0.019911
0.011496
0.000000
0.000000
0.022992
0.000000
0.000000
0.000000
0.007234
0.00000
0.00000
0.00000
Nicola, G.
Nicholas, R.A.
Davies, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
3
90.00
90.00
120.00
50.22
50.22
138.25
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
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
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
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
C
N
75
N
C
N
76
N
O
N
77
N
S
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
N
N
85
R
C
N
86
N
C
N
87
N
O
N
88
N
C
N
89
N
S
N
90
N
O
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
N
N
99
S
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
O
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
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
O
N
127
N
O
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
N
C
N
139
N
C
N
140
N
O
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
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
N
C
Y
152
N
C
Y
153
N
N
Y
154
N
C
Y
155
N
C
Y
156
N
N
N
157
N
O
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
H
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
S
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
O
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
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
N
N
194
S
C
N
195
N
C
N
196
N
O
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
O
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
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
C
N
223
N
N
N
224
N
O
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
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
N
N
241
S
C
N
242
N
C
N
243
N
O
N
244
N
C
N
245
N
C
N
246
N
S
N
247
N
C
N
248
N
O
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
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
Y
270
N
C
N
271
N
O
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
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
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
N
N
301
S
C
N
302
N
C
N
303
N
O
N
304
N
C
N
305
N
O
N
306
N
O
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
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
R
C
N
319
N
O
N
320
N
C
N
321
N
O
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
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
N
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
N
345
N
O
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
N
369
N
O
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
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
O
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
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
doub
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
doub
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
doub
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
doub
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
doub
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
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
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
Y
149
N
sing
Y
150
N
doub
Y
151
N
doub
N
152
N
sing
Y
153
N
sing
N
154
N
sing
Y
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
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
sing
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
sing
N
187
N
sing
N
188
N
doub
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
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
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
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
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
Y
257
N
doub
Y
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
261
N
doub
N
262
N
sing
Y
263
N
doub
N
264
N
sing
Y
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
doub
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
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
Y
326
N
doub
Y
327
N
sing
Y
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
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
N
348
N
sing
N
349
N
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
Y
354
N
doub
Y
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
358
N
doub
N
359
N
sing
Y
360
N
doub
N
361
N
sing
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
doub
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
UK
Biochem.J.
BIJOAK
0043
0264-6021
392
55
63
10.1042/BJ20050449
16038617
A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli.
2005
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
276
616
623
10.1074/jbc.M004471200
CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF
PENICILLIN-BINDING PROTEIN 5 AT 2.3 A RESOLUTION
2001
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
253
2584
2588
Effects of sulfhydryl reagents on the binding and release of penicillin G by D-alanine carboxypeptidase 1A of Escherichia coli
1978
10.2210/pdb1nzu/pdb
pdb_00001nzu
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
mirrors
IMAGE PLATE
2001-07-30
RIGAKU RAXIS IV
Osmic mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
39841.117
Penicillin-binding protein 5
3.4.16.4
1
man
polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
174
nat
water
D-alanyl-D-alanine carboxypeptidase fraction A, DD-peptidase, DD-carboxypeptidase, PBP-5
no
no
DDLNIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGN
PVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYS
SARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVM
GGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELH
APLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEGNFGDPVID
DDLNIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGN
PVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYS
SARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVM
GGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELH
APLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEGNFGDPVID
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
Escherichia
sample
DACA
562
Escherichia coli
562
Escherichia coli
MC1061
plasmid
PBR322
1
2.53
51.30
VAPOR DIFFUSION, HANGING DROP
5.5
24% PEG 4000, 100 mM magnesium acetate, 100 mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
294
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_remark
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2004-03-02
1
1
2008-04-29
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_remark.text
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal Structure Of A Deacylation-Defective Mutant Of Penicillin-Binding Protein 5 At 2.3 A Resolution
Crystal Structure Of A Deacylation-Defective Mutant Of Penicillin-Binding Protein 5 At 1.9 A Resolution
The crystal structure of wild type penicillin-binding protein 5 from E. coli
SEQUENCE
THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5
TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY
DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX AMINO
ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO
READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE
RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST
29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING
FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING
MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT
PRESENT IN THIS CONSTRUCT.
