0.023871
0.000000
0.000000
0.000000
0.019210
0.000000
0.000000
0.000000
0.010862
0.00000
0.00000
0.00000
Cui, K.
Zhu, L.
Lu, W.
Huang, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.891
52.057
92.064
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
Co 2
58.933
COBALT (II) ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O S
78.133
DIMETHYL SULFOXIDE
non-polymer
C8 H18 N2 O4 S
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
non-polymer
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
C17 H16 O4
284.307
2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
non-polymer
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
CO
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
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
H
N
89
N
S
N
90
N
O
N
91
N
C
N
92
N
C
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
N
N
100
N
C
N
101
N
C
N
102
N
N
N
103
N
C
N
104
N
C
N
105
N
C
N
106
N
C
N
107
N
O
N
108
N
C
N
109
N
C
N
110
N
S
N
111
N
O
N
112
N
O
N
113
N
O
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
N
N
133
S
C
N
134
N
C
N
135
N
O
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
O
N
140
N
N
N
141
N
O
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
N
N
153
S
C
N
154
N
C
N
155
N
O
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
O
N
160
N
O
N
161
N
O
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
N
N
172
N
C
N
173
N
C
N
174
N
O
N
175
N
O
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
N
N
182
S
C
N
183
N
C
N
184
N
O
N
185
N
C
Y
186
N
C
Y
187
N
N
Y
188
N
C
Y
189
N
C
Y
190
N
N
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
O
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
S
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
O
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
N
N
228
S
C
N
229
N
C
N
230
N
O
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
C
N
235
N
O
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
N
N
250
S
C
N
251
N
C
N
252
N
O
N
253
N
C
N
254
N
C
N
255
N
C
N
256
N
C
N
257
N
N
N
258
N
O
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
S
N
281
N
C
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
N
N
295
S
C
N
296
N
C
N
297
N
O
N
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
Y
303
N
C
Y
304
N
C
N
305
N
O
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
N
N
318
S
C
N
319
N
C
N
320
N
O
N
321
N
C
N
322
N
C
N
323
N
C
N
324
N
O
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
H
N
333
N
H
N
334
N
C
N
335
N
O
Y
336
N
C
N
337
N
O
N
338
N
C
N
339
N
O
Y
340
N
C
N
341
N
O
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
N
349
N
C
Y
350
N
C
N
351
N
C
Y
352
N
C
Y
353
N
C
N
354
N
C
N
355
N
H
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
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
N
376
N
O
N
377
N
O
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
R
C
N
390
N
O
N
391
N
C
N
392
N
O
