0.009000
0.005196
0.000000
0.000000
0.010393
0.000000
0.000000
0.000000
0.007932
0.00000
0.00000
0.00000
Vinothkumar, K.R.
voskya, O.
Kuettler, E.V.
Brouwer, A.J.
Liskamp, R.M.J.
Verhelst, S.H.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
111.109
111.109
126.067
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
C17 H17 N O3
283.322
2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate
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
R
C
N
75
R
C
N
76
S
C
N
77
S
C
N
78
R
C
N
79
N
C
N
80
N
C
N
81
N
C
N
82
N
C
N
83
N
C
N
84
N
C
N
85
N
C
N
86
N
C
N
87
N
C
N
88
N
C
N
89
N
O
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
O
N
94
N
O
N
95
N
H
N
96
N
H
N
97
N
H
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
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
CL
N
126
N
N
N
127
R
C
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
S
N
132
N
O
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
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
N
C
N
145
N
C
N
146
N
C
N
147
N
O
N
148
N
N
N
149
N
O
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
H
N
159
N
H
N
160
N
N
N
161
S
C
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
C
N
167
N
O
N
168
N
O
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
N
N
180
N
C
N
181
N
C
N
182
N
O
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
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
N
C
Y
194
N
C
Y
195
N
N
Y
196
N
C
Y
197
N
C
Y
198
N
N
N
199
N
O
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
O
N
211
N
H
N
212
N
H
N
213
N
N
N
214
S
C
N
215
N
C
N
216
N
O
N
217
S
C
N
218
N
C
N
219
N
C
N
220
N
C
N
221
N
O
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
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
N
N
236
S
C
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
C
N
243
N
O
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
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
N
N
258
S
C
N
259
N
C
N
260
N
O
N
261
N
C
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
N
N
266
N
O
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
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
N
N
283
S
C
N
284
N
C
N
285
N
O
N
286
N
C
N
287
N
C
N
288
N
S
N
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
N
N
303
S
C
N
304
N
C
N
305
N
O
N
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
C
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
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
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
N
330
N
C
N
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
N
347
N
O
N
348
N
O
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
O
N
357
N
C
N
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
N
Y
364
N
C
Y
365
N
C
N
366
N
C
N
367
N
O
N
368
N
O
N
369
N
C
N
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
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
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
R
C
N
399
N
O
N
400
N
C
N
401
N
O
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
Y
419
N
N
Y
420
N
C
Y
421
N
C
Y
422
N
C
Y
423
N
C
Y
424
N
C
N
425
N
O
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
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
N
N
439
S
C
N
440
N
C
N
441
N
O
N
442
N
C
Y
443
N
C
Y
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
N
449
N
O
N
450
N
O
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
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
N
N
463
S
C
N
464
N
C
N
465
N
O
N
466
N
C
N
467
N
C
N
468
N
C
N
469
N
O
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
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
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
doub
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
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
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
sing
N
159
N
doub
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
doub
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
sing
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
Y
191
N
sing
Y
192
N
doub
Y
193
N
doub
N
194
N
sing
Y
195
N
sing
N
196
N
sing
Y
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
doub
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
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
sing
N
249
N
sing
N
250
N
sing
N
251
N
doub
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
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
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
sing
N
294
N
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
Y
299
N
doub
Y
300
N
sing
Y
301
N
sing
N
302
N
sing
Y
303
N
doub
N
304
N
sing
Y
305
N
doub
N
306
N
sing
Y
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
doub
N
318
N
sing
N
319
N
sing
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
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
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
doub
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
sing
Y
346
N
doub
Y
347
N
doub
Y
348
N
sing
N
349
N
sing
Y
350
N
doub
Y
351
N
sing
N
352
N
sing
N
353
N
doub
N
354
N
sing
N
355
N
sing
N
356
N
sing
Y
357
N
sing
Y
358
N
doub
Y
359
N
doub
Y
360
N
sing
Y
361
N
doub
Y
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
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
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
doub
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
sing
N
402
N
doub
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
Y
407
N
doub
Y
408
N
sing
Y
409
N
sing
N
410
N
sing
Y
411
N
doub
Y
412
N
sing
Y
413
N
sing
N
414
N
sing
Y
415
N
sing
Y
416
N
doub
N
417
N
sing
Y
418
N
doub
N
419
N
sing
Y
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
doub
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
Y
435
N
doub
Y
436
N
sing
Y
437
N
sing
N
438
N
sing
Y
439
N
doub
N
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
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
sing
N
454
N
doub
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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
110
2472
10.1073/PNAS.1215076110
23359682
Activity-Based Probes for Rhomboid Proteases Discovered in a Mass Spectrometry-Based Assay.
