0.023743
0.000000
0.000000
0.000000
0.018879
0.000000
0.000000
0.000000
0.010839
0.00000
0.00000
0.00000
Cai, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
42.117
52.970
92.259
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
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
C21 H21 N O5
367.395
4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE
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
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
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
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
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
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
N
N
129
N
C
N
130
N
C
N
131
N
O
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
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
N
148
N
O
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
H
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
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
H
N
184
N
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
O
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
H
N
206
N
N
N
207
S
C
N
208
N
C
N
209
N
O
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
N
N
215
N
O
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
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
S
N
238
N
C
N
239
N
O
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
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
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
C
N
281
N
O
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
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
O
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
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
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
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
N
333
N
O
N
334
N
O
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
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
C
N
352
N
C
N
353
N
O
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
N
369
N
C
N
370
N
C
N
371
N
N
N
372
N
C
N
373
N
O
N
374
N
C
N
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
N
379
N
O
N
380
N
C
N
381
N
O
N
382
N
C
Y
383
N
C
N
384
N
O
N
385
N
C
N
386
N
O
N
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
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
H
N
412
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
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
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
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
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
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
doub
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
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
Y
348
N
doub
Y
349
N
sing
N
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
N
355
N
sing
Y
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
doub
N
366
N
sing
N
367
E
doub
N
368
N
sing
N
369
N
sing
N
370
N
sing
Y
371
N
sing
Y
372
N
doub
Y
373
N
doub
N
374
N
sing
N
375
N
sing
Y
376
N
sing
N
377
N
sing
N
378
N
doub
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
Y
384
N
doub
N
385
N
sing
N
386
N
doub
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
Y
391
N
sing
N
392
N
sing
N
393
N
sing
Y
394
N
doub
N
395
N
sing
N
396
N
sing
US
Protein Sci.
PRCIEI
0795
0961-8368
15
2071
2081
10.1110/ps.062238406
16882991
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation
2006
10.2210/pdb2ew5/pdb
pdb_00002ew5
