0.009159
0.000000
0.002463
0.000000
0.012417
0.000000
0.000000
0.000000
0.019543
0.00000
0.00000
0.00000
Akaji, K.
Konno, H.
Mitsui, H.
Teruya, K.
Hattori, Y.
Ozaki, T.
Kusunoki, M.
Sanjho, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
105.05
90.00
109.185
80.533
52.987
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C9 H17 N O2
171.237
n
2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
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
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 H10 N3 O 1
140.163
n
L-histidinal
L-peptide linking
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
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
O
N
3
N
C
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
N
N
22
S
C
N
23
N
C
N
24
N
O
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
C
N
29
N
C
N
30
N
C
N
31
N
C
N
32
N
O
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
H
N
49
N
H
N
50
N
N
N
51
S
C
N
52
N
C
N
53
N
O
N
54
N
C
N
55
N
C
N
56
N
C
N
57
N
N
N
58
N
C
N
59
N
N
N
60
N
N
N
61
N
O
N
62
N
H
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
N
N
78
S
C
N
79
N
C
N
80
N
O
N
81
N
C
N
82
N
C
N
83
N
O
N
84
N
N
N
85
N
O
N
86
N
H
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
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
O
N
101
N
O
N
102
N
O
N
103
N
H
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
N
N
111
R
C
N
112
N
C
N
113
N
O
N
114
N
C
N
115
N
S
N
116
N
O
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
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
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
O
N
153
N
O
N
154
N
H
N
155
N
H
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
N
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
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
Y
178
N
C
Y
179
N
N
Y
180
N
C
Y
181
N
C
Y
182
N
N
N
183
N
O
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
H
N
193
N
H
N
194
N
O
N
195
N
H
N
196
N
H
N
197
N
N
N
198
S
C
N
199
N
C
Y
200
N
C
Y
201
N
N
Y
202
N
C
Y
203
N
C
Y
204
N
N
N
205
N
C
N
206
N
O
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
S
C
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
O
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
N
C
N
244
N
C
N
245
N
C
N
246
N
C
N
247
N
O
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
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
N
N
262
S
C
N
263
N
C
N
264
N
O
N
265
N
C
N
266
N
C
N
267
N
C
N
268
N
C
N
269
N
N
N
270
N
O
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
N
N
287
S
C
N
288
N
C
N
289
N
O
N
290
N
C
N
291
N
C
N
292
N
S
N
293
N
C
N
294
N
O
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
N
N
307
S
C
N
308
N
C
N
309
N
O
N
310
N
C
Y
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
N
317
N
O
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
N
N
330
S
C
N
331
N
C
N
332
N
O
N
333
N
C
N
334
N
C
N
335
N
C
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
O
N
352
N
O
N
353
N
H
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
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
R
C
N
365
N
O
N
366
N
C
N
367
N
O
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
N
N
378
S
C
N
379
N
C
N
380
N
O
N
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
N
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
N
391
N
O
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
N
N
405
S
C
N
406
N
C
N
407
N
O
N
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
Y
413
N
C
Y
414
N
C
N
415
N
O
N
416
N
O
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
H
N
428
N
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
N
C
N
433
N
C
N
434
N
C
N
435
N
O
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
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
doub
N
14
N
sing
N
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
doub
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
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
doub
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
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
doub
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
doub
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
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
doub
N
125
N
sing
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
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
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
sing
N
159
N
sing
N
160
N
sing
N
161
N
doub
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
Y
175
N
sing
Y
176
N
doub
Y
177
N
doub
N
178
N
sing
Y
179
N
sing
N
180
N
sing
Y
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
Y
187
N
sing
Y
188
N
sing
Y
189
N
doub
N
190
N
doub
Y
191
N
doub
Y
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
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
doub
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
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
doub
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
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
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
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
doub
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
Y
303
N
doub
Y
304
N
sing
Y
305
N
sing
N
306
N
sing
Y
307
N
doub
N
308
N
sing
Y
309
N
doub
N
310
N
sing
Y
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
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
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
doub
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
Y
372
N
doub
Y
373
N
sing
Y
374
N
sing
N
375
N
sing
Y
376
N
doub
Y
377
N
sing
Y
378
N
sing
N
379
N
sing
Y
380
N
sing
Y
381
N
doub
N
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
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
doub
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
Y
400
N
doub
Y
401
N
sing
Y
402
N
sing
N
403
N
sing
Y
404
N
doub
N
405
N
sing
Y
406
N
doub
N
407
N
sing
Y
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
doub
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
sing
N
430
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
54
7962
7973
10.1021/jm200870n
22014094
Structure-Based Design, Synthesis, and Evaluation of Peptide-Mimetic SARS 3CL Protease Inhibitors.