2013
10.2210/pdb3zeb/pdb
pdb_00003zeb
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
PIXEL
2012-05-24
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
I02
Diamond
0.9795
SYNCHROTRON
DIAMOND BEAMLINE I02
THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 FORMS ESTER BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE CREATES A SECOND COVALENT BOND.
20214.020
RHOMBOID PROTEASE GLPG
3.4.21.105
CORE TM DOMAIN, RESIDUES 92-270
1
man
polymer
283.322
2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
306.395
nonyl beta-D-glucopyranoside
5
man
non-polymer
18.015
water
18
nat
water
INTRAMEMBRANE SERINE PROTEASE, GLPG
no
no
RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGS
GKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMAN
GAHIAGLAVGLAMAFVDSL
RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGS
GKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMAN
GAHIAGLAVGLAMAFVDSL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
469008
ESCHERICHIA COLI
469008
ESCHERICHIA COLI
BL21(DE3)
C41
PET
PLASMID
1
3.5
64.8
NONE
VAPOR DIFFUSION, HANGING DROP
7.0
2M AMMONIUM CHLORIDE, 0.1 M BIS-TRIS PH7.0, 298K
298
exptl_crystal_grow
pdbx_database_proc
pdbx_database_status
struct_biol
struct_conn
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_database_status
pdbx_entity_nonpoly
struct_conn
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
Data collection
Derived calculations
Experimental preparation
Other
Data collection
Derived calculations
Other
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2013-02-13
1
1
2013-03-06
1
2
2019-02-27
1
3
2020-07-29
1
4
2023-12-20
_exptl_crystal_grow.method
_exptl_crystal_grow.temp
_pdbx_database_status.recvd_author_approval
_struct_conn.pdbx_leaving_atom_flag
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_database_status.status_code_sf
_pdbx_entity_nonpoly.name
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
b-nonylglucoside
PDBE
Y
PDBE
2012-12-04
REL
REL
SV1
2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate
CL
CHLORIDE ION
BNG
nonyl beta-D-glucopyranoside
HOH
water
2-PHENYLETHYL 2-(4-AZANYL-2-METHANOYL-PHENYL)ETHANOATE (SV1): THE
NUCLEOPHILIC ATTACK OF SER 201 ON ISOCOUMARIN OPENS THE
RING AND FORMS AN ESTER BOND. A SUBSEQUENT REACTION WITH
HIS 150 RESULTS IN TWIN COVALENTLY BONDED MOLECULE.
