0.018553
0.000000
0.000000
0.000000
0.017198
0.000000
0.000000
0.000000
0.016313
0.00000
0.00000
0.00000
Romano, K.P.
Schiffer, C.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
53.900
58.146
61.300
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
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
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
Zn 2
65.409
ZINC ION
non-polymer
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
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
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
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
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
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
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
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
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
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
S
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
O
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
R
C
N
314
N
O
N
315
N
C
N
316
N
O
N
317
N
H
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
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
N
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
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
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
N
364
N
O
N
365
N
O
N
366
N
H
N
367
N
H
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
N
382
N
C
N
383
N
C
N
384
N
O
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
ZN
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
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
doub
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
N
107
N
sing
N
108
N
doub
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
doub
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
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
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
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
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
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
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
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
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
doub
N
291
N
doub
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
doub
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
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
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
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
US
J.Virol.
JOVIAM
0825
1098-5514
85
6106
6116
10.1128/JVI.00377-11
21507982
Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease.
2011
10.2210/pdb3rc4/pdb
pdb_00003rc4
1
2010-10-28
SINGLE WAVELENGTH
M
x-ray
1
1.0
14-BM-C
APS
SYNCHROTRON
APS BEAMLINE 14-BM-C
21487.330
NS3/4A Protease
UNP residues 36-218
A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, V1044E, L1047Q, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S
1
man
polymer
1270.451
Product TRIF
1
syn
polymer
96.063
SULFATE ION
1
syn
non-polymer
65.409
ZINC ION
1
syn
non-polymer
18.015
water
154
nat
water
no
no
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQTFLATSINGVLWTVYHGA
GTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSA
GGPLLCPAGHAVGIFRAAVSTRGVAKAVDFIPVESLETTMRSP