2011
10.2210/pdb3avz/pdb
pdb_00003avz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
95
1
CCD
2010-01-27
ADSC QUANTUM 4r
Triangular with an asymmetric angle of 7.8 degree
SINGLE WAVELENGTH
M
x-ray
1
0.978
1.0
BL-6A
Photon Factory
0.978
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-6A
33832.602
3C-Like Proteinase
3.4.22.69
R188I
1
man
polymer
576.709
peptide ACE-SER-ALA-VAL-ALC-HIS-H
1
syn
polymer
18.015
water
18
nat
water
3CL-PRO, 3CLp, nsp5
no
no
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGH
SMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFC
YMHHMELPTGVHAGTDLEGKFYGPFVDIQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGH
SMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFC
YMHHMELPTGVHAGTDLEGKFYGPFVDIQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ
A
polypeptide(L)
no
yes
(ACE)SAV(ALC)(HSV)
XSAVAH
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
SARS-CoV
sample
1a
227859
SARS coronavirus
562
Escherichia coli
BL21(DE3)
Plasmid
pMAL-3CL-R188I
1
3.27
62.36
VAPOR DIFFUSION, HANGING DROP
6.0
9-11%(w/v) PEG 20000, 100mM MES pH 6.0, 5mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Other
Structure summary
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2011-12-14
1
1
2012-12-12
1
2
2015-07-01
1
3
2023-11-01
1
4
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
PDBJ
Y
PDBJ
2011-03-09
REL
REL
HOH
water
The peptide was chemically synthesized.
sample
2ZU5
PDB
experimental model
Enzyme inhibitor
peptide ACE-SER-ALA-VAL-ALC-HIS-H
Peptide-like
HOH
1
3
HOH
HOH
401
A
HOH
2
3
HOH
HOH
402
A
HOH
3
3
HOH
HOH
403
A
HOH
4
3
HOH
HOH
404
A
HOH
5
3
HOH
HOH
405
A
HOH
6
3
HOH
HOH
406
A
HOH
7
3
HOH
HOH
407
A
HOH
8
3
HOH
HOH
408
A
HOH
9
3
HOH
HOH
409
A
HOH
10
3
HOH
HOH
410
A
HOH
11
3
HOH
HOH
411
A
HOH
12
3
HOH
HOH
412
A
HOH
13
3
HOH
HOH
413
A
HOH
14
3
HOH
HOH
414
A
HOH
15
3
HOH
HOH
415
A
HOH
16
3
HOH
HOH
416
A
HOH
17
3
HOH
HOH
417
A
HOH
18
3
HOH
HOH
418
A
SER
1
n
1
SER
1
A
GLY
2
n
2
GLY
2
A
PHE
3
n
3
PHE
3
A
ARG
4
n
4
ARG
4
A
LYS
5
n
5
LYS
5
A
MET
6
n
6
MET
6
A
ALA
7
n
7
ALA
7
A
PHE
8
n
8
PHE
8
A
PRO
9
n
9
PRO
9
A
SER
10
n
10
SER
10
A
GLY
11
n
11
GLY
11
A
LYS
12
n
12
LYS
12
A
VAL
13
n
13
VAL
13
A
GLU
14
n
14
GLU
14
A
GLY
15
n
15
GLY
15
A
CYS
16
n
16
CYS