2XOV
PDB ENTRY 2XOV
PDB
experimental model
SV1
401
2
SV1
SV1
401
A
CL
402
3
CL
CL
402
A
BNG
403
4
BNG
BNG
403
A
BNG
404
4
BNG
BNG
404
A
BNG
405
4
BNG
BNG
405
A
BNG
406
4
BNG
BNG
406
A
BNG
407
4
BNG
BNG
407
A
HOH
2001
5
HOH
HOH
2001
A
HOH
2002
5
HOH
HOH
2002
A
HOH
2003
5
HOH
HOH
2003
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2006
5
HOH
HOH
2006
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2008
5
HOH
HOH
2008
A
HOH
2009
5
HOH
HOH
2009
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2011
5
HOH
HOH
2011
A
HOH
2012
5
HOH
HOH
2012
A
HOH
2013
5
HOH
HOH
2013
A
HOH
2014
5
HOH
HOH
2014
A
HOH
2015
5
HOH
HOH
2015
A
HOH
2016
5
HOH
HOH
2016
A
HOH
2017
5
HOH
HOH
2017
A
HOH
2018
5
HOH
HOH
2018
A
ARG
92
n
1
ARG
92
A
ALA
93
n
2
ALA
93
A
GLY
94
n
3
GLY
94
A
PRO
95
n
4
PRO
95
A
VAL
96
n
5
VAL
96
A
THR
97
n
6
THR
97
A
TRP
98
n
7
TRP
98
A
VAL
99
n
8
VAL
99
A
MET
100
n
9
MET
100
A
MET
101
n
10
MET
101
A
ILE
102
n
11
ILE
102
A
ALA
103
n
12
ALA
103
A
CYS
104
n
13
CYS
104
A
VAL
105
n
14
VAL
105
A
VAL
106
n
15
VAL
106
A
VAL
107
n
16
VAL
107
A
PHE
108
n
17
PHE
108
A
ILE
109
n
18
ILE
109
A
ALA
110
n
19
ALA
110
A
MET
111
n
20
MET
111
A
GLN
112
n
21
GLN
112
A
ILE
113
n
22
ILE
113
A
LEU
114
n
23
LEU
114
A
GLY
115
n
24
GLY
115
A
ASP
116
n
25
ASP
116
A
GLN
117
n
26
GLN
117
A
GLU
118
n
27
GLU
118
A
VAL
119
n
28
VAL
119
A
MET
120
n
29
MET
120
A
LEU
121
n
30
LEU
121
A
TRP
122
n
31
TRP
122
A
LEU
123
n
32
LEU
123
A
ALA
124
n
33
ALA
124
A
TRP
125
n
34
TRP
125
A
PRO
126
n
35
PRO
126
A
PHE
127
n
36
PHE
127
A
ASP
128
n
37
ASP
128
A
PRO
129
n
38
PRO
129
A
THR
130
n
39
THR
130
A
LEU
131
n
40
LEU
131
A
LYS
132
n
41
LYS
132
A
PHE
133
n
42
PHE
133
A
GLU
134
n
43
GLU
134
A
PHE
135
n
44
PHE
135
A
TRP
136
n
45
TRP
136
A
ARG
137
n
46
ARG
137
A
TYR
138
n
47
TYR
138
A
PHE
139
n
48
PHE
139
A
THR
140
n
49
THR
140
A
HIS
141
n
50
HIS
141
A
ALA
142
n
51
ALA
142
A
LEU
143
n
52
LEU
143
A
MET
144
n
53
MET
144
A
HIS
145
n
54
HIS
145
A
PHE
146
n
55
PHE
146
A
SER
147
n
56
SER
147
A
LEU
148
n
57
LEU
148
A
MET
149
n
58
MET
149
A
HIS
150
n
59
HIS
150
A
ILE
151
n
60
ILE
151
A
LEU
152
n
61
LEU
152
A
PHE
153
n
62
PHE
153
A
ASN
154
n
63
ASN
154
A
LEU
155
n
64
LEU
155
A
LEU
156
n