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQTFLATSINGVLWTVYHGA
GTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSA
GGPLLCPAGHAVGIFRAAVSTRGVAKAVDFIPVESLETTMRSP
A
polypeptide(L)
no
no
PPPPPPPPSSTPC
PPPPPPPPSSTPC
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
sample
1
203
31646
Hepatitis C virus subtype 1a
469008
Escherichia coli
BL21(DE3)
plasmid
Biological sequence
pET28a
1
2.12
41.97
VAPOR DIFFUSION, HANGING DROP
6.5
20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
entity
entity_name_com
entity_src_gen
pdbx_entity_src_syn
struct
struct_ref
struct_ref_seq
struct_ref_seq_dif
software
citation
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Database references
Source and taxonomy
Structure summary
Refinement description
Database references
Derived calculations
Data collection
Refinement description
1
0
2011-05-04
1
1
2011-07-13
1
2
2017-06-28
1
3
2017-11-08
1
4
2023-07-26
1
5
2023-09-13
_entity.pdbx_description
_entity.pdbx_fragment
_entity.pdbx_mutation
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
_entity_src_gen.pdbx_gene_src_gene
_entity_src_gen.pdbx_seq_type
_pdbx_entity_src_syn.pdbx_beg_seq_num
_pdbx_entity_src_syn.pdbx_end_seq_num
_struct.pdbx_descriptor
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.language
_software.location
_software.name
_software.type
_software.version
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.title
_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_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_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_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2011-03-30
REL
REL
SO4
SULFATE ION
ZN
ZINC ION
HOH
water
9606
human
Homo sapiens
sample
1
13
THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.
3M5M
PDB entry 3M5M
PDB
experimental model
SO4
1
3
SO4
SO4
1
A
ZN
1
4
ZN
ZN
1183
A
HOH
2
5
HOH
HOH
2
A
HOH
3
5
HOH
HOH
3
A
HOH
4
5
HOH
HOH
4
A
HOH
5
5
HOH
HOH
5
A
HOH
6
5
HOH
HOH
6
A
HOH
7
5
HOH
HOH
7
A
HOH
8
5
HOH
HOH
8
A
HOH
9
5
HOH
HOH
9
A
HOH
10
5
HOH
HOH
10
A
HOH
11
5
HOH
HOH
11
A
HOH
12
5
HOH
HOH
12
A
HOH
13
5
HOH
HOH
13
A
HOH
14
5
HOH
HOH
14
A
HOH
15
5
HOH
HOH
15
A
HOH
16
5
HOH
HOH
16
A
HOH
17
5
HOH
HOH
17
A
HOH
18
5
HOH
HOH
18
A
HOH
19
5
HOH
HOH
19
A
HOH
20
5
HOH
HOH
20
A
HOH
21
5
HOH
HOH
21
A
HOH
22
5
HOH
HOH
22
A
HOH
23
5
HOH
HOH
23
A
HOH
24
5
HOH
HOH
24
A
HOH
25
5
HOH
HOH
25
A
HOH
26
5
HOH
HOH
26
A
HOH
27
5
HOH
HOH
27
A
HOH
28
5
HOH
HOH
28
A
HOH
29
5
HOH
HOH
29
A
HOH
30
5
HOH
HOH
30
A
HOH
31
5
HOH
HOH
31
A
HOH
32
5
HOH
HOH
32
A
HOH
33
5
HOH
HOH
33
A
HOH
34
5
HOH
HOH
34
A
HOH
35
5
HOH
HOH
35
A
HOH
36
5
HOH
HOH
36
A
HOH
37
5
HOH
HOH
37
A
HOH
38
5
HOH
HOH
38
A
HOH
39
5
HOH
HOH
39
A
HOH
40
5
HOH
HOH
40
A
HOH
41
5
HOH
HOH
41
A
HOH
42
5
HOH
HOH
42
A
HOH
43
5
HOH
HOH
43
A
HOH
44
5
HOH
HOH
44
A
HOH
45
5
HOH
HOH
45
A
HOH
46
5
HOH
HOH
46
A
HOH
47
5
HOH
HOH
47
A
HOH
48
5
HOH
HOH
48
A
HOH
49
5
HOH
HOH
49
A
HOH
50
5
HOH
HOH
50
A
HOH
51
5
HOH
HOH
51
A
HOH
52
5
HOH
HOH
52
A
HOH
53
5
HOH
HOH
53
A
HOH
54
5
HOH
HOH
54
A
HOH
55
5
HOH
HOH
55
A
HOH
56
5
HOH
HOH
56
A
HOH
57
5
HOH
HOH
57
A
HOH
58
5
HOH
HOH
58
A
HOH
59
5
HOH
HOH
59
A
HOH
60
5
HOH
HOH
60
A
HOH
61
5
HOH
HOH
61
A
HOH
62
5
HOH
HOH
62
A
HOH
63
5
HOH
HOH
63
A
HOH
64
5
HOH
HOH
64
A
HOH
65
5
HOH
HOH
65
A
HOH
66
5
HOH
HOH
66
A
HOH
67
5
HOH
HOH
67
A
HOH
68
5
HOH
HOH
68
A
HOH
69
5
HOH
HOH
69
A
HOH
70
5
HOH
HOH
70
A
HOH
71
5
HOH
HOH
71
A
HOH
72
5
HOH
HOH
72
A
HOH
