A
O
LEU
88
A
O
LEU
88
A
N
MET
91
A
N
MET
91
A
O
LEU
94
A
O
LEU
94
A
N
PHE
63
A
N
PHE
63
A
O
ASN
84
A
O
ASN
84
1
A
LYS
16
-100.18
78.70
1
A
CYS
75
-149.84
47.90
PROTEIN.PARAM
PROTEIN.TOP
CPG_NOH.PARAM
CPG_NOH.TOP
ION.PARAM
ION.TOP
WATER.PARAM
WATER.TOP
27.3
5.62
0.00
0.00
5.62
0.00
11.24
0.2513
0.009
0.203
0.203
2.1
20.0
722
6785
10.6
86.3
RANDOM
1
RESTRAINED
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
PDB ENTRY 1ONC
FLAT
67.3609
0.39614
0.30
0.23
5.00
0.22
0.17
2.1
20.0
107
1000
45
0
848
0.01
1.3
22.7
0.91
1.10
1.50
1.61
2.00
2.04
2.00
3.03
2.50
0.297
0.029
0.209
2.23
102
804
6
11.3
71
6.8
2.100
20.000
1OJ1
53962
2.000
0.07500
1
17.5000
3.000
98.6
0.04500
2.10
2.14
3.450
1
98.2
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
Nonproductive and Novel Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with (2,5 CpG) and d(ApCpGpA)
1
N
N
2
N
N
3
N
N
4
N
N
A
ASP
2
A
ASP
2
HELX_P
A
HIS
10
A
HIS
10
1
1
9
A
LYS
18
A
LYS
18
HELX_P
A
MET
23
A
MET
23
1
2
6
A
ARG
40
A
ARG
40
HELX_P
A
LEU
47
A
LEU
47
1
3
8
disulf
2.029
A
CYS
19
A
SG
CYS
19
1_555
A
CYS
68
A
SG
CYS
68
1_555
disulf
2.031
A
CYS
30
A
SG
CYS
30
1_555
A
CYS
75
A
SG
CYS
75
1_555
disulf
2.029
A
CYS
48
A
SG
CYS
48
1_555
A
CYS
90
A
SG
CYS
90
1_555
disulf
2.032
A
CYS
87
A
SG
CYS
87
1_555
A
CYS
104
A
SG
CYS
104
1_555
covale
1.332
both
A
PCA
1
A
C
PCA
1
1_555
A
ASP
2
A
N
ASP
2
1_555
HYDROLASE
CYTOTOXIC RIBONUCLEASES, ANTI-TUMOR ACTIVITY, SIALIC BINDING AND NUCLEOTIDE BINDING, HYDROLASE
A
LEU
73
A
LEU
73
1
A
PRO
74
A
PRO
74
0.54
Q9DFY5
UNP
1
Q9DFY5
24
128
1OJ1
1
105
Q9DFY5
A
1
1
105
1
ASP
conflict
ASN
53
1OJ1
A
Q9DFY5
UNP
76
53
2
3
3
2
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
11
A
LEU
11
A
THR
12
A
THR
12
A
ILE
37
A
ILE
37
A
PHE
38
A
PHE
38
A
THR
33
A
THR
33
A
THR
35
A
THR
35
A
GLN
67
A
GLN
67
A
LYS
72
A
LYS
72
A
HIS
76
A
HIS
76
A
ASP
80
A
ASP
80
A
THR
55
A
THR
55
A
LEU
58
A
LEU
58
A
ILE
86
A
ILE
86
A
MET
91
A
MET
91
A
LEU
94
A
LEU
94
A
VAL
101
A
VAL
101
A
PHE
63
A
PHE
63
A
TYR
64
A
TYR
64
A
THR
83
A
THR
83
A
ASN
84
A
ASN
84
BINDING SITE FOR RESIDUE SO4 A1107
Software
6
BINDING SITE FOR RESIDUE CG2 A1106
Software
13
A
LYS
9
A
LYS
9
6
1_555
A
HIS
10
A
HIS
10
6
1_555
A
PHE
98
A
PHE
98
6
1_555
A
CG2
1106
B
CG2
6
1_555
A
HOH
2101
D
HOH
6
1_555
A
HOH
2107
D
HOH
6
1_555
A
HIS
10
A
HIS
10
13
1_555
A
ASN
34
A
ASN
34
13
1_555
A
THR
35
A
THR
35
13
1_555
A
LYS
49
A
LYS
49
13
1_555
A
ASN
50
A
ASN
50
13
1_555
A
GLN
67
A
GLN
67
13
1_555
A
ASN
69
A
ASN
69
13
1_555
A
PHE
98
A
PHE
98
13
1_555
A
ALA
99
A
ALA
99
13
1_555
A
GLY
100
A
GLY
100
13
1_555
A
VAL
101
A
VAL
101
13
1_555
A
SO4
1107
C
SO4
13
1_555
A
HOH
2106
D
HOH
13
1_555
96
P 43 21 2