65
LEU
156
A
TRP
157
n
66
TRP
157
A
TRP
158
n
67
TRP
158
A
TRP
159
n
68
TRP
159
A
TYR
160
n
69
TYR
160
A
LEU
161
n
70
LEU
161
A
GLY
162
n
71
GLY
162
A
GLY
163
n
72
GLY
163
A
ALA
164
n
73
ALA
164
A
VAL
165
n
74
VAL
165
A
GLU
166
n
75
GLU
166
A
LYS
167
n
76
LYS
167
A
ARG
168
n
77
ARG
168
A
LEU
169
n
78
LEU
169
A
GLY
170
n
79
GLY
170
A
SER
171
n
80
SER
171
A
GLY
172
n
81
GLY
172
A
LYS
173
n
82
LYS
173
A
LEU
174
n
83
LEU
174
A
ILE
175
n
84
ILE
175
A
VAL
176
n
85
VAL
176
A
ILE
177
n
86
ILE
177
A
THR
178
n
87
THR
178
A
LEU
179
n
88
LEU
179
A
ILE
180
n
89
ILE
180
A
SER
181
n
90
SER
181
A
ALA
182
n
91
ALA
182
A
LEU
183
n
92
LEU
183
A
LEU
184
n
93
LEU
184
A
SER
185
n
94
SER
185
A
GLY
186
n
95
GLY
186
A
TYR
187
n
96
TYR
187
A
VAL
188
n
97
VAL
188
A
GLN
189
n
98
GLN
189
A
GLN
190
n
99
GLN
190
A
LYS
191
n
100
LYS
191
A
PHE
192
n
101
PHE
192
A
SER
193
n
102
SER
193
A
GLY
194
n
103
GLY
194
A
PRO
195
n
104
PRO
195
A
TRP
196
n
105
TRP
196
A
PHE
197
n
106
PHE
197
A
GLY
198
n
107
GLY
198
A
GLY
199
n
108
GLY
199
A
LEU
200
n
109
LEU
200
A
SER
201
n
110
SER
201
A
GLY
202
n
111
GLY
202
A
VAL
203
n
112
VAL
203
A
VAL
204
n
113
VAL
204
A
TYR
205
n
114
TYR
205
A
ALA
206
n
115
ALA
206
A
LEU
207
n
116
LEU
207
A
MET
208
n
117
MET
208
A
GLY
209
n
118
GLY
209
A
TYR
210
n
119
TYR
210
A
VAL
211
n
120
VAL
211
A
TRP
212
n
121
TRP
212
A
LEU
213
n
122
LEU
213
A
ARG
214
n
123
ARG
214
A
GLY
215
n
124
GLY
215
A
GLU
216
n
125
GLU
216
A
ARG
217
n
126
ARG
217
A
ASP
218
n
127
ASP
218
A
PRO
219
n
128
PRO
219
A
GLN
220
n
129
GLN
220
A
SER
221
n
130
SER
221
A
GLY
222
n
131
GLY
222
A
ILE
223
n
132
ILE
223
A
TYR
224
n
133
TYR
224
A
LEU
225
n
134
LEU
225
A
GLN
226
n
135
GLN
226
A
ARG
227
n
136
ARG
227
A
GLY
228
n
137
GLY
228
A
LEU
229
n
138
LEU
229
A
ILE
230
n
139
ILE
230
A
ILE
231
n
140
ILE
231
A
PHE
232
n
141
PHE
232
A
ALA
233
n
142
ALA
233
A
LEU
234
n
143
LEU
234
A
ILE
235
n
144
ILE
235
A
TRP
236
n
145
TRP
236
A
ILE
237
n
146
ILE
237
A
VAL
238
n
147
VAL
238
A
ALA
239
n
148
ALA
239
A
GLY
240
n
149
GLY
240
A
TRP
241
n
150
TRP
241
A
PHE
242
n
151
PHE
242
A
ASP
243
n
152
ASP
243
A
LEU
244
n
153
LEU
244
A
PHE
245
n
154
PHE
245
A
GLY
246
n
155
GLY
246
A
MET
247
n
156
MET
247
A
SER