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
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
N
C
Y
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
N
413
N
O
N
414
N
O
N
415
N
H
N
416
N
H
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
N
N
427
S
C
N
428
N
C
N
429
N
O
N
430
N
C
N
431
N
C
N
432
N
C
N
433
N
O
N
434
N
H
N
435
N
H
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
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
doub
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
doub
N
122
N
doub
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
doub
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
doub
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
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
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
doub
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
Y
182
N
sing
Y
183
N
doub
Y
184
N
doub
N
185
N
sing
Y
186
N
sing
N
187
N
sing
Y
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
doub
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
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
doub
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
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
sing
N
284
N
sing
N
285
N
doub
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
Y
290
N
doub
Y
291
N
sing
Y
292
N
sing
N
293
N
sing
Y
294
N
doub
N
295
N
sing
Y
296
N
doub
N
297
N
sing
Y
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
Y
323
N
doub
Y
324
N
sing
N
325
N
sing
N
326
N
sing
Y
327
N
sing
N
328
N
doub
Y
329
N
doub
Y
330
N
doub
Y
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
Y
336
N
doub
N
337
E
doub
Y
338
N
doub
N
339
N
sing
Y
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
sing
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
doub
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
doub
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
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
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
sing
N
406
N
sing
N
407
N
sing
N
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
doub
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
To be Published
0353
Identification of Novel Peptide Deformylase Inhibitors from Natural Products
10.2210/pdb4e9a/pdb
pdb_00004e9a
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
CCD
2011-11-22
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
BL17U
SSRF
1
SYNCHROTRON
SSRF BEAMLINE BL17U
21008.465
Peptide deformylase 11
3.5.1.88
UNP RESIDUES 2-164
1
man
polymer
58.933
COBALT (II) ION
1
syn
non-polymer
284.307
2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
1
syn
non-polymer
238.305
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
1
syn
non-polymer
78.133
DIMETHYL SULFOXIDE
2
syn
non-polymer
18.015
water
87
nat
water
PDF 11, Polypeptide deformylase 11
no
no
ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINP
KFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFE
KELKELQKKQKHKLEHHHHHH
ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINP
KFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFE
KELKELQKKQKHKLEHHHHHH
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
n
n
sample
def, def11
210
Helicobacter pylori
562
Escherichia coli
BL21(DE3)
Plasmid
pET22b
1
2.39
48.52
EVAPORATION
7.5
HEPES, MPD, pH 7.5, EVAPORATION, temperature 290K
290
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-04-24
1
1
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
PDBJ
2012-03-20
REL
REL
CO
COBALT (II) ION
QAP
2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
EPE
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
DMS
DIMETHYL SULFOXIDE
HOH
water
2EW7
PDB
experimental model
CO
300
2
CO
CO
201
A
C13
200
3
QAP
QAP
202
A
EPE
201
4
EPE
EPE
203
A
DMS
4001
5
DMS
DMS
204
A
DMS
4001
5
DMS
DMS
205
A
HOH
1
6
HOH
HOH
301
A
HOH
2
6
HOH
HOH
302
A
HOH
3
6
HOH
HOH
303
A
HOH
4
6
HOH
HOH
304
A
HOH
5
6
HOH
HOH
305
A
HOH
6
6
HOH
HOH
306
A
HOH
7
6
HOH
HOH
307
A
HOH
8
6
HOH
HOH
308
A
HOH
9
6
HOH
HOH
309
A
HOH
10
6
HOH
HOH
310
A
HOH
11
6
HOH
HOH
311
A
HOH
12
6
HOH
HOH
312
A
HOH
13
6
HOH
HOH
313
A
HOH
14
6
HOH
HOH
314
A
HOH
15
6
HOH
HOH
315
A
HOH
16
6
HOH
HOH
316
A
HOH
17
6
HOH
HOH
317
A
HOH
18
6
HOH
HOH
318
A
HOH
19
6
HOH
HOH
319
A
HOH
20
6
HOH
HOH
320
A
HOH
21
6
HOH
HOH
321
A
HOH
22
6
HOH
HOH
322
A
HOH
23
6
HOH
HOH
323
A
HOH
24
6
HOH
HOH
324
A
HOH
25
6
HOH
HOH
325
A
HOH
26
6
HOH
HOH
326
A
HOH
27
6
HOH
HOH
327
A
HOH
28
6
HOH
HOH
328
A
HOH
29
6
HOH
HOH
329
A
HOH
30
6
HOH
HOH
330
A
HOH
31
6
HOH
HOH
331
A
HOH
32
6
HOH
HOH
332
A
HOH
33
6
HOH
HOH
333
A
HOH
34
6
HOH
HOH
334
A
HOH
35
6
HOH
HOH
335
A
HOH
36
6
HOH
HOH
336
A
HOH
37
6
HOH
HOH
337
A
HOH
38
6
HOH
HOH
338
A
HOH
39
6
HOH
HOH
339
A
HOH
40
6
HOH
HOH
340
A
HOH
41
6
HOH
HOH
341
A
HOH
42
6
HOH
HOH
342
A
HOH
43
6
HOH
HOH
343
A
HOH
44
6
HOH
HOH
344
A
HOH
45
6
HOH
HOH
345
A
HOH
46
6
HOH
HOH
346
A
HOH
47
6
HOH
HOH
347
A
HOH
48
6
HOH
HOH
348
A
HOH
49
6
HOH
HOH
349
A
HOH
50
6
HOH
HOH
350
A
HOH
51
6
HOH
HOH
351
A
HOH
52
6
HOH
HOH
352
A
HOH
53
6
HOH
HOH
353
A
HOH
54
6
HOH
HOH
354
A
HOH
55
6
HOH
HOH
355
A
HOH
56
6
HOH
HOH
356
A
HOH
57
6
HOH
HOH
357
A
HOH
58
6
HOH
HOH
358
A
HOH
59
6
HOH
HOH
359
A
HOH
60
6
HOH
HOH
360
A
HOH
61
6
HOH
HOH
361
A
HOH
62
6
HOH
HOH
362
A
HOH
63
6
HOH
HOH
363
A
HOH
64
6
HOH
HOH
364
A
HOH
65
6
HOH
HOH
365
A
HOH
66
6
HOH
HOH
366
A
HOH
67
6
HOH
HOH
367
A
HOH
68
6
HOH
HOH
368
A
HOH
69
6
HOH
HOH
369
A
HOH
70
6
HOH
HOH
370
A
HOH
71
6
HOH
HOH
371
A
HOH
72
6
HOH
HOH
372
A
HOH
73
6
HOH
HOH
373
A
HOH
74
6
HOH
HOH
374
A
HOH
75
6
HOH
HOH
375
A
HOH
76
6
HOH
HOH
376
A
HOH
77
6
HOH
HOH
377
A
HOH
78
6
HOH
HOH
378
A
HOH
79
6
HOH
HOH
379
A
HOH
80
6
HOH
HOH
380
A
HOH
81
6
HOH
HOH
381
A
HOH
82
6
HOH
HOH
382
A
HOH
83
6
HOH
HOH
383
A
HOH
84
6
HOH
HOH
384
A
HOH
85
6
HOH
HOH
385
A
HOH
86
6
HOH
HOH
386
A
HOH
87
6
HOH
HOH
387
A
ALA
2
n
1
ALA
