0.008979
0.005184
0.000000
0.000000
0.010369
0.000000
0.000000
0.000000
0.008030
0.00000
0.00000
0.00000
Ticha, A.
Stanchev, S.
Vinothkumar, K.R.
Mikles, D.C.
Pachl, P.
Svehlova, K.
Nguyen, M.T.N.
Verhelst, S.H.L.
Johnson, D.
Bachovchin, D.
Lepsik, M.
Majer, P.
Strisovsky, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
111.365
111.365
124.539
C2 H4 O
44.053
ACETYL GROUP
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
C15 H30 O6
306.395
n
nonyl beta-D-glucopyranoside
Beta-NONYLGLUCOSIDE; nonyl beta-D-glucoside; nonyl D-glucoside; nonyl glucoside
D-saccharide
Cl -1
35.453
CHLORIDE 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
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
C13 H20 N2 O2
236.310
(2~{R},3~{S})-3-azanyl-~{N}-[(2,5-dimethylphenyl)methyl]-2-oxidanyl-butanamide
non-polymer
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
N
N
29
N
C
N
30
N
N
N
31
N
N
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
N
N
49
S
C
N
50
N
C
N
51
N
O
N
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
O
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
R
C
N
82
R
C
N
83
S
C
N
84
S
C
N
85
R
C
N
86
N
C
N
87
N
C
N
88
N
C
N
89
N
C
N
90
N
C
N
91
N
C
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
O
N
98
N
O
N
99
N
O
N
100
N
O
N
101
N
O
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
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
CL
N
133
N
N
N
134
R
C
N
135
N
C
N
136
N
O
N
137
N
C
N
138
N
S
N
139
N
O
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
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
N
C
N
152
N
C
N
153
N
C
N
154
N
O
N
155
N
N
N
156
N
O
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
H
N
166
N
H
N
167
N
N
N
168
S
C
N
169
N
C
N
170
N
O
N
171
N
C
N
172
N
C
N
173
N
C
N
174
N
O
N
175
N
O
N
176
N
O
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
H
N
184
N
H
N
185
N
H
N
186
N
N
N
187
N
C
N
188
N
C
N
189
N
O
N
190
N
O
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
N
N
197
S
C
N
198
N
C
N
199
N
O
N
200
N
C
Y
201
N
C
Y
202
N
N
Y
203
N
C
Y
204
N
C
Y
205
N
N
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
O
N
218
N
H
N
219
N
H
N
220
N
N
N
221
S
C
N
222
N
C
N
223
N
O
N
224
S
C
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
O
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
H
N
240
N
H
N
241
N
H
N
242
N
N
N
243
S
C
N
244
N
C
N
245
N
O
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
C
N
250
N
O
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
H
N
262
N
H
N
263
N
H
N
264
N
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
C
N
272
N
N
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
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
N
N
290
S
C
N
291
N
C
N
292
N
O
N
293
N
C
N
294
N
C
N
295
N
S
N
296
N
C
N
297
N
O
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
H
N
307
N
H
N
308
N
H
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
N
320
N
O
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
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
N
337
N
C
N
338
N
C
N
339
N
O
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
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
N
354
N
O
N
355
N
O
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
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
R
C
N
368
N
O
N
369
N
C
N
370
N
O
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
H
N
378
N
H
N
379
N
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
N
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
N
394
N
O
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
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
C
Y
416
N
C
Y
417
N
C
N
418
N
O
N
419
N
O
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
H
N
429
N
H
N
430
N
H
N
431
N
N
N
432
S
C
N
433
N
C
N
434
N
O
N
435
N
C
N
436
N
C
N
437
N
C
N
438
N
O
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
447
N
H
N
448
N
H
N
449
N
H
N
450
N
O
N
451
N
C
N
452
R
C
N
453
N
O
N
454
S
C
N
455
N
C
N
456
N
N
N
457
N
N
N
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
N
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
N
466
N
C
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
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
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
doub
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
doub
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
doub
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
doub
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
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
sing
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
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
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
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
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
doub
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
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
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
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
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
Y
197
N
sing
Y
198
N
doub
Y
199
N
doub
N
200
N
sing
Y
201
N
sing
N
202
N
sing
Y
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
doub
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
sing
N
235
N
sing
N
236
N
doub
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
sing
N
256
N
sing
N
257
N
doub
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
sing
N
280
N
sing
N
281
N
doub
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
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
Y
305
N
doub
Y
306
N
sing
Y
307
N
sing
N
308
N
sing
Y
309
N
doub
N
310
N
sing
Y
311
N
doub
N
312
N
sing
Y
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
sing
N
322
N
sing
N
323
N
doub
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
sing
N
339
N
sing
N
340
N
doub
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
sing
N
352
N
sing
N
353
N
doub
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
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
Y
374
N
doub
Y
375
N
sing
Y
376
N
sing
N
377
N
sing
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
385
N
doub
N
386
N
sing
Y
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
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
Y
402
N
doub
Y
403
N
sing
Y
404
N
sing
N
405
N
sing
Y
406
N
doub
N
407
N
sing
Y
408
N
doub
N
409
N
sing
Y
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
sing
N
420
N
sing
N
421
N
doub
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
N
431
N
sing
N
432
N
sing
N
433
N
sing
Y
434
N
doub
Y
435
N
sing
Y
436
N
sing
Y
437
N
doub
Y
438
N
doub
Y
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
doub
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
sing
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
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
US
Cell Chem Biol
2451-9456
24
1523
1536.e4
10.1016/j.chembiol.2017.09.007
29107700
General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.