16
A
MET
17
n
17
MET
17
A
VAL
18
n
18
VAL
18
A
GLN
19
n
19
GLN
19
A
VAL
20
n
20
VAL
20
A
THR
21
n
21
THR
21
A
CYS
22
n
22
CYS
22
A
GLY
23
n
23
GLY
23
A
THR
24
n
24
THR
24
A
THR
25
n
25
THR
25
A
THR
26
n
26
THR
26
A
LEU
27
n
27
LEU
27
A
ASN
28
n
28
ASN
28
A
GLY
29
n
29
GLY
29
A
LEU
30
n
30
LEU
30
A
TRP
31
n
31
TRP
31
A
LEU
32
n
32
LEU
32
A
ASP
33
n
33
ASP
33
A
ASP
34
n
34
ASP
34
A
THR
35
n
35
THR
35
A
VAL
36
n
36
VAL
36
A
TYR
37
n
37
TYR
37
A
CYS
38
n
38
CYS
38
A
PRO
39
n
39
PRO
39
A
ARG
40
n
40
ARG
40
A
HIS
41
n
41
HIS
41
A
VAL
42
n
42
VAL
42
A
ILE
43
n
43
ILE
43
A
CYS
44
n
44
CYS
44
A
THR
45
n
45
THR
45
A
ALA
46
n
46
ALA
46
A
GLU
47
n
47
GLU
47
A
ASP
48
n
48
ASP
48
A
MET
49
n
49
MET
49
A
LEU
50
n
50
LEU
50
A
ASN
51
n
51
ASN
51
A
PRO
52
n
52
PRO
52
A
ASN
53
n
53
ASN
53
A
TYR
54
n
54
TYR
54
A
GLU
55
n
55
GLU
55
A
ASP
56
n
56
ASP
56
A
LEU
57
n
57
LEU
57
A
LEU
58
n
58
LEU
58
A
ILE
59
n
59
ILE
59
A
ARG
60
n
60
ARG
60
A
LYS
61
n
61
LYS
61
A
SER
62
n
62
SER
62
A
ASN
63
n
63
ASN
63
A
HIS
64
n
64
HIS
64
A
SER
65
n
65
SER
65
A
PHE
66
n
66
PHE
66
A
LEU
67
n
67
LEU
67
A
VAL
68
n
68
VAL
68
A
GLN
69
n
69
GLN
69
A
ALA
70
n
70
ALA
70
A
GLY
71
n
71
GLY
71
A
ASN
72
n
72
ASN
72
A
VAL
73
n
73
VAL
73
A
GLN
74
n
74
GLN
74
A
LEU
75
n
75
LEU
75
A
ARG
76
n
76
ARG
76
A
VAL
77
n
77
VAL
77
A
ILE
78
n
78
ILE
78
A
GLY
79
n
79
GLY
79
A
HIS
80
n
80
HIS
80
A
SER
81
n
81
SER
81
A
MET
82
n
82
MET
82
A
GLN
83
n
83
GLN
83
A
ASN
84
n
84
ASN
84
A
CYS
85
n
85
CYS
85
A
LEU
86
n
86
LEU
86
A
LEU
87
n
87
LEU
87
A
ARG
88
n
88
ARG
88
A
LEU
89
n
89
LEU
89
A
LYS
90
n
90
LYS
90
A
VAL
91
n
91
VAL
91
A
ASP
92
n
92
ASP
92
A
THR
93
n
93
THR
93
A
SER
94
n
94
SER
94
A
ASN
95
n
95
ASN
95
A
PRO
96
n
96
PRO
96
A
LYS
97
n
97
LYS
97
A
THR
98
n
98
THR
98
A
PRO
99
n
99
PRO
99
A
LYS
100
n
100
LYS
100
A
TYR
101
n
101
TYR
101
A
LYS
102
n
102
LYS
102
A
PHE
103
n
103
PHE
103
A
VAL
104
n
104
VAL
104
A
ARG
105
n
105
ARG
105
A
ILE
106
n
106
ILE
106
A
GLN
107
n
107
GLN
107
A
PRO
108
n
108
PRO
108
A
GLY
109
n
109
GLY
109
A
GLN
110
n
110
GLN
110
A
THR
111
n
111
THR
111
A
PHE
112
n
112
PHE
112
A
SER
113
n
113
SER
113
A
VAL
114
n
114
VAL
114
A
LEU
115
n
115
LEU
115
A
ALA
116
n
116
ALA
116
A
CYS
117
n
117
CYS
117
A
TYR
118
n
118
TYR
118
A
ASN
119
n
119
ASN
119
A