2
A
LEU
3
n
2
LEU
3
A
LEU
4
n
3
LEU
4
A
GLU
5
n
4
GLU
5
A
ILE
6
n
5
ILE
6
A
ILE
7
n
6
ILE
7
A
HIS
8
n
7
HIS
8
A
TYR
9
n
8
TYR
9
A
PRO
10
n
9
PRO
10
A
SER
11
n
10
SER
11
A
LYS
12
n
11
LYS
12
A
ILE
13
n
12
ILE
13
A
LEU
14
n
13
LEU
14
A
ARG
15
n
14
ARG
15
A
THR
16
n
15
THR
16
A
ILE
17
n
16
ILE
17
A
SER
18
n
17
SER
18
A
LYS
19
n
18
LYS
19
A
GLU
20
n
19
GLU
20
A
VAL
21
n
20
VAL
21
A
VAL
22
n
21
VAL
22
A
SER
23
n
22
SER
23
A
PHE
24
n
23
PHE
24
A
ASP
25
n
24
ASP
25
A
ALA
26
n
25
ALA
26
A
LYS
27
n
26
LYS
27
A
LEU
28
n
27
LEU
28
A
HIS
29
n
28
HIS
29
A
GLN
30
n
29
GLN
30
A
GLN
31
n
30
GLN
31
A
LEU
32
n
31
LEU
32
A
ASP
33
n
32
ASP
33
A
ASP
34
n
33
ASP
34
A
MET
35
n
34
MET
35
A
TYR
36
n
35
TYR
36
A
GLU
37
n
36
GLU
37
A
THR
38
n
37
THR
38
A
MET
39
n
38
MET
39
A
ILE
40
n
39
ILE
40
A
ALA
41
n
40
ALA
41
A
SER
42
n
41
SER
42
A
GLU
43
n
42
GLU
43
A
GLY
44
n
43
GLY
44
A
ILE
45
n
44
ILE
45
A
GLY
46
n
45
GLY
46
A
LEU
47
n
46
LEU
47
A
ALA
48
n
47
ALA
48
A
ALA
49
n
48
ALA
49
A
ILE
50
n
49
ILE
50
A
GLN
51
n
50
GLN
51
A
VAL
52
n
51
VAL
52
A
GLY
53
n
52
GLY
53
A
LEU
54
n
53
LEU
54
A
PRO
55
n
54
PRO
55
A
LEU
56
n
55
LEU
56
A
ARG
57
n
56
ARG
57
A
MET
58
n
57
MET
58
A
LEU
59
n
58
LEU
59
A
ILE
60
n
59
ILE
60
A
ILE
61
n
60
ILE
61
A
ASN
62
n
61
ASN
62
A
LEU
63
n
62
LEU
63
A
PRO
64
n
63
PRO
64
A
GLN
65
n
64
GLN
65
A
GLU
66
n
65
GLU
66
A
ASP
67
n
66
ASP
67
A
GLY
68
n
67
GLY
68
A
VAL
69
n
68
VAL
69
A
GLN
70
n
69
GLN
70
A
HIS
71
n
70
HIS
71
A
LYS
72
n
71
LYS
72
A
GLU
73
n
72
GLU
73
A
ASP
74
n
73
ASP
74
A
CYS
75
n
74
CYS
75
A
LEU
76
n
75
LEU
76
A
GLU
77
n
76
GLU
77
A
ILE
78
n
77
ILE
78
A
ILE
79
n
78
ILE
79
A
ASN
80
n
79
ASN
80
A
PRO
81
n
80
PRO
81
A
LYS
82
n
81
LYS
82
A
PHE
83
n
82
PHE
83
A
ILE
84
n
83
ILE
84
A
GLU
85
n
84
GLU
85
A
THR
86
n
85
THR
86
A
GLY
87
n
86
GLY
87
A
GLY
88
n
87
GLY
88
A
SER
89
n
88
SER
89
A
MET
90
n
89
MET
90
A
MET
91
n
90
MET
91
A
TYR
92
n
91
TYR
92
A
LYS
93
n
92
LYS
93
A
GLU
94
n
93
GLU
94
A
GLY
95
n
94
GLY
95
A
CYS
96
n
95
CYS
96
A
LEU
97
n
96
LEU
97
A
SER
98
n
97
SER
98
A
VAL
99
n
98
VAL
99
A
PRO
100
n
99
PRO
100
A
GLY
101
n
100
GLY
101
A
PHE
102
n
101
PHE
102
A
TYR
103
n
102
TYR
103
A
GLU
104
n
103
GLU
104
A
GLU
105
n
104
GLU
105
A
VAL
106
n
105
VAL
106
A
GLU
107
n
106
GLU
107
A
ARG
108
n
107
ARG
108
A
PHE
109
n
108
PHE
109
A
GLU
110
n
109
GLU
110
A
LYS
111
n
110
LYS
111
A
VAL
112
n
111
VAL
112
A
LYS
113
n
112
LYS
113
A
ILE
114
n
113
ILE
114
A
GLU
115
n
114
GLU
115
A
TYR
116
n
115
TYR
116
A
GLN
117
n
116
GLN
117
A
ASN
118
n
117
ASN
118
A
ARG
119
n
118
ARG
119
A
PHE
120
n
119
PHE
120
A
ALA
121
n
120
ALA
121
A
GLU
122
n
121
GLU
122
A
VAL
123
n
122
VAL
123
A
LYS
124
n
123
LYS
124
A
VAL
125
n
124
VAL
125
A
LEU
126
n
125
LEU
126
A
GLU
127
n
126
GLU
127
A
ALA
128
n
127
ALA
128
A
SER
129
n
128
SER
129
A
GLU
130
n
129
GLU
130
A
LEU
131
n
130
LEU
131
A
LEU
132
n
131
LEU
132
A
ALA
133
n
132
ALA
133
A
VAL
134
n
133
VAL
134
A
ALA
135
n
134
ALA
135
A
ILE
136
n
135
ILE
136
A