2017
10.2210/pdb5mtf/pdb
pdb_00005mtf
100
1
PIXEL
2016-04-20
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.918408
1.0
14.1
BESSY
0.918408
SYNCHROTRON
BESSY BEAMLINE 14.1
21513.568
Rhomboid protease GlpG
3.4.21.105
1
man
polymer
814.013
inhibitor
1
syn
polymer
35.453
CHLORIDE ION
2
syn
non-polymer
306.395
nonyl beta-D-glucopyranoside
5
man
non-polymer
18.015
water
68
nat
water
Intramembrane serine protease
no
no
AALRERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVE
KRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFG
MSMANGAHIAGLAVGLAMAFVDSLNARKRK
AALRERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVE
KRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFG
MSMANGAHIAGLAVGLAMAFVDSLNARKRK
A
polypeptide(L)
no
yes
(ACE)RVRH(W6Q)
XRVRHX
C
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
S88 / ExPEC
sample
1
190
glpG, ECS88_3813
585035
Escherichia coli O45:K1 (strain S88 / ExPEC)
469008
Escherichia coli BL21(DE3)
C43
Biological sequence
pET25
1
3.53
65.15
VAPOR DIFFUSION, HANGING DROP
3M NH4Cl, 25mM Bis Tris pH7
298
citation
entity_src_gen
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Database references
Source and taxonomy
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2017-11-15
1
1
2018-01-03
1
2
2018-01-24
1
3
2020-07-29
1
4
2024-01-17
_citation.journal_volume
_citation.page_first
_citation.page_last
_entity_src_gen.host_org_common_name
_entity_src_gen.pdbx_host_org_scientific_name
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
b-nonylglucoside
N
PDBE
Y
PDBE
2017-01-09
REL
REL
CL
CHLORIDE ION
BNG
nonyl beta-D-glucopyranoside
HOH
water
32630
synthetic construct
sample
1
6
4QNZ
PDB
experimental model
CL
302
3
CL
CL
301
A
CL
303
3
CL
CL
302
A
BNG
304
4
BNG
BNG
303
A
BNG
305
4
BNG
BNG
304
A
BNG
306
4
BNG
BNG
305
A
BNG
307
4
BNG
BNG
306
A
BNG
308
4
BNG
BNG
307
A
HOH
401
5
HOH
HOH
401
A
HOH
402
5
HOH
HOH
402
A
HOH
403
5
HOH
HOH
403
A
HOH
404
5
HOH
HOH
404
A
HOH
405
5
HOH
HOH
405
A
HOH
406
5
HOH
HOH
406
A
HOH
407
5
HOH
HOH
407
A
HOH
408
5
HOH
HOH
408
A
HOH
409
5
HOH
HOH
409
A
HOH
410
5
HOH
HOH
410
A
HOH
411
5
HOH
HOH
411
A
HOH
412
5
HOH
HOH
412
A
HOH
413
5
HOH
HOH
413
A
HOH
414
5
HOH
HOH
414
A
HOH
415
5
HOH
HOH
415
A
HOH
416
5
HOH
HOH
416
A
HOH
417
5
HOH
HOH
417
A
HOH
418
5
HOH
HOH
418
A
HOH
419
5
HOH
HOH
419
A
HOH
420
5
HOH
HOH
420
A
HOH
421
5