73
5
HOH
HOH
73
A
HOH
74
5
HOH
HOH
74
A
HOH
75
5
HOH
HOH
75
A
HOH
76
5
HOH
HOH
76
A
HOH
77
5
HOH
HOH
77
A
HOH
78
5
HOH
HOH
78
A
HOH
79
5
HOH
HOH
79
A
HOH
80
5
HOH
HOH
80
A
HOH
81
5
HOH
HOH
81
A
HOH
82
5
HOH
HOH
82
A
HOH
83
5
HOH
HOH
83
A
HOH
84
5
HOH
HOH
84
A
HOH
85
5
HOH
HOH
85
A
HOH
86
5
HOH
HOH
86
A
HOH
87
5
HOH
HOH
87
A
HOH
88
5
HOH
HOH
88
A
HOH
89
5
HOH
HOH
89
A
HOH
90
5
HOH
HOH
90
A
HOH
91
5
HOH
HOH
91
A
HOH
92
5
HOH
HOH
92
A
HOH
93
5
HOH
HOH
93
A
HOH
94
5
HOH
HOH
94
A
HOH
95
5
HOH
HOH
95
A
HOH
96
5
HOH
HOH
96
A
HOH
97
5
HOH
HOH
97
A
HOH
98
5
HOH
HOH
98
A
HOH
99
5
HOH
HOH
99
A
HOH
100
5
HOH
HOH
100
A
HOH
101
5
HOH
HOH
101
A
HOH
102
5
HOH
HOH
102
A
HOH
103
5
HOH
HOH
103
A
HOH
104
5
HOH
HOH
104
A
HOH
105
5
HOH
HOH
105
A
HOH
106
5
HOH
HOH
106
A
HOH
107
5
HOH
HOH
107
A
HOH
108
5
HOH
HOH
108
A
HOH
109
5
HOH
HOH
109
A
HOH
110
5
HOH
HOH
110
A
HOH
111
5
HOH
HOH
111
A
HOH
112
5
HOH
HOH
112
A
HOH
113
5
HOH
HOH
113
A
HOH
114
5
HOH
HOH
114
A
HOH
115
5
HOH
HOH
115
A
HOH
116
5
HOH
HOH
116
A
HOH
117
5
HOH
HOH
117
A
HOH
118
5
HOH
HOH
118
A
HOH
119
5
HOH
HOH
119
A
HOH
120
5
HOH
HOH
120
A
HOH
121
5
HOH
HOH
121
A
HOH
122
5
HOH
HOH
122
A
HOH
123
5
HOH
HOH
123
A
HOH
124
5
HOH
HOH
124
A
HOH
126
5
HOH
HOH
126
A
HOH
127
5
HOH
HOH
127
A
HOH
128
5
HOH
HOH
128
A
HOH
129
5
HOH
HOH
129
A
HOH
130
5
HOH
HOH
130
A
HOH
131
5
HOH
HOH
131
A
HOH
132
5
HOH
HOH
132
A
HOH
133
5
HOH
HOH
133
A
HOH
134
5
HOH
HOH
134
A
HOH
135
5
HOH
HOH
135
A
HOH
136
5
HOH
HOH
136
A
HOH
137
5
HOH
HOH
137
A
HOH
138
5
HOH
HOH
138
A
HOH
139
5
HOH
HOH
139
A
HOH
140
5
HOH
HOH
140
A
HOH
141
5
HOH
HOH
141
A
HOH
142
5
HOH
HOH
142
A
HOH
143
5
HOH
HOH
143
A
HOH
144
5
HOH
HOH
144
A
HOH
145
5
HOH
HOH
145
A
HOH
146
5
HOH
HOH
146
A
HOH
147
5
HOH
HOH
147
A
HOH
148
5
HOH
HOH
148
A
HOH
149
5
HOH
HOH
149
A
HOH
150
5
HOH
HOH
150
A
HOH
151
5
HOH
HOH
151
A
HOH
152
5
HOH
HOH
152
A
HOH
153
5
HOH
HOH
153
A
HOH
154
5
HOH
HOH
154
A
HOH
1
5
HOH
HOH
1184
A
HOH
125
5
HOH
HOH
125
B
n
1
980
A
n
2
981
A
HIS
982
n
3
HIS
982
A
MET
983
n
4
MET
983
A
ALA
984
n
5
ALA
984
A
SER
985
n
6
SER
985
A
MET
986
n
7
MET
986
A
LYS
987
n
8
LYS
987
A
LYS
988
n
9
LYS
988
A
LYS
989
n
10
LYS
989
A
GLY
990
n
11
GLY
990
A
SER
991
n
12
SER
991
A
VAL
992
n
13
VAL
992
A
VAL
993
n
14
VAL
993
A
ILE
994
n
15
ILE
994
A
VAL
995
n
16
VAL
995
A
GLY
996
n
17
GLY
996
A
ARG
997
n
18
ARG
997
A
ILE
998
n
19
ILE
998
A
ASN
999
n
20
ASN
999
A
LEU
1000
n
21
LEU
1000
A
SER
1001
n
22
SER
1001
A
GLY
1002
n
23
GLY
1002
A
ASP
1003
n
24
ASP
1003
A
THR
1004
n
25
THR
1004
A
ALA
1005
n
26
ALA
1005
A
TYR
1006
n
27
TYR
1006
A
ALA
1007
n
28
ALA
1007
A
GLN
1008
n
29
GLN
1008
A
GLN
1009
n
30
GLN
1009
A
THR
1010
n
31
THR
1010
A
ARG
1011
n
32
ARG
1011
A
GLY
1012
n
33
GLY
1012
A
GLU
1013
n
34
GLU
1013
A
GLU
1014
n
35
GLU
1014
A
GLY
1015
n
36
GLY
1015
A
CYS
1016
n
37
CYS
1016
A
GLN
1017
n
38
GLN
1017
A
GLU
1018
n
39
GLU
1018
A
THR
1019
n
40
THR
1019
A
SER
1020
n
41
SER
1020
A
GLN
1021
n
42
GLN
1021
A
THR
1022
n
43
THR
1022
A
GLY
1023
n
44
GLY
1023
A
ARG
1024
n
45
ARG
1024
A
ASP
1025
n
46
ASP
1025
A
LYS
1026
n
47
LYS
1026
A
ASN
1027
n
48
ASN
1027
A
GLN
1028
n
49
GLN
1028
A
VAL
1029
n
50
VAL
1029
A
GLU
1030
n
51
GLU
1030
A
GLY
1031
n
52
GLY
1031
A
GLU
1032
n
53
GLU
1032
A
VAL
1033
n
54
VAL
1033
A
GLN
1034
n
55
GLN
1034
A
ILE
1035
n
56
ILE
1035
A
VAL
1036
n
57
VAL
1036
A
SER
1037
n
58
SER
1037
A
THR
1038
n
59
THR
1038
A
ALA
1039
n
60
ALA
1039
A
THR
1040
n
61
THR