GLY
120
n
120
GLY
120
A
SER
121
n
121
SER
121
A
PRO
122
n
122
PRO
122
A
SER
123
n
123
SER
123
A
GLY
124
n
124
GLY
124
A
VAL
125
n
125
VAL
125
A
TYR
126
n
126
TYR
126
A
GLN
127
n
127
GLN
127
A
CYS
128
n
128
CYS
128
A
ALA
129
n
129
ALA
129
A
MET
130
n
130
MET
130
A
ARG
131
n
131
ARG
131
A
PRO
132
n
132
PRO
132
A
ASN
133
n
133
ASN
133
A
HIS
134
n
134
HIS
134
A
THR
135
n
135
THR
135
A
ILE
136
n
136
ILE
136
A
LYS
137
n
137
LYS
137
A
GLY
138
n
138
GLY
138
A
SER
139
n
139
SER
139
A
PHE
140
n
140
PHE
140
A
LEU
141
n
141
LEU
141
A
ASN
142
n
142
ASN
142
A
GLY
143
n
143
GLY
143
A
SER
144
n
144
SER
144
A
CYS
145
n
145
CYS
145
A
GLY
146
n
146
GLY
146
A
SER
147
n
147
SER
147
A
VAL
148
n
148
VAL
148
A
GLY
149
n
149
GLY
149
A
PHE
150
n
150
PHE
150
A
ASN
151
n
151
ASN
151
A
ILE
152
n
152
ILE
152
A
ASP
153
n
153
ASP
153
A
TYR
154
n
154
TYR
154
A
ASP
155
n
155
ASP
155
A
CYS
156
n
156
CYS
156
A
VAL
157
n
157
VAL
157
A
SER
158
n
158
SER
158
A
PHE
159
n
159
PHE
159
A
CYS
160
n
160
CYS
160
A
TYR
161
n
161
TYR
161
A
MET
162
n
162
MET
162
A
HIS
163
n
163
HIS
163
A
HIS
164
n
164
HIS
164
A
MET
165
n
165
MET
165
A
GLU
166
n
166
GLU
166
A
LEU
167
n
167
LEU
167
A
PRO
168
n
168
PRO
168
A
THR
169
n
169
THR
169
A
GLY
170
n
170
GLY
170
A
VAL
171
n
171
VAL
171
A
HIS
172
n
172
HIS
172
A
ALA
173
n
173
ALA
173
A
GLY
174
n
174
GLY
174
A
THR
175
n
175
THR
175
A
ASP
176
n
176
ASP
176
A
LEU
177
n
177
LEU
177
A
GLU
178
n
178
GLU
178
A
GLY
179
n
179
GLY
179
A
LYS
180
n
180
LYS
180
A
PHE
181
n
181
PHE
181
A
TYR
182
n
182
TYR
182
A
GLY
183
n
183
GLY
183
A
PRO
184
n
184
PRO
184
A
PHE
185
n
185
PHE
185
A
VAL
186
n
186
VAL
186
A
ASP
187
n
187
ASP
187
A
ILE
188
n
188
ILE
188
A
GLN
189
n
189
GLN
189
A
THR
190
n
190
THR
190
A
ALA
191
n
191
ALA
191
A
GLN
192
n
192
GLN
192
A
ALA
193
n
193
ALA
193
A
ALA
194
n
194
ALA
194
A
GLY
195
n
195
GLY
195
A
THR
196
n
196
THR
196
A
ASP
197
n
197
ASP
197
A
THR
198
n
198
THR
198
A
THR
199
n
199
THR
199
A
ILE
200
n
200
ILE
200
A
THR
201
n
201
THR
201
A
LEU
202
n
202
LEU
202
A
ASN
203
n
203
ASN
203
A
VAL
204
n
204
VAL
204
A
LEU
205
n
205
LEU
205
A
ALA
206
n
206
ALA
206
A
TRP
207
n
207
TRP
207
A
LEU
208
n
208
LEU
208
A
TYR
209
n
209
TYR
209
A
ALA
210
n
210
ALA
210
A
ALA
211
n
211
ALA
211
A
VAL
212
n
212
VAL