HOH
HOH
421
A
HOH
422
5
HOH
HOH
422
A
HOH
423
5
HOH
HOH
423
A
HOH
424
5
HOH
HOH
424
A
HOH
425
5
HOH
HOH
425
A
HOH
426
5
HOH
HOH
426
A
HOH
427
5
HOH
HOH
427
A
HOH
428
5
HOH
HOH
428
A
HOH
429
5
HOH
HOH
429
A
HOH
430
5
HOH
HOH
430
A
HOH
431
5
HOH
HOH
431
A
HOH
432
5
HOH
HOH
432
A
HOH
433
5
HOH
HOH
433
A
HOH
434
5
HOH
HOH
434
A
HOH
435
5
HOH
HOH
435
A
HOH
436
5
HOH
HOH
436
A
HOH
437
5
HOH
HOH
437
A
HOH
438
5
HOH
HOH
438
A
HOH
439
5
HOH
HOH
439
A
HOH
440
5
HOH
HOH
440
A
HOH
441
5
HOH
HOH
441
A
HOH
442
5
HOH
HOH
442
A
HOH
443
5
HOH
HOH
443
A
HOH
444
5
HOH
HOH
444
A
HOH
445
5
HOH
HOH
445
A
HOH
446
5
HOH
HOH
446
A
HOH
447
5
HOH
HOH
447
A
HOH
448
5
HOH
HOH
448
A
HOH
449
5
HOH
HOH
449
A
HOH
450
5
HOH
HOH
450
A
HOH
451
5
HOH
HOH
451
A
HOH
452
5
HOH
HOH
452
A
HOH
453
5
HOH
HOH
453
A
HOH
454
5
HOH
HOH
454
A
HOH
455
5
HOH
HOH
455
A
HOH
456
5
HOH
HOH
456
A
HOH
457
5
HOH
HOH
457
A
HOH
458
5
HOH
HOH
458
A
HOH
459
5
HOH
HOH
459
A
HOH
460
5
HOH
HOH
460
A
HOH
461
5
HOH
HOH
461
A
HOH
462
5
HOH
HOH
462
A
HOH
101
5
HOH
HOH
101
C
HOH
102
5
HOH
HOH
102
C
HOH
103
5
HOH
HOH
103
C
HOH
104
5
HOH
HOH
104
C
HOH
105
5
HOH
HOH
105
C
HOH
106
5
HOH
HOH
106
C
0.505
44.970
2.140
n
1
87
A
n
2
88
A
n
3
89
A
n
4
90
A
GLU
91
n
5
GLU
91
A
ARG
92
n
6
ARG
92
A
ALA
93
n
7
ALA
93
A
GLY
94
n
8
GLY
94
A
PRO
95
n
9
PRO
95
A
VAL
96
n
10
VAL
96
A
THR
97
n
11
THR
97
A
TRP
98
n
12
TRP
98
A
VAL
99
n
13
VAL
99
A
MET
100
n
14
MET
100
A
MET
101
n
15
MET
101
A
ILE
102
n
16
ILE
102
A
ALA
103
n
17
ALA
103
A
CYS
104
n
18
CYS
104
A
VAL
105
n
19
VAL
105
A
VAL
106
n
20
VAL
106
A
VAL
107
n
21
VAL
107
A
PHE
108
n
22
PHE
108
A
ILE
109
n
23
ILE
109
A
ALA
110
n
24
ALA
110
A
MET
111
n
25
MET
111
A
GLN
112
n
26
GLN
112
A
ILE
113
n
27
ILE
113
A
LEU
114
n
28
LEU
114
A
GLY
115
n
29
GLY
115
A
ASP
116
n
30
ASP
116
A
GLN
117
n
31
GLN
117
A
GLU
118
n
32
GLU
118
A
VAL
119
n
33
VAL
119
A
MET
120
n
34
MET
120
A
LEU
121
n
35
LEU
121
A
TRP
122
n
36
TRP
122
A
LEU
123
n
37
LEU
123
A
ALA
124
n
38
ALA
124
A
TRP
125
n
39
TRP
125
A
PRO
126
n
40
PRO
126
A
PHE
127
n
41
PHE
127
A
ASP
128
n
42
ASP
128
A
PRO
129
n
43
PRO
129
A
THR
130
n
44
THR
130
A
LEU
131
n
45
LEU
131
A
LYS
132
n
46
LYS
132
A
PHE
133
n
47
PHE
133
A
GLU
134
n
48
GLU
134
A
PHE
135
n
49
PHE
135
A
TRP
136
n
50
TRP
136
A
ARG
137
n
51
ARG
137
A
TYR
138
n
52
TYR
138
A
PHE
139
n
53
PHE
139
A
THR
140
n
54
THR
140
A
HIS
141