1040
A
GLN
1041
n
62
GLN
1041
A
THR
1042
n
63
THR
1042
A
PHE
1043
n
64
PHE
1043
A
LEU
1044
n
65
LEU
1044
A
ALA
1045
n
66
ALA
1045
A
THR
1046
n
67
THR
1046
A
SER
1047
n
68
SER
1047
A
ILE
1048
n
69
ILE
1048
A
ASN
1049
n
70
ASN
1049
A
GLY
1050
n
71
GLY
1050
A
VAL
1051
n
72
VAL
1051
A
LEU
1052
n
73
LEU
1052
A
TRP
1053
n
74
TRP
1053
A
THR
1054
n
75
THR
1054
A
VAL
1055
n
76
VAL
1055
A
TYR
1056
n
77
TYR
1056
A
HIS
1057
n
78
HIS
1057
A
GLY
1058
n
79
GLY
1058
A
ALA
1059
n
80
ALA
1059
A
GLY
1060
n
81
GLY
1060
A
THR
1061
n
82
THR
1061
A
ARG
1062
n
83
ARG
1062
A
THR
1063
n
84
THR
1063
A
ILE
1064
n
85
ILE
1064
A
ALA
1065
n
86
ALA
1065
A
SER
1066
n
87
SER
1066
A
PRO
1067
n
88
PRO
1067
A
LYS
1068
n
89
LYS
1068
A
GLY
1069
n
90
GLY
1069
A
PRO
1070
n
91
PRO
1070
A
VAL
1071
n
92
VAL
1071
A
THR
1072
n
93
THR
1072
A
GLN
1073
n
94
GLN
1073
A
MET
1074
n
95
MET
1074
A
TYR
1075
n
96
TYR
1075
A
THR
1076
n
97
THR
1076
A
ASN
1077
n
98
ASN
1077
A
VAL
1078
n
99
VAL
1078
A
ASP
1079
n
100
ASP
1079
A
LYS
1080
n
101
LYS
1080
A
ASP
1081
n
102
ASP
1081
A
LEU
1082
n
103
LEU
1082
A
VAL
1083
n
104
VAL
1083
A
GLY
1084
n
105
GLY
1084
A
TRP
1085
n
106
TRP
1085
A
GLN
1086
n
107
GLN
1086
A
ALA
1087
n
108
ALA
1087
A
PRO
1088
n
109
PRO
1088
A
GLN
1089
n
110
GLN
1089
A
GLY
1090
n
111
GLY
1090
A
SER
1091
n
112
SER
1091
A
ARG
1092
n
113
ARG
1092
A
SER
1093
n
114
SER
1093
A
LEU
1094
n
115
LEU
1094
A
THR
1095
n
116
THR
1095
A
PRO
1096
n
117
PRO
1096
A
CYS
1097
n
118
CYS
1097
A
THR
1098
n
119
THR
1098
A
CYS
1099
n
120
CYS
1099
A
GLY
1100
n
121
GLY
1100
A
SER
1101
n
122
SER
1101
A
SER
1102
n
123
SER
1102
A
ASP
1103
n
124
ASP
1103
A
LEU
1104
n
125
LEU
1104
A
TYR
1105
n
126
TYR
1105
A
LEU
1106
n
127
LEU
1106
A
VAL
1107
n
128
VAL
1107
A
THR
1108
n
129
THR
1108
A
ARG
1109
n
130
ARG
1109
A
HIS
1110
n
131
HIS
1110
A
ALA
1111
n
132
ALA
1111
A
ASP
1112
n
133
ASP
1112
A
VAL
1113
n
134
VAL
1113
A
ILE
1114
n
135
ILE
1114
A
PRO
1115
n
136
PRO
1115
A
VAL
1116
n
137
VAL
1116
A
ARG
1117
n
138
ARG
1117
A
ARG
1118
n
139
ARG
1118
A
ARG
1119
n
140
ARG
1119
A
GLY
1120
n
141
GLY
1120
A
ASP
1121
n
142
ASP
1121
A
SER
1122
n
143
SER
1122
A
ARG
1123
n
144
ARG
1123
A
GLY
1124
n
145
GLY
1124
A
SER
1125
n
146
SER
1125
A
LEU
1126
n
147
LEU
1126
A
LEU
1127
n
148
LEU
1127
A
SER
1128
n
149
SER
1128
A
PRO
1129
n
150
PRO
1129
A
ARG
1130
n
151
ARG
1130
A
PRO
1131
n
152
PRO
1131
A
ILE
1132
n
153
ILE
1132
A
SER
1133
n
154
SER
1133
A
TYR
1134
n
155
TYR
1134
A
LEU
1135
n
156
LEU
1135
A
LYS
1136
n
157
LYS
1136
A
GLY
1137
n
158
GLY
1137
A
SER
1138
n
159
SER
1138
A
ALA
1139
n
160
ALA
1139
A
GLY
1140
n
161
GLY
1140
A
GLY
1141
n
162
GLY
1141
A
PRO
1142
n
163
PRO
1142
A
LEU
1143
n
164
LEU
1143
A
LEU
1144
n
165
LEU
1144
A
CYS
1145
n
166
CYS
1145
A
PRO
1146
n
167
PRO
1146
A
ALA
1147
n
168
ALA
1147
A
GLY
1148
n
169
GLY
1148
A
HIS
1149
n
170
HIS
1149
A
ALA
1150
n
171
ALA
1150
A
VAL
1151
n
172
VAL
1151
A
GLY
1152
n
173
GLY
1152
A
ILE
1153
n
174
ILE
1153
A
PHE
1154
n
175
PHE
1154
A
ARG
1155
n
176
ARG
1155
A
ALA
1156
n
177
ALA
1156
A
ALA
1157
n
178
ALA
1157
A
VAL
1158
n
179
VAL
1158
A
SER
1159
n
180
SER
1159
A
THR
1160
n
181
THR
1160
A
ARG
1161
n
182
ARG
1161
A
GLY
1162
n
183
GLY
1162
A
VAL
1163
n
184
VAL
1163
A
ALA
1164
n
185
ALA
1164
A
LYS
1165
n
186
LYS
1165
A
ALA
1166
n
187
ALA
1166
A
VAL
1167
n
188
VAL
1167
A
ASP
1168
n
189
ASP
1168
A
PHE
1169
n
190
PHE
1169
A
ILE
1170
n
191
ILE
1170
A
PRO
1171
n
192
PRO
1171
A