212
A
ILE
213
n
213
ILE
213
A
ASN
214
n
214
ASN
214
A
GLY
215
n
215
GLY
215
A
ASP
216
n
216
ASP
216
A
ARG
217
n
217
ARG
217
A
TRP
218
n
218
TRP
218
A
PHE
219
n
219
PHE
219
A
LEU
220
n
220
LEU
220
A
ASN
221
n
221
ASN
221
A
ARG
222
n
222
ARG
222
A
PHE
223
n
223
PHE
223
A
THR
224
n
224
THR
224
A
THR
225
n
225
THR
225
A
THR
226
n
226
THR
226
A
LEU
227
n
227
LEU
227
A
ASN
228
n
228
ASN
228
A
ASP
229
n
229
ASP
229
A
PHE
230
n
230
PHE
230
A
ASN
231
n
231
ASN
231
A
LEU
232
n
232
LEU
232
A
VAL
233
n
233
VAL
233
A
ALA
234
n
234
ALA
234
A
MET
235
n
235
MET
235
A
LYS
236
n
236
LYS
236
A
TYR
237
n
237
TYR
237
A
ASN
238
n
238
ASN
238
A
TYR
239
n
239
TYR
239
A
GLU
240
n
240
GLU
240
A
PRO
241
n
241
PRO
241
A
LEU
242
n
242
LEU
242
A
THR
243
n
243
THR
243
A
GLN
244
n
244
GLN
244
A
ASP
245
n
245
ASP
245
A
HIS
246
n
246
HIS
246
A
VAL
247
n
247
VAL
247
A
ASP
248
n
248
ASP
248
A
ILE
249
n
249
ILE
249
A
LEU
250
n
250
LEU
250
A
GLY
251
n
251
GLY
251
A
PRO
252
n
252
PRO
252
A
LEU
253
n
253
LEU
253
A
SER
254
n
254
SER
254
A
ALA
255
n
255
ALA
255
A
GLN
256
n
256
GLN
256
A
THR
257
n
257
THR
257
A
GLY
258
n
258
GLY
258
A
ILE
259
n
259
ILE
259
A
ALA
260
n
260
ALA
260
A
VAL
261
n
261
VAL
261
A
LEU
262
n
262
LEU
262
A
ASP
263
n
263
ASP
263
A
MET
264
n
264
MET
264
A
CYS
265
n
265
CYS
265
A
ALA
266
n
266
ALA
266
A
ALA
267
n
267
ALA
267
A
LEU
268
n
268
LEU
268
A
LYS
269
n
269
LYS
269
A
GLU
270
n
270
GLU
270
A
LEU
271
n
271
LEU
271
A
LEU
272
n
272
LEU
272
A
GLN
273
n
273
GLN
273
A
ASN
274
n
274
ASN
274
A
GLY
275
n
275
GLY
275
A
MET
276
n
276
MET
276
A
ASN
277
n
277
ASN
277
A
GLY
278
n
278
GLY
278
A
ARG
279
n
279
ARG
279
A
THR
280
n
280
THR
280
A
ILE
281
n
281
ILE
281
A
LEU
282
n
282
LEU
282
A
GLY
283
n
283
GLY
283
A
SER
284
n
284
SER
284
A
THR
285
n
285
THR
285
A
ILE
286
n
286
ILE
286
A
LEU
287
n
287
LEU
287
A
GLU
288
n
288
GLU
288
A
ASP
289
n
289
ASP
289
A
GLU
290
n
290
GLU
290
A
PHE
291
n
291
PHE
291
A
THR
292
n
292
THR
292
A
PRO
293
n
293
PRO
293
A
PHE
294
n
294
PHE
294
A
ASP
295
n
295
ASP
295
A
VAL
296
n
296
VAL
296
A
VAL
297
n
297
VAL
297
A
ARG
298
n
298
ARG
298
A
GLN
299
n
299
GLN
299
A
CYS
300
n
300
CYS
300
A
n
301
301
A
n
302
302
A
n
303
303
A
n
304
304
A
n
305
305
A
n
306
306
A
ACE
1
n
1
ACE
1
B
SER
2
n
2
SER
2
B
ALA