n
55
HIS
141
A
ALA
142
n
56
ALA
142
A
LEU
143
n
57
LEU
143
A
MET
144
n
58
MET
144
A
HIS
145
n
59
HIS
145
A
PHE
146
n
60
PHE
146
A
SER
147
n
61
SER
147
A
LEU
148
n
62
LEU
148
A
MET
149
n
63
MET
149
A
HIS
150
n
64
HIS
150
A
ILE
151
n
65
ILE
151
A
LEU
152
n
66
LEU
152
A
PHE
153
n
67
PHE
153
A
ASN
154
n
68
ASN
154
A
LEU
155
n
69
LEU
155
A
LEU
156
n
70
LEU
156
A
TRP
157
n
71
TRP
157
A
TRP
158
n
72
TRP
158
A
TRP
159
n
73
TRP
159
A
TYR
160
n
74
TYR
160
A
LEU
161
n
75
LEU
161
A
GLY
162
n
76
GLY
162
A
GLY
163
n
77
GLY
163
A
ALA
164
n
78
ALA
164
A
VAL
165
n
79
VAL
165
A
GLU
166
n
80
GLU
166
A
LYS
167
n
81
LYS
167
A
ARG
168
n
82
ARG
168
A
LEU
169
n
83
LEU
169
A
GLY
170
n
84
GLY
170
A
SER
171
n
85
SER
171
A
GLY
172
n
86
GLY
172
A
LYS
173
n
87
LYS
173
A
LEU
174
n
88
LEU
174
A
ILE
175
n
89
ILE
175
A
VAL
176
n
90
VAL
176
A
ILE
177
n
91
ILE
177
A
THR
178
n
92
THR
178
A
LEU
179
n
93
LEU
179
A
ILE
180
n
94
ILE
180
A
SER
181
n
95
SER
181
A
ALA
182
n
96
ALA
182
A
LEU
183
n
97
LEU
183
A
LEU
184
n
98
LEU
184
A
SER
185
n
99
SER
185
A
GLY
186
n
100
GLY
186
A
TYR
187
n
101
TYR
187
A
VAL
188
n
102
VAL
188
A
GLN
189
n
103
GLN
189
A
GLN
190
n
104
GLN
190
A
LYS
191
n
105
LYS
191
A
PHE
192
n
106
PHE
192
A
SER
193
n
107
SER
193
A
GLY
194
n
108
GLY
194
A
PRO
195
n
109
PRO
195
A
TRP
196
n
110
TRP
196
A
PHE
197
n
111
PHE
197
A
GLY
198
n
112
GLY
198
A
GLY
199
n
113
GLY
199
A
LEU
200
n
114
LEU
200
A
SER
201
n
115
SER
201
A
GLY
202
n
116
GLY
202
A
VAL
203
n
117
VAL
203
A
VAL
204
n
118
VAL
204
A
TYR
205
n
119
TYR
205
A
ALA
206
n
120
ALA
206
A
LEU
207
n
121
LEU
207
A
MET
208
n
122
MET
208
A
GLY
209
n
123
GLY
209
A
TYR
210
n
124
TYR
210
A
VAL
211
n
125
VAL
211
A
TRP
212
n
126
TRP
212
A
LEU
213
n
127
LEU
213
A
ARG
214
n
128
ARG
214
A
GLY
215
n
129
GLY
215
A
GLU
216
n
130
GLU
216
A
ARG
217
n
131
ARG
217
A
ASP
218
n
132
ASP
218
A
PRO
219
n
133
PRO
219
A
GLN
220
n
134
GLN
220
A
SER
221
n
135
SER
221
A
GLY
222
n
136
GLY
222
A
ILE
223
n
137
ILE
223
A
TYR
224
n
138
TYR
224
A
LEU
225
n
139
LEU
225
A
GLN
226
n
140
GLN
226
A
ARG
227
n
141
ARG
227
A
GLY
228
n
142
GLY
228
A
LEU
229
n
143
LEU
229
A
ILE
230
n
144
ILE
230
A
ILE
231
n
145
ILE
231
A
PHE
232
n
146
PHE
232
A
ALA
233
n
147
ALA
233
A
LEU
234
n
148
LEU
234
A
ILE
235
n
149
ILE
235
A
TRP
236
n
150
TRP
236
A
ILE
237
n
151
ILE
237
A
VAL
238
n
152
VAL
238
A
ALA
239
n
153
ALA
239
A
GLY
240