RCSB
Y
RCSB
2003-02-19
REL
REL
BME
BETA-MERCAPTOETHANOL
HOH
water
1HD8
PDB ENTRY 1HD8
PDB
experimental model
BME
400
2
BME
BME
400
A
HOH
1
3
HOH
HOH
401
A
HOH
2
3
HOH
HOH
402
A
HOH
3
3
HOH
HOH
403
A
HOH
4
3
HOH
HOH
404
A
HOH
5
3
HOH
HOH
405
A
HOH
6
3
HOH
HOH
406
A
HOH
7
3
HOH
HOH
407
A
HOH
8
3
HOH
HOH
408
A
HOH
9
3
HOH
HOH
409
A
HOH
10
3
HOH
HOH
410
A
HOH
11
3
HOH
HOH
411
A
HOH
12
3
HOH
HOH
412
A
HOH
13
3
HOH
HOH
413
A
HOH
14
3
HOH
HOH
414
A
HOH
15
3
HOH
HOH
415
A
HOH
16
3
HOH
HOH
416
A
HOH
17
3
HOH
HOH
417
A
HOH
18
3
HOH
HOH
418
A
HOH
19
3
HOH
HOH
419
A
HOH
20
3
HOH
HOH
420
A
HOH
21
3
HOH
HOH
421
A
HOH
22
3
HOH
HOH
422
A
HOH
23
3
HOH
HOH
423
A
HOH
24
3
HOH
HOH
424
A
HOH
25
3
HOH
HOH
425
A
HOH
26
3
HOH
HOH
426
A
HOH
27
3
HOH
HOH
427
A
HOH
28
3
HOH
HOH
428
A
HOH
29
3
HOH
HOH
429
A
HOH
30
3
HOH
HOH
430
A
HOH
31
3
HOH
HOH
431
A
HOH
32
3
HOH
HOH
432
A
HOH
33
3
HOH
HOH
433
A
HOH
34
3
HOH
HOH
434
A
HOH
35
3
HOH
HOH
435
A
HOH
36
3
HOH
HOH
436
A
HOH
37
3
HOH
HOH
437
A
HOH
38
3
HOH
HOH
438
A
HOH
39
3
HOH
HOH
439
A
HOH
40
3
HOH
HOH
440
A
HOH
41
3
HOH
HOH
441
A
HOH
42
3
HOH
HOH
442
A
HOH
43
3
HOH
HOH
443
A
HOH
44
3
HOH
HOH
444
A
HOH
45
3
HOH
HOH
445
A
HOH
46
3
HOH
HOH
446
A
HOH
47
3
HOH
HOH
447
A
HOH
48
3
HOH
HOH
448
A
HOH
49
3
HOH
HOH
449
A
HOH
50
3
HOH
HOH
450
A
HOH
51
3
HOH
HOH
451
A
HOH
52
3
HOH
HOH
452
A
HOH
53
3
HOH
HOH
453
A
HOH
54
3
HOH
HOH
454
A
HOH
55
3
HOH
HOH
455
A
HOH
56
3
HOH
HOH
456
A
HOH
57
3
HOH
HOH
457
A
HOH
58
3
HOH
HOH
458
A
HOH
59
3
HOH
HOH
459
A
HOH
60
3
HOH
HOH
460
A
HOH
61
3
HOH
HOH
461
A
HOH
62
3
HOH
HOH
462
A
HOH
63
3
HOH
HOH
463
A
HOH
64
3
HOH
HOH
464
A
HOH
65
3
HOH
HOH
465
A
HOH
66
3
HOH
HOH
466
A
HOH
67
3
HOH
HOH
467
A
HOH
68
3
HOH
HOH
468
A
HOH
69
3
HOH
HOH
469
A
HOH
70
3
HOH
HOH
470
A
HOH
71
3
HOH
HOH
471
A
HOH
72
3
HOH
HOH
472
A
HOH
73
3
HOH
HOH
473
A
HOH
74
3
HOH
HOH
474
A
HOH
75
3
HOH
HOH
475
A
HOH
76
3
HOH
HOH
476
A
HOH
77
3
HOH
HOH
477
A
HOH
78
3
HOH
HOH
478
A
HOH
79
3
HOH
HOH
479
A
HOH
80
3
HOH
HOH
480
A
HOH
81
3
HOH
HOH
481
A
HOH
82
3
HOH
HOH
482
A
HOH
83
3
HOH
HOH
483
A
HOH
84
3
HOH
HOH
484
A
HOH
85
3
HOH
HOH
485
A
HOH
86
3
HOH
HOH
486
A
HOH
87
3
HOH
HOH
487
A
HOH
88
3
HOH
HOH
488
A
HOH
89
3
HOH
HOH
489
A
HOH
90
3
HOH
HOH
490
A
HOH
91
3
HOH
HOH
491
A
HOH
92
3
HOH
HOH
492
A
HOH
93
3
HOH
HOH
493
A
HOH
94
3
HOH
HOH
494
A
HOH
95
3
HOH
HOH
495
A
HOH