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
OSMIC MIRRORS
IMAGE PLATE
2004-06-25
RIGAKU RAXIS IV
OSCILLATION
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
21008.465
peptide deformylase
3.5.1.88
1
man
polymer
58.933
COBALT (II) ION
1
syn
non-polymer
367.395
4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE
1
syn
non-polymer
18.015
water
125
nat
water
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
Helicobacter
Escherichia
Escherichia coli
sample
210
Helicobacter pylori
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
PET22B(+)
1
2.45
49.77
VAPOR DIFFUSION, HANGING DROP
7.8
60-70% MPD in 0.1M pH7.8 Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2006-10-24
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2023-10-25
_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_asym_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_asym_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_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
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Helicobacter Pylori peptide deformylase in complex with inhibitor
Helicobacter Pylori peptide deformylase
RCSB
Y
PDBJ
2005-11-02
REL
REL
CO
COBALT (II) ION
Y12
4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE
HOH
water
1IX1
PDB
experimental model
CO
300
2
CO
CO
300
A
Y12
200
3
Y12
Y12
200
A
HOH
1
4
HOH
HOH
301
A
HOH
2
4
HOH
HOH
302
A
HOH
3
4
HOH
HOH
303
A
HOH
4
4
HOH
HOH
304
A
HOH
5
4
HOH
HOH
305
A
HOH
6
4
HOH
HOH
306
A
HOH
7
4
HOH
HOH
307
A
HOH
8
4
HOH
HOH
308
A
HOH
9
4
HOH
HOH
309
A
HOH
10
4
HOH
HOH
310
A
HOH
11
4
HOH
HOH
311
A
HOH
12
4
HOH
HOH
312
A
HOH
13
4
HOH
HOH
313
A
HOH
14
4
HOH
HOH
314
A
HOH
15
4
HOH
HOH
315
A
HOH
16
4
HOH
HOH
316
A
HOH
17
4
HOH
HOH
317
A
HOH
18
4
HOH
HOH
318
A
HOH
19
4
HOH
HOH
319
A
HOH
20
4
HOH
HOH
320
A
HOH
21
4
HOH
HOH
321
A
HOH
22
4
HOH
HOH
322
A
HOH
23
4
HOH
HOH
323
A
HOH
24
4
HOH
HOH
324
A
HOH
25
4
HOH
HOH
325
A
HOH
26
4
HOH
HOH
326
A
HOH
27
4
HOH
HOH
327
A
HOH
28
4
HOH
HOH
328
A
HOH
29
4
HOH
HOH
329
A
HOH
30
4
HOH
HOH
330
A
HOH
31
4
HOH
HOH
331
A
HOH
32
4
HOH
HOH
332
A
HOH
33
4
HOH
HOH
333
A
HOH
34
4
HOH
HOH
334
A
HOH
35
4
HOH
HOH
335
A
HOH
36
4
HOH
HOH
336
A
HOH
37
4
HOH
HOH
337
A
HOH
38
4
HOH
HOH
338
A
HOH
39
4
HOH
HOH
339
A
HOH
40
4
HOH
HOH
340
A
HOH
41
4
HOH
HOH
341
A
HOH
42
4
HOH
HOH
342
A
HOH
43
4
HOH
HOH
343
A
HOH
44
4
HOH
HOH
344
A
HOH
45
4
HOH
HOH
345
A
HOH
46
4
HOH
HOH
346
A
HOH
47
4
HOH
HOH
347
A
HOH
48
4
HOH
HOH
348
A
HOH
49
4
HOH
HOH
349
A
HOH
50
4
HOH
HOH
350
A
HOH
51
4
HOH
HOH
351
A
HOH
52
4
HOH
HOH
352
A
HOH
53
4
HOH
HOH
353
A
HOH
54
4
HOH
HOH
354
A
HOH
55
4
HOH
HOH
355
A
HOH
56
4
HOH
HOH
356
A
HOH
57
4
HOH
HOH
357
A
HOH
58
4
HOH
HOH
358
A
HOH
59
4
HOH
HOH
359
A
HOH
60
4
HOH
HOH
360
A
HOH
61
4
HOH
HOH
361
A
HOH
62
4
HOH
HOH
362
A
HOH
63
4
HOH
HOH
363
A
HOH
64
4
HOH
HOH
364
A
HOH
65
4
HOH
HOH
365
A
HOH
66
4
HOH
HOH
366
A
HOH
67
4
HOH
HOH
367
A
HOH
68
4
HOH
HOH
368
A
HOH
69
4
HOH
HOH
369
A
HOH
70
4
HOH
HOH
370
A
HOH
71
4
HOH
HOH
371
A
HOH
72
4
HOH
HOH
372
A
HOH
73
4
HOH
HOH
373
A
HOH
74
4
HOH
HOH
374
A
HOH
75
4
HOH
HOH
375
A
HOH
76
4
HOH
HOH
376
A
HOH
77
4
HOH
HOH
377
A
HOH
78
4
HOH
HOH
378
A
HOH
79
4
HOH
HOH
379
A
HOH
80
4
HOH
HOH
380
A
HOH
81
4
HOH
HOH
381
A
HOH
82
4
HOH
HOH
382
A
HOH
83
4
HOH
HOH
383
A
HOH
84
4
HOH
HOH
384
A
HOH
85
4
HOH
HOH
385
A
HOH
86
4
HOH
HOH
386
A
HOH
87
4
HOH
HOH
387
A
HOH
88
4
HOH
HOH
388
A
HOH
89
4
HOH
HOH
389
A
HOH
90
4
HOH
HOH
390
A
HOH
91
4
HOH
HOH
391
A
HOH
92
4
HOH
HOH
392
A
HOH
93
4
HOH
HOH
393
A
HOH
94
4
HOH
HOH
394
A
HOH
95
4
HOH
HOH
395
A
HOH
96
4
HOH
HOH
396
A
HOH
97
4
HOH
HOH
397