GLN
137
n
136
GLN
137
A
HIS
138
n
137
HIS
138
A
GLU
139
n
138
GLU
139
A
ILE
140
n
139
ILE
140
A
ASP
141
n
140
ASP
141
A
HIS
142
n
141
HIS
142
A
LEU
143
n
142
LEU
143
A
ASN
144
n
143
ASN
144
A
GLY
145
n
144
GLY
145
A
VAL
146
n
145
VAL
146
A
LEU
147
n
146
LEU
147
A
PHE
148
n
147
PHE
148
A
VAL
149
n
148
VAL
149
A
ASP
150
n
149
ASP
150
A
LYS
151
n
150
LYS
151
A
LEU
152
n
151
LEU
152
A
SER
153
n
152
SER
153
A
ILE
154
n
153
ILE
154
A
LEU
155
n
154
LEU
155
A
LYS
156
n
155
LYS
156
A
ARG
157
n
156
ARG
157
A
LYS
158
n
157
LYS
158
A
LYS
159
n
158
LYS
159
A
PHE
160
n
159
PHE
160
A
GLU
161
n
160
GLU
161
A
LYS
162
n
161
LYS
162
A
GLU
163
n
162
GLU
163
A
LEU
164
n
163
LEU
164
A
n
164
165
A
n
165
166
A
n
166
167
A
n
167
168
A
n
168
169
A
n
169
170
A
n
170
171
A
n
171
172
A
n
172
173
A
n
173
174
A
n
174
175
A
n
175
176
A
n
176
177
A
n
177
178
A
n
178
179
A
n
179
180
A
n
180
181
A
n
181
182
A
author_and_software_defined_assembly
PISA
1
monomeric
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
201
B
CO
CO
1_555
A
HIS
142
A
NE2
HIS
141
1_555
107.1
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
201
B
CO
CO
1_555
A
HOH
332
G
O
HOH
1_555
107.8
A
HIS
142
A
NE2
HIS
141
1_555
A
CO
201
B
CO
CO
1_555
A
HOH
332
G
O
HOH
1_555
94.5
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
47
A
N
LEU
46
A
O
ILE
60
A
O
ILE
59
A
N
ILE
61
A
N
ILE
60
A
O
LEU
76
A
O
LEU
75
A
N
ILE
84
A
N
ILE
83
A
O
LYS
113
A
O
LYS
112
A
N
TYR
116
A
N
TYR
115
A
O
LYS
124
A
O
LYS
123
A
N
MET
90
A
N
MET
89
A
O
ARG
108
A
O
ARG
107
1
A
LYS
165
A
LYS
164
1
Y
1
A
GLU
166
A
GLU
165
1
Y
1
A
LEU
167
A
LEU
166
1
Y
1
A
GLN
168
A
GLN
167
1
Y
1
A
LYS
169
A
LYS
168
1
Y
1
A
LYS
170
A
LYS
169
1
Y
1
A
GLN
171
A
GLN
170
1
Y
1
A
LYS
172
A
LYS
171
1
Y
1
A
HIS
173
A
HIS
172
1
Y
1
A
LYS
174
A
LYS
173
1
Y
1
A
LEU
175
A
LEU
174
1
Y
1
A
GLU
176
A
GLU
175
1
Y
1
A
HIS
177
A
HIS
176
1
Y
1
A
HIS
178
A
HIS
177
1
Y
1
A
HIS
179
A
HIS
178
1
Y
1
A
HIS
180
A
HIS
179
1
Y
1
A
HIS
181
A
HIS
180
1
Y
1
A
HIS
182
A
HIS
181
1
Y
1
A
A
O
O
HOH
HOH
364
365
1.90
1
A
A
O
O
PRO
HOH
64
344
1.92
1
A
A
O
O
HOH
HOH
377
384
1.98
1
A
A
O
O
HOH
HOH
362
381
2.01
1
A
A
O
O
HOH
HOH
362
378
2.02
1
A
A
NZ
O
LYS
HOH
82
386
2.06
1
A
A
O
O
HOH
HOH
366
369
2.06
1
A
A
OE2
O
GLU
HOH
85
360
2.08
1
A
A
O
O
HOH
HOH
313
382
2.09
1
A
A
OE2
O
GLU
HOH
104
376
2.17
1
A
GLN
65
-82.59
-154.46
1
A
GLU
130
56.48
-138.98
-0.4800
0.0000
-0.0000
0.3879
-0.0000
0.0921
0.2302
0.2076
0.2088
1.662
34.48
1229
24141
5.09
98.84
0.16
1
1.35
MOLECULAR REPLACEMENT
19.82
1.11
1.30
2EW7
ML
FLAT BULK SOLVENT MODEL
52.855
0.377
1.662
34.48
87
1440
45
0
1308
0.007
1372
1.098
1841
18.000
536
0.073
205
0.004
229
0.2680
0.2692
1.7282
112
2458
9
97.00
0.2502
0.2297
1.8068
141
2539
9
100.00
0.2115
0.1931
1.9021
150
2515
9
100.00
0.1882
0.1827
2.0212
142
2536
9
100.00
0.2162
0.1771
2.1773
146
2533
9
100.00
0.2070
0.1930
2.3963
118
2576
9
100.00
0.2266
0.1957
2.7429
143
2577
9
100.00
0.2113
0.1991