248
n
157
SER
248
A
MET
249
n
158
MET
249
A
ALA
250
n
159
ALA
250
A
ASN
251
n
160
ASN
251
A
GLY
252
n
161
GLY
252
A
ALA
253
n
162
ALA
253
A
HIS
254
n
163
HIS
254
A
ILE
255
n
164
ILE
255
A
ALA
256
n
165
ALA
256
A
GLY
257
n
166
GLY
257
A
LEU
258
n
167
LEU
258
A
ALA
259
n
168
ALA
259
A
VAL
260
n
169
VAL
260
A
GLY
261
n
170
GLY
261
A
LEU
262
n
171
LEU
262
A
ALA
263
n
172
ALA
263
A
MET
264
n
173
MET
264
A
ALA
265
n
174
ALA
265
A
PHE
266
n
175
PHE
266
A
VAL
267
n
176
VAL
267
A
ASP
268
n
177
ASP
268
A
SER
269
n
178
SER
269
A
LEU
270
n
179
LEU
270
A
author_and_software_defined_assembly
PISA
1
monomeric
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
1
A
CG
GLN
220
A
CG
GLN
129
1
Y
1
A
CD
GLN
220
A
CD
GLN
129
1
Y
1
A
OE1
GLN
220
A
OE1
GLN
129
1
Y
1
A
NE2
GLN
220
A
NE2
GLN
129
1
Y
1
A
C1
BNG
403
D
C1
BNG
1
1
N
1
A
C2
BNG
403
D
C2
BNG
1
1
N
1
A
C3
BNG
403
D
C3
BNG
1
1
N
1
A
C4
BNG
403
D
C4
BNG
1
1
N
1
A
C5
BNG
403
D
C5
BNG
1
1
N
1
A
C6
BNG
403
D
C6
BNG
1
1
N
1
A
O1
BNG
403
D
O1
BNG
1
1
N
1
A
O2
BNG
403
D
O2
BNG
1
1
N
1
A
O3
BNG
403
D
O3
BNG
1
1
N
1
A
O4
BNG
403
D
O4
BNG
1
1
N
1
A
O5
BNG
403
D
O5
BNG
1
1
N
1
A
O6
BNG
403
D
O6
BNG
1
1
N
1
A
C1
BNG
404
E
C1
BNG
1
1
N
1
A
C2
BNG
404
E
C2
BNG
1
1
N
1
A
C3
BNG
404
E
C3
BNG
1
1
N
1
A
C4
BNG
404
E
C4
BNG
1
1
N
1
A
C5
BNG
404
E
C5
BNG
1
1
N
1
A
C6
BNG
404
E
C6
BNG
1
1
N
1
A
C8'
BNG
404
E
C8'
BNG
1
1
N
1
A
C9'
BNG
404
E
C9'
BNG
1
1
N
1
A
O1
BNG
404
E
O1
BNG
1
1
N
1
A
O2
BNG
404
E
O2
BNG
1
1
N
1
A
O3
BNG
404
E
O3
BNG
1
1
N
1
A
O4
BNG
404
E
O4
BNG
1
1
N
1
A
O5
BNG
404
E
O5
BNG
1
1
N
1
A
O6
BNG
404
E
O6
BNG
1
1
N
1
A
C1
BNG
405
F
C1
BNG
1
1
N
1
A
C2
BNG
405
F
C2
BNG
1
1
N
1
A
C3
BNG
405
F
C3
BNG
1
1
N
1
A
C4
BNG
405
F
C4
BNG
1
1
N
1
A
C5
BNG
405
F
C5
BNG
1
1
N
1
A
C6
BNG
405
F
C6
BNG
1
1
N
1
A
C6'
BNG
405
F
C6'
BNG
1
1
N
1
A
C7'
BNG
405
F
C7'
BNG
1
1
N
1
A
C8'
BNG
405
F
C8'
BNG
1
1
N
1
A
C9'
BNG
405
F
C9'
BNG
1
1
N
1
A
O1
BNG
405
F
O1
BNG
1
1
N
1
A
O2
BNG
405
F
O2
BNG
1
1
N
1
A
O3
BNG
405
F
O3
BNG
1
1
N
1
A
O4
BNG
405
F
O4
BNG
1
1
N
1
A
O5
BNG
405
F
O5
BNG
1
1
N
1
A
O6
BNG
405
F
O6
BNG
1
1
N
1
A
C1
BNG
407
H
C1
BNG
1
1
N
1
A
C2
BNG
407
H
C2
BNG
1
1
N
1
A
C3
BNG
407
H
C3
BNG
1
1
N
1
A
C4
BNG
407
H
C4