A
HOH
98
4
HOH
HOH
398
A
HOH
99
4
HOH
HOH
399
A
HOH
100
4
HOH
HOH
400
A
HOH
101
4
HOH
HOH
401
A
HOH
102
4
HOH
HOH
402
A
HOH
103
4
HOH
HOH
403
A
HOH
104
4
HOH
HOH
404
A
HOH
105
4
HOH
HOH
405
A
HOH
106
4
HOH
HOH
406
A
HOH
107
4
HOH
HOH
407
A
HOH
108
4
HOH
HOH
408
A
HOH
109
4
HOH
HOH
409
A
HOH
110
4
HOH
HOH
410
A
HOH
111
4
HOH
HOH
411
A
HOH
112
4
HOH
HOH
412
A
HOH
113
4
HOH
HOH
413
A
HOH
114
4
HOH
HOH
414
A
HOH
115
4
HOH
HOH
415
A
HOH
116
4
HOH
HOH
416
A
HOH
117
4
HOH
HOH
417
A
HOH
118
4
HOH
HOH
418
A
HOH
119
4
HOH
HOH
419
A
HOH
120
4
HOH
HOH
420
A
HOH
121
4
HOH
HOH
421
A
HOH
122
4
HOH
HOH
422
A
HOH
123
4
HOH
HOH
423
A
HOH
124
4
HOH
HOH
424
A
HOH
125
4
HOH
HOH
425
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
LYS
165
n
164
LYS
165
A
GLU
166
n
165
GLU
166
A
LEU
167
n
166
LEU
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_defined_assembly
1
monomeric
A
CYS
96
A
SG
CYS
95
1_555
A
CO
300
B
CO
CO
1_555
A
HIS
138
A
NE2
HIS
137
1_555
106.8
A
CYS
96
A
SG
CYS
95
1_555
A
CO
300
B
CO
CO
1_555
A
HIS
142
A
NE2
HIS
141
1_555
96.8
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
300
B
CO
CO
1_555
A
HIS
142
A
NE2
HIS
141
1_555
108.0
A
CYS
96
A
SG
CYS
95
1_555
A
CO
300
B
CO
CO
1_555
A
HOH
424
D
O
HOH
1_555
126.0
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
300
B
CO
CO
1_555
A
HOH
424
D
O
HOH
1_555
114.4
A
HIS
142
A
NE2
HIS
141
1_555
A
CO
300
B
CO
CO
1_555
A
HOH
424
D
O
HOH
1_555
101.9
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
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
LYS
72
-46.61
-13.79
1
A
VAL
99
-141.90
57.34
1
A
TYR
116
-160.69
-168.52
1
A
GLU
130
54.34
-138.79
protein_rep.param
protein.top
water_rep.param
lig.top
ion.param
ion.top
lig.param
water.top
21.2
-2.89
0.00
0.00
1.63
0.00
1.25
0.254
0.011
0.201
0.213
0.201
2.2
12.0
537
10633
10633
5.1
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
1IX1
Engh & Huber
0.30
0.23
5.00
0.21
0.15
2.2
12.0
125
1487
28
0
1334
0.007
1.2
22.3
0.73
1.31
1.50
2.07
2.00
2.13
2.00
3.19
2.50
0.256
0.029
0.214
2.34
78
1649
6
4.5
97.1
14.2
2.2
12.0
2EW5
10663
10663
1.0
1.0
0.075
1
8.1
3.3
97.7
0.19
2.20
2.28
3.3
1019
3.2
96.6
data reduction
TRUNCATE
refinement
CNS
data scaling
CCP4
(TRUNCATE)
phasing
CNS
Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor
1
N
N
2
N
N
3
N
N
4
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
167
A
LEU
166
1
7
15
metalc
2.396
A
CYS
96
A
SG
CYS
95
1_555
A
CO
300
B
CO
CO
1_555
metalc
2.217
A
HIS
138
A
NE2
HIS
137
1_555
A
CO
300
B
CO
CO
1_555
metalc
2.157
A
HIS
142
A
NE2
HIS
141
1_555
A
CO
300
B
CO
CO
1_555
metalc
2.018
A
CO
300
B
CO
CO
1_555
A
HOH
424
D
O
HOH
1_555
HYDROLASE
Cobalt Helicobacter pylori peptide deformylase, inhibitor, HYDROLASE
A
TYR
9
A
TYR
8
1
A
PRO
10
A
PRO
9
0.38
Q672W7_HELPY
UNP
1
2
Q672W7
2
174
2EW5
2
174
Q672W7
A
1
1
173
1
expression tag
LEU
175
2EW5
A
Q672W7
UNP
174
1
expression tag
GLU
176
2EW5
A
Q672W7
UNP
175
1
expression tag
HIS
177
2EW5
A
Q672W7
UNP
176
1
expression tag
HIS
178
2EW5
A
Q672W7
UNP
177
1
expression tag
HIS
179
2EW5
A
Q672W7
UNP
178
1
expression tag
HIS
180
2EW5
A
Q672W7
UNP
179
1
expression tag
HIS
181
2EW5
A
Q672W7
UNP
180
1
expression tag
HIS
182
2EW5
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 300
A
CO
300
Software
5
BINDING SITE FOR RESIDUE Y12 A 200
A
Y12
200
Software
15
A
GLN
51
A
GLN
50
5
1_555
A
CYS
96
A
CYS
95
5
1_555
A
HIS
138
A
HIS
137
5
1_555
A
HIS
142
A
HIS
141
5
1_555
A
HOH
424
D
HOH
5
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
TYR
92
A
TYR
91
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
19
P 21 21 21