n
154
GLY
240
A
TRP
241
n
155
TRP
241
A
PHE
242
n
156
PHE
242
A
ASP
243
n
157
ASP
243
A
LEU
244
n
158
LEU
244
A
PHE
245
n
159
PHE
245
A
GLY
246
n
160
GLY
246
A
MET
247
n
161
MET
247
A
SER
248
n
162
SER
248
A
MET
249
n
163
MET
249
A
ALA
250
n
164
ALA
250
A
ASN
251
n
165
ASN
251
A
GLY
252
n
166
GLY
252
A
ALA
253
n
167
ALA
253
A
HIS
254
n
168
HIS
254
A
ILE
255
n
169
ILE
255
A
ALA
256
n
170
ALA
256
A
GLY
257
n
171
GLY
257
A
LEU
258
n
172
LEU
258
A
ALA
259
n
173
ALA
259
A
VAL
260
n
174
VAL
260
A
GLY
261
n
175
GLY
261
A
LEU
262
n
176
LEU
262
A
ALA
263
n
177
ALA
263
A
MET
264
n
178
MET
264
A
ALA
265
n
179
ALA
265
A
PHE
266
n
180
PHE
266
A
VAL
267
n
181
VAL
267
A
ASP
268
n
182
ASP
268
A
SER
269
n
183
SER
269
A
LEU
270
n
184
LEU
270
A
ASN
271
n
185
ASN
271
A
n
186
272
A
n
187
273
A
n
188
274
A
n
189
275
A
n
190
276
A
ACE
7
n
1
ACE
7
C
ARG
8
n
2
ARG
8
C
VAL
9
n
3
VAL
9
C
ARG
10
n
4
ARG
10
C
HIS
11
n
5
HIS
11
C
W6Q
12
n
6
W6Q
12
C
software_defined_assembly
PISA
12
dodecameric
32290
-281
43680
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-y,x-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-x+y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
5_555
x-y,-y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_555
-x,-x+y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
C1
BNG
304
F
C1
BNG
1
1
N
1
A
C2
BNG
304
F
C2
BNG
1
1
N
1
A
C3
BNG
304
F
C3
BNG
1
1
N
1
A
C4
BNG
304
F
C4
BNG
1
1
N
1
A
C5
BNG
304
F
C5
BNG
1
1
N
1
A
C6
BNG
304
F
C6
BNG
1
1
N
1
A
C1'
BNG
304
F
C1'
BNG
1
1
N
1
A
C2'
BNG
304
F
C2'
BNG
1
1
N
1
A
O1
BNG
304
F
O1
BNG
1
1
N
1
A
O2
BNG
304
F
O2
BNG
1
1
N
1
A
O3
BNG
304
F
O3
BNG
1
1
N
1
A
O4
BNG
304
F
O4
BNG
1
1
N
1
A
O5
BNG
304
F
O5
BNG
1
1
N
1
A
O6
BNG
304
F
O6
BNG
1
1
N
1
A
C1
BNG
305
G
C1
BNG
1
1
N
1
A
C2
BNG
305
G
C2
BNG
1
1
N
1
A
C3
BNG
305
G
C3
BNG
1
1
N
1
A
C4
BNG
305
G
C4
BNG
1
1
N
1
A
C5
BNG
305
G
C5
BNG
1
1
N
1
A
C6
BNG
305
G
C6
BNG
1
1
N
1
A
C1'
BNG
305
G
C1'
BNG
1
1
N
1
A
C2'
BNG
305
G
C2'
BNG
1
1
N
1
A
O1
BNG
305
G
O1
BNG
1
1
N
1
A
O2
BNG
305
G
O2
BNG
1
1
N
1
A
O3
BNG
305
G
O3
BNG
1
1
N
1
A
O4
BNG
305
G
O4
BNG
1
1
N
1
A
O5
BNG
305
G
O5
BNG
1
1
N
1
A
O6
BNG
305
G
O6
BNG
1
1
N
1
A
C2'
BNG
306
H
C2'
BNG
1
1
N
1
A
C3'
BNG
306
H
C3'
BNG
1
1
N
1
A
C4'
BNG
306
H
C4'
BNG
1
1
N
1
A
C5'
BNG
306
H
C5'
BNG
1
1
N
1
A
C6'
BNG
306
H
C6'
BNG
1
1
N
1
A
C7'
BNG
306
H
C7'
BNG
1
1