VAL
1172
n
193
VAL
1172
A
GLU
1173
n
194
GLU
1173
A
SER
1174
n
195
SER
1174
A
LEU
1175
n
196
LEU
1175
A
GLU
1176
n
197
GLU
1176
A
THR
1177
n
198
THR
1177
A
THR
1178
n
199
THR
1178
A
MET
1179
n
200
MET
1179
A
ARG
1180
n
201
ARG
1180
A
n
202
1181
A
n
203
1182
A
n
1
-5
B
n
2
-4
B
n
3
-3
B
n
4
-2
B
n
5
-1
B
n
6
0
B
n
7
1
B
PRO
2
n
8
PRO
2
B
SER
3
n
9
SER
3
B
SER
4
n
10
SER
4
B
THR
5
n
11
THR
5
B
PRO
6
n
12
PRO
6
B
CYS
7
n
13
CYS
7
B
-1.7823
0.7102
1.6656
0.9844
5.0628
10.0373
0.2191
0.1987
0.3847
-0.2349
0.1366
-0.2172
0.2994
-0.0441
-0.3557
0.8206
0.0933
0.2956
0.3112
0.0893
0.3270
refined
6.5914
-19.0221
0.0618
X-RAY DIFFRACTION
3.2661
-0.4576
-1.0216
5.0704
1.9273
6.1039
0.1252
-0.3630
0.2242
0.3922
0.0349
-0.1878
-0.2634
0.1646
-0.1602
0.1475
-0.0297
0.0080
0.0899
0.0105
0.0810
refined
2.2944
2.2228
24.0661
X-RAY DIFFRACTION
4.7783
-1.3893
-3.7098
5.0444
1.5870
6.7520
0.0480
-0.2505
-0.0943
0.0061
-0.0103
-0.1777
-0.0628
0.3074
-0.0376
0.0951
-0.0140
0.0027
0.0509
0.0116
0.0792
refined
4.3542
5.0541
19.1889
X-RAY DIFFRACTION
3.6902
-2.4761
0.0284
8.6292
0.3902
9.3404
0.1117
0.0342
-0.0421
-0.4865
-0.1232
-0.5930
-0.2830
0.3021
0.0115
0.0842
-0.0030
0.0895
0.0710
0.0187
0.1325
refined
11.3756
-5.2400
11.0437
X-RAY DIFFRACTION
27.2976
2.2577
-6.2850
9.0159
-0.6672
8.0380
0.2694
-0.6946
0.7118
0.1737
-0.1806
-0.3935
-0.2905
0.4806
-0.0888
0.1227
-0.0470
-0.0258
0.0729
-0.0027
0.1065
refined
6.2091
-1.5412
26.4446
X-RAY DIFFRACTION
4.0738
0.5896
0.1853
7.2052
2.0442
14.3512
0.2631
0.2259
-0.1387
-0.4870
-0.0474
0.0278
0.1105
-0.5606
-0.2157
0.0929
0.0193
-0.0082
0.0978
0.0257
0.1014
refined
-0.0347
-5.1531
13.3611
X-RAY DIFFRACTION
2.3506
0.2558
-0.3347
1.8094
0.4405
1.0801
0.0746
-0.0101
-0.0336
0.0044
-0.0858
-0.0632
0.0536
-0.0214
0.0111
0.0949
0.0076
-0.0032
0.0874
0.0246
0.0751
refined
-1.3421
-11.2751
20.2017
X-RAY DIFFRACTION
7.6127
2.6533
-1.3024
3.0491
-0.6936
1.9166
0.2061
-0.2184
-0.1919
0.0587
-0.2319
-0.3548
0.0746
0.1980
0.0258
0.0699
0.0236
-0.0002
0.0646
0.0170
0.1251
refined
5.9188
-16.4491
19.4225
X-RAY DIFFRACTION
6.6288
2.2171
2.0585
2.1932
1.2554
3.1856
0.0294
0.0384
-0.1622
0.1504
-0.0782
-0.1374
0.0528
0.0982
0.0488
0.0945
0.0181
-0.0059
0.0785
0.0155
0.0939
refined
-0.9753
-15.6395
22.1808
X-RAY DIFFRACTION
14.0323
1.4679
-10.1598
2.0903
-1.1236
7.5990
-0.2270
-0.6181
-0.1708
0.1287
-0.0940
-0.1479
-0.0443
0.3285
0.3210
0.1813
-0.0019
-0.0299
0.2556
-0.0413
0.1375
refined
-1.5202
-8.0593
35.2373
X-RAY DIFFRACTION
14.2651
4.6252
-6.7156
3.0451
-7.3299
15.8821
0.4853
-1.1612
0.9696
0.0828
-0.1802
0.0542
-0.0590
0.3621
-0.3051
0.0781
-0.0078
0.0826
0.1498
-0.1898
0.3407
refined
-14.3151
-1.4691
33.2003
X-RAY DIFFRACTION
8.2642
7.9203
-3.5921
17.3775
-6.6563
17.3618
0.0682
0.3922
0.4473
-0.7403
0.1442
1.3296
-0.0092
0.3174
-0.2124
0.1051
0.0177
-0.0198
0.0759
-0.0058
0.2404
refined
-6.9609
3.3816
21.2654
X-RAY DIFFRACTION
8.1576
1.8196
-2.5992
0.8246
-1.1265
2.7618
0.1627
-0.3600
0.5970
0.0534
0.1507
0.0792
-0.1155
-0.0233
-0.3134
0.0748
0.0036
0.0543
0.1608
-0.0323
0.1214
refined
-17.7132
-5.5714
30.6129
X-RAY DIFFRACTION
5.2785
-3.5988
0.5569
12.4215
-9.1512
5.4841
0.1442
-0.0098
0.5952
-0.2093
0.3629
0.5604
-0.0628
-0.2844
-0.5071
0.1801
0.0381
0.0785
0.1891
0.0153
0.2683
refined
-20.8640
-1.2831
26.0205
X-RAY DIFFRACTION
30.8502
-11.7222
0.8019
7.4563
-5.9410
5.2008
0.1247
0.6573
1.6429
0.2477