3
n
3
ALA
3
B
VAL
4
n
4
VAL
4
B
ALC
5
n
5
ALC
5
B
HSO
6
n
6
HSV
6
B
author_and_software_defined_assembly
PISA
2
dimeric
1220
-9
13740
B
ALC
5
2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
B
ALC
5
ALA
B
HSV
6
L-HISTIDINAL
B
HSV
6
HIS
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
VAL
73
A
O
VAL
73
A
N
ALA
70
A
N
ALA
70
A
O
LEU
67
A
O
LEU
67
A
N
THR
21
A
N
THR
21
A
N
VAL
20
A
N
VAL
20
A
O
LEU
27
A
O
LEU
27
A
N
LEU
30
A
N
LEU
30
A
O
TYR
37
A
O
TYR
37
A
N
CYS
38
A
N
CYS
38
A
O
LEU
87
A
O
LEU
87
A
O
ARG
88
A
O
ARG
88
A
N
SER
81
A
N
SER
81
A
N
LYS
102
A
N
LYS
102
A
O
PHE
159
A
O
PHE
159
A
N
MET
162
A
N
MET
162
A
O
THR
175
A
O
THR
175
A
O
SER
123
A
O
SER
123
A
N
ALA
116
A
N
ALA
116
A
N
SER
113
A
N
SER
113
A
O
PHE
150
A
O
PHE
150
A
N
ASN
151
A
N
ASN
151
A
O
SER
158
A
O
SER
158
A
N
GLU
166
A
N
GLU
166
B
O
VAL
4
B
O
VAL
4
1
A
SER
301
A
SER
301
1
Y
1
A
GLY
302
A
GLY
302
1
Y
1
A
VAL
303
A
VAL
303
1
Y
1
A
THR
304
A
THR
304
1
Y
1
A
PHE
305
A
PHE
305
1
Y
1
A
GLN
306
A
GLN
306
1
Y
1
-12.96
1.60
122.70
109.74
B
B
B
O
C
N
ACE
ACE
SER
1
1
2
Y
1
A
ASP
33
58.06
-125.80
1
A
ASN
51
-167.52
92.64
1
A
ASN
84
61.86
-125.33
1
A
TYR
154
57.15
-130.75
1
A
ALA
260
-44.09
150.59
63.180
0.01
0.00
-0.27
-0.09
0.00
-0.07
0.946
0.931
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.26261
0.22125
0.22351
2.46
43.45
765
15377
14594
5.0
95.17
10.281
0.234
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.270
0.80
0.80
1.40
2ZU5
MAXIMUM LIKELIHOOD
MASK
2.46
43.45
18
2383
0
0
2365
0.018
0.022
2418
1.781
1.961
3285
7.324
5.000
299
38.649
24.434
106
18.927
15.000
385
20.500
15.000
11
0.119
0.200
373
0.008
0.021
1837
0.931
1.500
1493
1.727
2.000
2415
2.243
3.000
925
3.578
4.500
870
0.371
0.304
2.527
36
669
705
20
59.09
2.46
50.00
3AVZ
15377
0
-3
0.122
0.122
1
16.736
7.4
97.4
0.487
2.50
2.54
2.526
0.487
1
5.7
83.2
data collection
HKL-2000
phasing
MOLREP
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
Structure of SARS 3CL protease with peptidic aldehyde inhibitor containing cyclohexyl side chain
1
N
N
2
N
N
3
N
N
A
SER
10
A
SER
10
HELX_P
A
GLY
15
A
GLY
15
1
1
6
A
HIS
41
A
HIS
41
HELX_P
A
CYS
44
A
CYS
44
5
2
4
A
GLU
47
A
GLU
47
HELX_P
A
ASN
51
A
ASN
51
5
3
5
A
ASN
53
A
ASN
53
HELX_P
A
ILE
59
A
ILE
59
1