N
1
A
C8'
BNG
306
H
C8'
BNG
1
1
N
1
A
C9'
BNG
306
H
C9'
BNG
1
1
N
1
A
C2'
BNG
307
I
C2'
BNG
1
1
N
1
A
C3'
BNG
307
I
C3'
BNG
1
1
N
1
A
C4'
BNG
307
I
C4'
BNG
1
1
N
1
A
C5'
BNG
307
I
C5'
BNG
1
1
N
1
A
C6'
BNG
307
I
C6'
BNG
1
1
N
1
A
C7'
BNG
307
I
C7'
BNG
1
1
N
1
A
C8'
BNG
307
I
C8'
BNG
1
1
N
1
A
C9'
BNG
307
I
C9'
BNG
1
1
N
1
A
ALA
87
A
ALA
1
1
Y
1
A
ALA
88
A
ALA
2
1
Y
1
A
LEU
89
A
LEU
3
1
Y
1
A
ARG
90
A
ARG
4
1
Y
1
A
ALA
272
A
ALA
186
1
Y
1
A
ARG
273
A
ARG
187
1
Y
1
A
LYS
274
A
LYS
188
1
Y
1
A
ARG
275
A
ARG
189
1
Y
1
A
LYS
276
A
LYS
190
1
Y
1
-6.04
0.90
118.30
112.26
A
A
A
CB
CG
OD2
ASP
ASP
ASP
116
116
116
N
1
3.26
0.50
120.30
123.56
C
C
C
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
35.73
0.03000
0.01000
0.00000
0.03000
0.00000
-0.08000
HYDROGENS HAVE BEEN ADDED IN THE RIDING
0.192
0.167
0.169
1.79
44.97
1411
26791
5.000
99.8
4.530
0.066
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.088
0.087
4QNZ
1.79
44.97
68
1636
80
0
1488
37.88
1.787
44.970
5MTF
28202
1
18.6400
5.000
99.8
1.79
1.90
1.860
1
4.95
99.6
refinement
REFMAC
data extraction
PDB_EXTRACT
3.22
data reduction
XDS
phasing
MOLREP
N
A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
5
N
N
A
GLY
94
A
GLY
8
HELX_P
A
GLY
115
A
GLY
29
1
AA1
22
A
GLY
115
A
GLY
29
HELX_P
A
ALA
124
A
ALA
38
1
AA2
10
A
ASP
128
A
ASP
42
HELX_P
A
LYS
132
A
LYS
46
5
AA3
5
A
TRP
136
A
TRP
50
HELX_P
A
HIS
141
A
HIS
55
1
AA4
6
A
ALA
142
A
ALA
56
HELX_P
A
MET
144
A
MET
58
5
AA5
3
A
SER
147
A
SER
61
HELX_P
A
GLY
170
A
GLY
84
1
AA6
24
A
GLY
170
A
GLY
84
HELX_P
A
GLY
194
A
GLY
108
1
AA7
25
A
LEU
200
A
LEU
114
HELX_P
A
ASP
218
A
ASP
132
1
AA8
19
A
PRO
219
A
PRO
133
HELX_P
A
GLY
222
A
GLY
136
5
AA9
4
A
GLN
226
A
GLN
140
HELX_P
A
PHE
242
A
PHE
156
1
AB1
17
A
ALA
250
A
ALA
164
HELX_P
A
LEU
270
A
LEU
184
1
AB2
21
covale
1.380
none
A
SER
201
A
OG
SER
115
1_555
C
W6Q
12
B
C7
W6Q
6
1_555
covale
1.352
both
C
ACE
7
B
C
ACE
1
1_555
C
ARG
8
B
N
ARG
2
1_555
covale
1.463
one
C
HIS
11
B
C
HIS
5
1_555
C
W6Q
12
B
N1
W6Q
6
1_555
HYDROLASE
Rhomboid protease, specificity, inhibition, ketoamide, hydrolase
GLPG_ECO45
UNP
1
87
B7MDQ0
AALRERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVE
KRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFG
MSMANGAHIAGLAVGLAMAFVDSLNARKRK
5MTF
PDB
2
1
5MTF
87
276
5MTF
87
276
B7MDQ0
A
1
1
190
7
12
5MTF
7
12
5MTF
C
2
1
6
155
H 3 2