3.4553
124
2598
9
99.00
0.2546
0.2280
34.4913
153
2580
9
95.00
1.66
34.484
4E9A
24141
1
data collection
HKL-2000
refinement
PHENIX
(phenix.refine: 1.7.3_928)
data reduction
HKL-2000
data scaling
HKL-2000
Structure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
6
N
N
A
SER
11
A
SER
10
HELX_P
A
THR
16
A
THR
15
5
1
6
A
ASP
25
A
ASP
24
HELX_P
A
SER
42
A
SER
41
1
2
18
A
ILE
50
A
ILE
49
HELX_P
A
GLY
53
A
GLY
52
5
3
4
A
HIS
71
A
HIS
70
HELX_P
A
CYS
75
A
CYS
74
5
4
5
A
GLU
130
A
GLU
129
HELX_P
A
ASN
144
A
ASN
143
1
5
15
A
LEU
147
A
LEU
146
HELX_P
A
LEU
152
A
LEU
151
5
6
6
A
SER
153
A
SER
152
HELX_P
A
LEU
164
A
LEU
163
1
7
12
metalc
2.132
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
201
B
CO
CO
1_555
metalc
2.134
A
HIS
142
A
NE2
HIS
141
1_555
A
CO
201
B
CO
CO
1_555
metalc
2.204
A
CO
201
B
CO
CO
1_555
A
HOH
332
G
O
HOH
1_555
HYDROLASE
Hydrolase
A
TYR
9
A
TYR
8
1
A
PRO
10
A
PRO
9
8.01
Q672W7_HELPX
UNP
1
2
Q672W7
ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINP
KFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFE
KELKELQKKQKHK
2
174
4E9A
2
174
Q672W7
A
1
1
173
1
expression tag
LEU
175
4E9A
A
Q672W7
UNP
174
1
expression tag
GLU
176
4E9A
A
Q672W7
UNP
175
1
expression tag
HIS
177
4E9A
A
Q672W7
UNP
176
1
expression tag
HIS
178
4E9A
A
Q672W7
UNP
177
1
expression tag
HIS
179
4E9A
A
Q672W7
UNP
178
1
expression tag
HIS
180
4E9A
A
Q672W7
UNP
179
1
expression tag
HIS
181
4E9A
A
Q672W7
UNP
180
1
expression tag
HIS
182
4E9A
A
Q672W7
UNP
181
5
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
46
A
GLY
45
A
ALA
48
A
ALA
47
A
MET
58
A
MET
57
A
ILE
61
A
ILE
60
A
LEU
76
A
LEU
75
A
GLY
87
A
GLY
86
A
LYS
111
A
LYS
110
A
GLN
117
A
GLN
116
A
VAL
123
A
VAL
122
A
SER
129
A
SER
128
A
MET
90
A
MET
89
A
GLU
94
A
GLU
93
A
GLU
104
A
GLU
103
A
ARG
108
A
ARG
107
BINDING SITE FOR RESIDUE CO A 201
A
CO
201
Software
4
BINDING SITE FOR RESIDUE QAP A 202
A
QAP
202
Software
15
BINDING SITE FOR RESIDUE EPE A 203
A
EPE
203
Software
5
BINDING SITE FOR RESIDUE DMS A 204
A
DMS
204
Software
3
BINDING SITE FOR RESIDUE DMS A 205
A
DMS
205
Software
4
A
CYS
96
A
CYS
95
4
1_555
A
HIS
138
A
HIS
137
4
1_555
A
HIS
142
A
HIS
141
4
1_555
A
HOH
332
G
HOH
4
1_555
A
SER
42
A
SER
41
15
1_555
A
GLY
44
A
GLY
43
15
1_555
A
ILE
45
A
ILE
44
15
1_555
A
GLY
46
A
GLY
45
15
1_555
A
GLU
94
A
GLU
93
15
1_555
A
GLY
95
A
GLY
94
15
1_555
A
CYS
96
A
CYS
95
15
1_555
A
LEU
97
A
LEU
96
15
1_555
A
PRO
100
A
PRO
99
15
1_555
A
GLY
101
A
GLY
100
15
1_555
A
TYR
103
A
TYR
102
15
1_555
A
LEU
131
A
LEU
130
15
1_555
A
HIS
138
A
HIS
137
15
1_555
A
GLU
139
A
GLU
138
15
1_555
A
HOH
307
G
HOH
15
1_555
A
ILE
17
A
ILE
16
5
1_555
A
GLU
20
A
GLU
19
5
1_555
A
ARG
57
A
ARG
56
5
1_555
A
ASN
144
A
ASN
143
5
1_555
A
HOH
358
G
HOH
5
1_555
A
ASN
62
A
ASN
61
3
1_555
A
LEU
63
A
LEU
62
3
1_555
A
ASP
74
A
ASP
73
3
1_555
A
SER
23
A
SER
22
4
1_555
A
ASP
25
A
ASP
24
4
1_555
A
LYS
27
A
LYS
26
4
1_555
A
GLN
31
A
GLN
30
4
1_555
19
P 21 21 21