0.3931
-0.3190
-0.3014
-0.5174
-0.5179
0.1385
0.0271
0.0133
0.1668
0.1165
0.3248
refined
-13.7648
1.0307
16.8831
X-RAY DIFFRACTION
4.5420
-0.6767
-2.3447
-0.1059
2.1331
15.8011
0.0959
-0.6274
0.7405
-0.0817
0.0043
-0.0264
-0.3481
0.0912
-0.1002
0.1497
-0.0306
0.0390
0.2535
-0.1159
0.2441
refined
-7.8018
-3.7719
33.3199
X-RAY DIFFRACTION
9.6925
-3.2663
0.4360
-0.1130
-0.4034
5.6394
0.0183
0.0750
0.0648
-0.0336
-0.1528
0.1111
0.2206
0.3727
0.1345
0.1469
-0.0134
0.0160
0.1503
0.0018
0.1470
refined
-10.1726
-8.9321
26.1077
X-RAY DIFFRACTION
1.5419
-4.1761
3.8924
10.2891
-4.1532
8.3939
0.1178
0.5537
-0.2926
-0.4667
0.1135
1.2879
-0.0275
-0.0277
-0.2314
0.1424
0.0638
0.0120
0.6276
0.2172
0.3422
refined
-21.9782
-3.0715
17.5764
X-RAY DIFFRACTION
20.0374
-8.3760
6.5262
6.1854
-7.3332
10.5561
0.1673
0.1133
-0.3041
0.0652
-0.0242
0.2027
-0.0497
0.0347
-0.1432
0.1103
-0.0149
0.0203
0.1196
0.0099
0.0589
refined
-13.9468
-10.6713
25.9813
X-RAY DIFFRACTION
14.2477
-3.6459
-6.8595
4.6329
-1.9177
3.5448
-0.3471
-0.8776
-0.6017
0.2578
0.1360
0.4240
0.1725
0.1446
0.2111
0.1545
-0.0440
-0.0322
0.1932
0.1026
0.1140
refined
-5.9745
-17.9455
31.7631
X-RAY DIFFRACTION
A
982
A
991
X-RAY DIFFRACTION
1
A
992
A
1004
X-RAY DIFFRACTION
2
A
1005
A
1012
X-RAY DIFFRACTION
3
A
1013
A
1027
X-RAY DIFFRACTION
4
A
1028
A
1033
X-RAY DIFFRACTION
5
A
1034
A
1041
X-RAY DIFFRACTION
6
A
1042
A
1063
X-RAY DIFFRACTION
7
A
1064
A
1078
X-RAY DIFFRACTION
8
A
1079
A
1088
X-RAY DIFFRACTION
9
A
1089
A
1101
X-RAY DIFFRACTION
10
A
1102
A
1106
X-RAY DIFFRACTION
11
A
1107
A
1112
X-RAY DIFFRACTION
12
A
1113
A
1122
X-RAY DIFFRACTION
13
A
1123
A
1129
X-RAY DIFFRACTION
14
A
1130
A
1139
X-RAY DIFFRACTION
15
A
1140
A
1149
X-RAY DIFFRACTION
16
A
1150
A
1155
X-RAY DIFFRACTION
17
A
1156
A
1166
X-RAY DIFFRACTION
18
A
1167
A
1171
X-RAY DIFFRACTION
19
A
1172
A
1179
X-RAY DIFFRACTION
20
author_and_software_defined_assembly
PISA
2
dimeric
830
-19
10010
A
CYS
1097
A
SG
CYS
118
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
CYS
1099
A
SG
CYS
120
1_555
109.7
A
CYS
1097
A
SG
CYS
118
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
CYS
1145
A
SG
CYS
166
1_555
109.7
A
CYS
1099
A
SG
CYS
120
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
CYS
1145
A
SG
CYS
166
1_555
117.1
A
CYS
1097
A
SG
CYS
118
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
HIS
1149
A
ND1
HIS
170
1_555
124.1
A
CYS
1099
A
SG
CYS
120
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
HIS
1149
A
ND1
HIS
170
1_555
105.9
A
CYS
1145
A
SG
CYS
166
1_555
A
ZN
1183
D
ZN
ZN
1_555
A
HIS
1149
A
ND1
HIS
170
1_555
89.8
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
1006
A
O
TYR
27
A
N
ASN
999
A
N
ASN
20
A
N
VAL
995
A
N
VAL
16
A
O
ILE
1035
A
O
ILE
56
A
N
GLN
1034
A
N
GLN
55
A
O
ALA
1045
A
O
ALA
66
A
N
THR
1046
A
N
THR
67
A
O
TRP
1053
A
O
TRP
74
A
N
LEU
1052
A
N
LEU
73
A
O
TRP
1085
A
O
TRP
106
A
O
LEU
1082
A
O
LEU
103
A
N
ASN
1077
A
N
ASN
98
B
O
THR
5
B
O
THR
11
A
N
ALA
1157
A
N
ALA
178
A
N
ALA
1156
A
N
ALA
177
A
O
ASP
1168
A
O
ASP
189
A
O
ALA
1164
A
O
ALA
185
A
N
ARG
1130
A
N
ARG
151
A
O
SER
1125
A
O
SER
146
A
N
ARG
1117
A
N
ARG
138
A
O
ILE
1114
A
O
ILE
135
A
N
LEU
1106
A
N
LEU
127
A
N
TYR
1105
A
N
TYR
126
A
O
LEU
1144
A
O
LEU
165
A
N
LEU
1143
A
N
LEU
164
A
O
VAL
1151
A
O
VAL
172
1
A
CG
HIS
982
A
CG
HIS
3
1
Y
1
A
ND1
HIS
982
A
ND1
HIS
3
1
Y
1
A
CD2
HIS
982
A
CD2
HIS
3
1
Y
1
A
CE1
HIS
982
A
CE1
HIS
3
1
Y
1
A