96
3
HOH
HOH
496
A
HOH
97
3
HOH
HOH
497
A
HOH
98
3
HOH
HOH
498
A
HOH
99
3
HOH
HOH
499
A
HOH
100
3
HOH
HOH
500
A
HOH
101
3
HOH
HOH
501
A
HOH
102
3
HOH
HOH
502
A
HOH
103
3
HOH
HOH
503
A
HOH
104
3
HOH
HOH
504
A
HOH
105
3
HOH
HOH
505
A
HOH
106
3
HOH
HOH
506
A
HOH
107
3
HOH
HOH
507
A
HOH
108
3
HOH
HOH
508
A
HOH
109
3
HOH
HOH
509
A
HOH
110
3
HOH
HOH
510
A
HOH
111
3
HOH
HOH
511
A
HOH
112
3
HOH
HOH
512
A
HOH
113
3
HOH
HOH
513
A
HOH
114
3
HOH
HOH
514
A
HOH
115
3
HOH
HOH
515
A
HOH
116
3
HOH
HOH
516
A
HOH
117
3
HOH
HOH
517
A
HOH
118
3
HOH
HOH
518
A
HOH
119
3
HOH
HOH
519
A
HOH
120
3
HOH
HOH
520
A
HOH
121
3
HOH
HOH
521
A
HOH
122
3
HOH
HOH
522
A
HOH
123
3
HOH
HOH
523
A
HOH
124
3
HOH
HOH
524
A
HOH
125
3
HOH
HOH
525
A
HOH
126
3
HOH
HOH
526
A
HOH
127
3
HOH
HOH
527
A
HOH
128
3
HOH
HOH
528
A
HOH
129
3
HOH
HOH
529
A
HOH
130
3
HOH
HOH
530
A
HOH
131
3
HOH
HOH
531
A
HOH
132
3
HOH
HOH
532
A
HOH
133
3
HOH
HOH
533
A
HOH
134
3
HOH
HOH
534
A
HOH
135
3
HOH
HOH
535
A
HOH
136
3
HOH
HOH
536
A
HOH
137
3
HOH
HOH
537
A
HOH
138
3
HOH
HOH
538
A
HOH
139
3
HOH
HOH
539
A
HOH
140
3
HOH
HOH
540
A
HOH
141
3
HOH
HOH
541
A
HOH
142
3
HOH
HOH
542
A
HOH
143
3
HOH
HOH
543
A
HOH
144
3
HOH
HOH
544
A
HOH
145
3
HOH
HOH
545
A
HOH
146
3
HOH
HOH
546
A
HOH
147
3
HOH
HOH
547
A
HOH
148
3
HOH
HOH
548
A
HOH
149
3
HOH
HOH
549
A
HOH
150
3
HOH
HOH
550
A
HOH
151
3
HOH
HOH
551
A
HOH
152
3
HOH
HOH
552
A
HOH
153
3
HOH
HOH
553
A
HOH
154
3
HOH
HOH
554
A
HOH
155
3
HOH
HOH
555
A
HOH
156
3
HOH
HOH
556
A
HOH
157
3
HOH
HOH
557
A
HOH
158
3
HOH
HOH
558
A
HOH
159
3
HOH
HOH
559
A
HOH
160
3
HOH
HOH
560
A
HOH
161
3
HOH
HOH
561
A
HOH
162
3
HOH
HOH
562
A
HOH
163
3
HOH
HOH
563
A
HOH
164
3
HOH
HOH
564
A
HOH
165
3
HOH
HOH
565
A
HOH
166
3
HOH
HOH
566
A
HOH
167
3
HOH
HOH
567
A
HOH
168
3
HOH
HOH
568
A
HOH
169
3
HOH
HOH
569
A
HOH
170
3
HOH
HOH
570
A
HOH
171
3
HOH
HOH
571
A
HOH
172
3
HOH
HOH
572
A
HOH
173
3
HOH
HOH
573
A
HOH
174
3
HOH
HOH
574
A
n
1
1
A
n
2
2
A
LEU
3
n
3
LEU
3
A
ASN
4
n
4
ASN
4
A
ILE
5
n
5
ILE
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
MET
8
n
8
MET
8
A
ILE
9
n
9
ILE
9
A
PRO
10
n
10
PRO
10
A
GLY
11
n
11
GLY
11
A
VAL
12
n
12
VAL
12
A
PRO
13
n
13
PRO
13
A
GLN
14
n
14
GLN
14
A
ILE
15
n
15
ILE
15
A
ASP
16
n
16
ASP
16
A
ALA
17
n
17
ALA
17
A
GLU
18
n
18
GLU
18
A
SER
19
n
19
SER
19
A
TYR
20
n
20
TYR
20
A
ILE
21
n
21
ILE
21
A
LEU
22
n
22
LEU