BNG
1
1
N
1
A
C5
BNG
407
H
C5
BNG
1
1
N
1
A
C6
BNG
407
H
C6
BNG
1
1
N
1
A
C6'
BNG
407
H
C6'
BNG
1
1
N
1
A
C7'
BNG
407
H
C7'
BNG
1
1
N
1
A
C8'
BNG
407
H
C8'
BNG
1
1
N
1
A
C9'
BNG
407
H
C9'
BNG
1
1
N
1
A
O1
BNG
407
H
O1
BNG
1
1
N
1
A
O2
BNG
407
H
O2
BNG
1
1
N
1
A
O3
BNG
407
H
O3
BNG
1
1
N
1
A
O4
BNG
407
H
O4
BNG
1
1
N
1
A
O5
BNG
407
H
O5
BNG
1
1
N
1
A
O6
BNG
407
H
O6
BNG
1
1
N
1
A
SER
269
-102.39
61.60
60.0
-1.30
-1.30
0.00
-1.30
0.00
4.21
0.950
0.935
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
0.24703
0.21386
0.21552
2.20
44.99
761
14556
5.0
99.33
5.099
0.132
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.203
0.179
0.80
0.80
1.20
PDB ENTRY 2XOV
MAXIMUM LIKELIHOOD
MASK
2.20
44.99
18
1513
69
0
1426
0.008
0.019
1554
0.001
0.020
1528
1.091
1.950
2107
0.744
3.000
3485
4.641
5.000
182
24.937
21.786
56
12.705
15.000
232
7.983
15.000
6
0.061
0.200
226
0.004
0.020
1718
0.001
0.020
393
2.897
5.672
720
2.894
5.666
718
4.104
8.481
898
4.104
8.487
899
2.958
6.267
834
2.957
6.268
835
4.729
9.228
1208
7.126
48.133
1836
7.069
48.113
1832
0.302
0.299
2.256
65
1020
20
95.93
47.4
2.20
44.95
3ZEB
15318
0.0
0.06
1
13.50
4.9
99.6
0.48
2.20
2.32
3.10
1
4.9
98.1
refinement
REFMAC
5.7.0032
data reduction
XDS
data scaling
SCALA
phasing
PHASER
A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
A
GLY
94
A
GLY
3
HELX_P
A
GLY
115
A
GLY
24
1
1
22
A
GLY
115
A
GLY
24
HELX_P
A
ALA
124
A
ALA
33
1
2
10
A
ASP
128
A
ASP
37
HELX_P
A
LYS
132
A
LYS
41
5
3
5
A
GLU
134
A
GLU
43
HELX_P
A
PHE
139
A
PHE
48
5
4
6
A
PHE
139
A
PHE
48
HELX_P
A
MET
144
A
MET
53
5
5
6
A
SER
147
A
SER
56
HELX_P
A
GLY
170
A
GLY
79
1
6
24
A
GLY
170
A
GLY
79
HELX_P
A
GLY
194
A
GLY
103
1
7
25
A
LEU
200
A
LEU
109
HELX_P
A
ASP
218
A
ASP
127
1
8
19
A
PRO
219
A
PRO
128
HELX_P
A
GLY
222
A
GLY
131
5
9
4
A
GLN
226
A
GLN
135
HELX_P
A
PHE
242
A
PHE
151
1
10
17
A
ALA
250
A
ALA
159
HELX_P
A
SER
269
A
SER
178
1
11
20
covale
1.502
one
A
HIS
150
A
ND1
HIS
59
1_555
A
SV1
401
B
C7
SV1
1_555
covale
1.479
one
A
SER
201
A
OG
SER
110
1_555
A
SV1
401
B
C
SV1
1_555
HYDROLASE
HYDROLASE, INTRA-MEMBRANE PROTEASE, SERINE PROTEASE, ACYL ENZYME
GLPG_ECOLI
UNP
1
P09391
92
270
3ZEB
92
270
P09391
A
1
1
179
155
H 3 2