NE2
HIS
982
A
NE2
HIS
3
1
Y
1
A
CG
LYS
988
A
CG
LYS
9
1
Y
1
A
CD
LYS
988
A
CD
LYS
9
1
Y
1
A
CE
LYS
988
A
CE
LYS
9
1
Y
1
A
NZ
LYS
988
A
NZ
LYS
9
1
Y
1
A
CG
GLU
1013
A
CG
GLU
34
1
Y
1
A
CD
GLU
1013
A
CD
GLU
34
1
Y
1
A
OE1
GLU
1013
A
OE1
GLU
34
1
Y
1
A
OE2
GLU
1013
A
OE2
GLU
34
1
Y
1
A
CG
GLU
1014
A
CG
GLU
35
1
Y
1
A
CD
GLU
1014
A
CD
GLU
35
1
Y
1
A
OE1
GLU
1014
A
OE1
GLU
35
1
Y
1
A
OE2
GLU
1014
A
OE2
GLU
35
1
Y
1
A
CG
GLN
1017
A
CG
GLN
38
1
Y
1
A
CD
GLN
1017
A
CD
GLN
38
1
Y
1
A
OE1
GLN
1017
A
OE1
GLN
38
1
Y
1
A
NE2
GLN
1017
A
NE2
GLN
38
1
Y
1
A
CG
GLU
1018
A
CG
GLU
39
1
Y
1
A
CD
GLU
1018
A
CD
GLU
39
1
Y
1
A
OE1
GLU
1018
A
OE1
GLU
39
1
Y
1
A
OE2
GLU
1018
A
OE2
GLU
39
1
Y
1
A
CG
GLN
1021
A
CG
GLN
42
1
Y
1
A
CD
GLN
1021
A
CD
GLN
42
1
Y
1
A
OE1
GLN
1021
A
OE1
GLN
42
1
Y
1
A
NE2
GLN
1021
A
NE2
GLN
42
1
Y
1
A
CG
LYS
1026
A
CG
LYS
47
1
Y
1
A
CD
LYS
1026
A
CD
LYS
47
1
Y
1
A
CE
LYS
1026
A
CE
LYS
47
1
Y
1
A
NZ
LYS
1026
A
NZ
LYS
47
1
Y
1
A
CG
GLN
1028
A
CG
GLN
49
1
Y
1
A
CD
GLN
1028
A
CD
GLN
49
1
Y
1
A
OE1
GLN
1028
A
OE1
GLN
49
1
Y
1
A
NE2
GLN
1028
A
NE2
GLN
49
1
Y
1
A
CG
ARG
1092
A
CG
ARG
113
1
Y
1
A
CD
ARG
1092
A
CD
ARG
113
1
Y
1
A
NE
ARG
1092
A
NE
ARG
113
1
Y
1
A
CZ
ARG
1092
A
CZ
ARG
113
1
Y
1
A
NH1
ARG
1092
A
NH1
ARG
113
1
Y
1
A
NH2
ARG
1092
A
NH2
ARG
113
1
Y
1
A
GLY
980
A
GLY
1
1
Y
1
A
SER
981
A
SER
2
1
Y
1
A
SER
1181
A
SER
202
1
Y
1
A
PRO
1182
A
PRO
203
1
Y
1
B
PRO
-5
B
PRO
1
1
Y
1
B
PRO
-4
B
PRO
2
1
Y
1
B
PRO
-3
B
PRO
3
1
Y
1
B
PRO
-2
B
PRO
4
1
Y
1
B
PRO
-1
B
PRO
5
1
Y
1
B
PRO
0
B
PRO
6
1
Y
1
B
PRO
1
B
PRO
7
1
Y
1
6.61
1.10
114.20
120.81
A
A
A
CA
CB
SG
CYS
CYS
CYS
1145
1145
1145
N
23.043
0.35
0.00
0.00
-1.53
0.00
1.18
0.958
0.944
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.21549
0.18641
0.18789
1.50
17.24
1416
26246
5.1
87.11
1.000
0.500
2.929
0.051
0.0855
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.086
0.086
0.80
0.80
1.40
PDB entry 3M5M
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.50
17.24
154
1637
6
0
1477
0.009
0.022
1510
0.001
0.020
1005
1.280
1.967
2057
0.826
3.000
2453
6.412
5.000
205
31.760
22.041
49
12.787
15.000
231
11.644
15.000
13
0.071
0.200
245
0.006
0.021
1699
0.001
0.020
296
0.597
1.500
1017
0.160
1.500
422
1.021
2.000
1633
1.519
3.000
493
2.343
4.500
423
0.283
0.224
1.535
96
2004
20
91.03
1.500
20.000
3RC4
27770
0.054
1
13.500
4.900
87.400
0.332
1.500
1.550
4.700
93.100
0.247
1.550
1.620
4.700
92.100
0.188
1.620
1.690
4.800
92.700
0.145
1.690
1.780
4.800
91.900
0.113
1.780
1.890
4.900
91.200
0.089
1.890
2.040
5.000
90.500
0.071
2.040
2.240
5.100
89.400
0.057
2.240
2.560
5.100
88.100
0.043
2.560
3.230
5.100
85.000
0.039
3.230
20.000
5.100
62.600
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
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
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
A
HIS
982
A
HIS
3
HELX_P
A
MET
986
A
MET
7
5
1
5
A
GLY
1012
A
GLY
33
HELX_P
A
GLY
1023
A
GLY
44
1
2
12
A
VAL
1055
A
VAL
76
HELX_P
A
GLY
1060
A
GLY
81
1
3
6
A
SER
1133
A
SER
154
HELX_P
A
LEU
1135
A
LEU
156
5
4
3
A
VAL
1172
A
VAL
193
HELX_P
A
ARG
1180
A
ARG
201
1
5
9
metalc
2.323
A
CYS
1097
A
SG
CYS
118
1_555
A
ZN
1183
D
ZN
ZN
1_555
metalc
2.194
A
CYS
1099
A
SG
CYS
120
1_555
A
ZN
1183
D
ZN
ZN
1_555
metalc
2.208
A
CYS
1145
A
SG
CYS
166
1_555
A
ZN
1183
D
ZN
ZN
1_555
metalc
2.176
A
HIS
1149
A
ND1
HIS
170
1_555
A
ZN
1183
D
ZN
ZN
1_555
HYDROLASE/HYDROLASE INHIBITOR