4
7
A
ARG
60
A
ARG
60
HELX_P
A
LYS
61
A
LYS
61
5
5
2
A
SER
62
A
SER
62
HELX_P
A
PHE
66
A
PHE
66
5
6
5
A
ILE
200
A
ILE
200
HELX_P
A
ASN
214
A
ASN
214
1
7
15
A
THR
226
A
THR
226
HELX_P
A
TYR
237
A
TYR
237
1
8
12
A
THR
243
A
THR
243
HELX_P
A
LEU
250
A
LEU
250
1
9
8
A
LEU
250
A
LEU
250
HELX_P
A
GLY
258
A
GLY
258
1
10
9
A
ALA
260
A
ALA
260
HELX_P
A
GLY
275
A
GLY
275
1
11
16
A
THR
292
A
THR
292
HELX_P
A
GLN
299
A
GLN
299
1
12
8
covale
1.335
both
sing
B
ACE
1
B
C
ACE
1
1_555
B
SER
2
B
N
SER
2
1_555
covale
1.329
both
sing
B
VAL
4
B
C
VAL
4
1_555
B
ALC
5
B
N
ALC
5
1_555
covale
1.329
both
B
ALC
5
B
C
ALC
5
1_555
B
HSV
6
B
N
HSV
6
1_555
HYDROLASE/HYDROLASE inhibitor
HYDROLASE PROTEINASE CONVERTING, DESIGNED INHIBITOR, HYDROLASE-HYDROLASE inhibitor complex
R1A_CVHSA
UNP
1
3241
P0C6U8
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGH
SMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFC
YMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQG
3AVZ
PDB
2
3AVZ
3241
3546
3AVZ
1
306
P0C6U8
A
1
1
306
1
6
3AVZ
1
6
3AVZ
B
2
1
6
1
ARG
engineered mutation
ILE
188
3AVZ
A
P0C6U8
UNP
3428
188
7
3
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
73
A
VAL
73
A
LEU
75
A
LEU
75
A
LEU
67
A
LEU
67
A
ALA
70
A
ALA
70
A
MET
17
A
MET
17
A
CYS
22
A
CYS
22
A
THR
25
A
THR
25
A
LEU
32
A
LEU
32
A
THR
35
A
THR
35
A
PRO
39
A
PRO
39
A
LEU
86
A
LEU
86
A
VAL
91
A
VAL
91
A
VAL
77
A
VAL
77
A
GLN
83
A
GLN
83
A
TYR
101
A
TYR
101
A
PHE
103
A
PHE
103
A
CYS
156
A
CYS
156
A
GLU
166
A
GLU
166
A
HIS
172
A
HIS
172
A
THR
175
A
THR
175
A
SER
121
A
SER
121
A
ALA
129
A
ALA
129
A
THR
111
A
THR
111
A
TYR
118
A
TYR
118
A
VAL
148
A
VAL
148
A
ASP
153
A
ASP
153
A
CYS
156
A
CYS
156
A
GLU
166
A
GLU
166
B
VAL
4
B
VAL
4
B
ALC
5
B
ALC
5
BINDING SITE FOR CHAIN B OF PEPTIDE ACE-SER-ALA-VAL-ALC-HIS-H
Software
15
A
HIS
41
A
HIS
41
15
1_555
A
ASN
142
A
ASN
142
15
1_555
A
GLY
143
A
GLY
143
15
1_555
A
SER
144
A
SER
144
15
1_555
A
CYS
145
A
CYS
145
15
1_555
A
HIS
163
A
HIS
163
15
1_555
A
HIS
164
A
HIS
164
15
1_555
A
MET
165
A
MET
165
15
1_555
A
GLU
166
A
GLU
166
15
1_555
A
ASP
187
A
ASP
187
15
1_555
A
ILE
188
A
ILE
188
15
1_555
A
GLN
189
A
GLN
189
15
1_555
A
THR
190
A
THR
190
15
1_555
A
ALA
191
A
ALA
191
15
1_555
A
GLN
192
A
GLN
192
15
1_555
5
C 1 2 1