drug resistance, drug design, Protease inhibitors, serine protease, HYDROLASE, chymotrypsin-like, HYDROLASE-HYDROLASE INHIBITOR complex
B
PRO
2
B
PRO
8
1
B
SER
3
B
SER
9
4.70
D6MZ98_9HEPC
UNP
1
36
D6MZ98
LAPITAYAQQTRGLLGCIVTSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVD
QDLVGWPAPQGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVC
TRGVAKAVDFIPVESLETTMRSP
3RC4
PDB
2
1
3RC4
36
218
3RC4
1000
1182
D6MZ98
A
1
21
203
-5
7
3RC4
-5
7
3RC4
B
2
1
13
1
expression tag
GLY
980
3RC4
A
D6MZ98
UNP
1
1
expression tag
SER
981
3RC4
A
D6MZ98
UNP
2
1
expression tag
HIS
982
3RC4
A
D6MZ98
UNP
3
1
expression tag
MET
983
3RC4
A
D6MZ98
UNP
4
1
expression tag
ALA
984
3RC4
A
D6MZ98
UNP
5
1
expression tag
SER
985
3RC4
A
D6MZ98
UNP
6
1
expression tag
MET
986
3RC4
A
D6MZ98
UNP
7
1
expression tag
LYS
987
3RC4
A
D6MZ98
UNP
8
1
expression tag
LYS
988
3RC4
A
D6MZ98
UNP
9
1
expression tag
LYS
989
3RC4
A
D6MZ98
UNP
10
1
expression tag
GLY
990
3RC4
A
D6MZ98
UNP
11
1
expression tag
SER
991
3RC4
A
D6MZ98
UNP
12
1
expression tag
VAL
992
3RC4
A
D6MZ98
UNP
13
1
expression tag
VAL
993
3RC4
A
D6MZ98
UNP
14
1
expression tag
ILE
994
3RC4
A
D6MZ98
UNP
15
1
expression tag
VAL
995
3RC4
A
D6MZ98
UNP
16
1
expression tag
GLY
996
3RC4
A
D6MZ98
UNP
17
1
expression tag
ARG
997
3RC4
A
D6MZ98
UNP
18
1
expression tag
ILE
998
3RC4
A
D6MZ98
UNP
19
1
expression tag
ASN
999
3RC4
A
D6MZ98
UNP
20
1
ALA
engineered mutation
SER
1001
3RC4
A
D6MZ98
UNP
37
22
1
PRO
engineered mutation
GLY
1002
3RC4
A
D6MZ98
UNP
38
23
1
ILE
engineered mutation
ASP
1003
3RC4
A
D6MZ98
UNP
39
24
1
LEU
engineered mutation
GLU
1013
3RC4
A
D6MZ98
UNP
49
34
1
LEU
engineered mutation
GLU
1014
3RC4
A
D6MZ98
UNP
50
35
1
ILE
engineered mutation
GLN
1017
3RC4
A
D6MZ98
UNP
53
38
1
VAL
engineered mutation
GLU
1018
3RC4
A
D6MZ98
UNP
54
39
1
LEU
engineered mutation
GLN
1021
3RC4
A
D6MZ98
UNP
57
42
1
CYS
engineered mutation
SER
1047
3RC4
A
D6MZ98
UNP
83
68
1
CYS
engineered mutation
LEU
1052
3RC4
A
D6MZ98
UNP
88
73
1
ILE
engineered mutation
THR
1072
3RC4
A
D6MZ98
UNP
108
93
1
GLN
engineered mutation
LYS
1080
3RC4
A
D6MZ98
UNP
116
101
1
PRO
engineered mutation
GLN
1086
3RC4
A
D6MZ98
UNP
122
107
1
ALA
engineered mutation
SER
1091
3RC4
A
D6MZ98
UNP
127
112
1
SER
engineered mutation
ALA
1139
3RC4
A
D6MZ98
UNP
175
160
1
CYS
engineered mutation
SER
1159
3RC4
A
D6MZ98
UNP
195
180
7
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
1006
A
TYR
27
A
GLN
1009
A
GLN
30
A
VAL
993
A
VAL
14
A
ASN
999
A
ASN
20
A
VAL
1033
A
VAL
54
A
SER
1037
A
SER
58
A
THR
1042
A
THR
63
A
ILE
1048
A
ILE
69
A
VAL
1051
A
VAL
72
A
THR
1054
A
THR
75
A
LEU
1082
A
LEU
103
A
GLN
1086
A
GLN
107
A
TYR
1075
A
TYR
96
A
ASN
1077
A
ASN
98
B
SER
4
B
SER
10
B
PRO
6
B
PRO
12
A
ALA
1150
A
ALA
171
A
THR
1160
A
THR
181
A
VAL
1163
A
VAL
184
A
PRO
1171
A
PRO
192
A
ARG
1123
A
ARG
144
A
PRO
1131
A
PRO
152
A
VAL
1113
A
VAL
134
A
ARG
1118
A
ARG
139
A
ASP
1103
A
ASP
124
A
VAL
1107
A
VAL
128
A
PRO
1142
A
PRO
163
A
LEU
1144
A
LEU
165
A
ALA
1150
A
ALA
171
A
THR
1160
A
THR
181
BINDING SITE FOR RESIDUE SO4 A 1
A
SO4
1
Software
7
BINDING SITE FOR RESIDUE ZN A 1183
A
ZN
1183
Software
4
A
HOH
16
E
HOH
7
1_555
A
HOH
37
E
HOH
7
1_555
A
HOH
38
E
HOH
7
3_545
A
HOH
142
E
HOH
7
1_555
A
TYR
1006
A
TYR
27
7
3_545
A
GLN
1008
A
GLN
29
7
3_545
A
TYR
1056
A
TYR
77
7
1_555
A
CYS
1097
A
CYS
118
4
1_555
A
CYS
1099
A
CYS
120
4
1_555
A
CYS
1145
A
CYS
166
4
1_555
A
HIS
1149
A
HIS
170
4
1_555
19
P 21 21 21