22
A
ILE
23
n
23
ILE
23
A
ASP
24
n
24
ASP
24
A
TYR
25
n
25
TYR
25
A
ASN
26
n
26
ASN
26
A
SER
27
n
27
SER
27
A
GLY
28
n
28
GLY
28
A
LYS
29
n
29
LYS
29
A
VAL
30
n
30
VAL
30
A
LEU
31
n
31
LEU
31
A
ALA
32
n
32
ALA
32
A
GLU
33
n
33
GLU
33
A
GLN
34
n
34
GLN
34
A
ASN
35
n
35
ASN
35
A
ALA
36
n
36
ALA
36
A
ASP
37
n
37
ASP
37
A
VAL
38
n
38
VAL
38
A
ARG
39
n
39
ARG
39
A
ARG
40
n
40
ARG
40
A
ASP
41
n
41
ASP
41
A
PRO
42
n
42
PRO
42
A
ALA
43
n
43
ALA
43
A
SER
44
n
44
SER
44
A
LEU
45
n
45
LEU
45
A
THR
46
n
46
THR
46
A
LYS
47
n
47
LYS
47
A
MET
48
n
48
MET
48
A
MET
49
n
49
MET
49
A
THR
50
n
50
THR
50
A
SER
51
n
51
SER
51
A
TYR
52
n
52
TYR
52
A
VAL
53
n
53
VAL
53
A
ILE
54
n
54
ILE
54
A
GLY
55
n
55
GLY
55
A
GLN
56
n
56
GLN
56
A
ALA
57
n
57
ALA
57
A
MET
58
n
58
MET
58
A
LYS
59
n
59
LYS
59
A
ALA
60
n
60
ALA
60
A
GLY
61
n
61
GLY
61
A
LYS
62
n
62
LYS
62
A
PHE
63
n
63
PHE
63
A
LYS
64
n
64
LYS
64
A
GLU
65
n
65
GLU
65
A
THR
66
n
66
THR
66
A
ASP
67
n
67
ASP
67
A
LEU
68
n
68
LEU
68
A
VAL
69
n
69
VAL
69
A
THR
70
n
70
THR
70
A
ILE
71
n
71
ILE
71
A
GLY
72
n
72
GLY
72
A
ASN
73
n
73
ASN
73
A
ASP
74
n
74
ASP
74
A
ALA
75
n
75
ALA
75
A
TRP
76
n
76
TRP
76
A
ALA
77
n
77
ALA
77
A
THR
78
n
78
THR
78
A
n
79
79
A
n
80
80
A
n
81
81
A
n
82
82
A
n
83
83
A
n
84
84
A
GLY
85
n
85
GLY
85
A
SER
86
n
86
SER
86
A
SER
87
n
87
SER
87
A
LEU
88
n
88
LEU
88
A
MET
89
n
89
MET
89
A
PHE
90
n
90
PHE
90
A
LEU
91
n
91
LEU
91
A
LYS
92
n
92
LYS
92
A
PRO
93
n
93
PRO
93
A
GLY
94
n
94
GLY
94
A
MET
95
n
95
MET
95
A
GLN
96
n
96
GLN
96
A
VAL
97
n
97
VAL
97
A
PRO
98
n
98
PRO
98
A
VAL
99
n
99
VAL
99
A
SER
100
n
100
SER
100
A
GLN
101
n
101
GLN
101
A
LEU
102
n
102
LEU
102
A
ILE
103
n
103
ILE
103
A
ARG
104
n
104
ARG
104
A
GLY
105
n
105
GLY
105
A
ILE
106
n
106
ILE
106
A
ASN
107
n
107
ASN
107
A
LEU
108
n
108
LEU
108
A
GLN
109
n
109
GLN
109
A
SER
110
n
110
SER
110
A
GLY
111
n
111
GLY
111
A
ASN
112
n
112
ASN
112
A
ASP
113
n
113
ASP
113
A
ALA
114
n
114
ALA
114
A
CYS
115
n
115
CYS
115
A
VAL
116
n
116
VAL
116
A
ALA
117
n
117
ALA
117
A
MET
118
n
118
MET
118
A
ALA
119
n
119
ALA
119
A
ASP
120
n
120
ASP
120
A
PHE
121
n
121
PHE
121
A
ALA
122
n
122
ALA
122
A
ALA
123
n
123
ALA
123
A
GLY
124
n
124
GLY
124
A
SER
125
n
125
SER
125
A
GLN
126
n
126
GLN
126
A
ASP
127
n
127
ASP
127
A
ALA
128
n
128
ALA
128
A
PHE
129
n
129
PHE
129
A
VAL
130
n
130
VAL
130
A
GLY
131
n
131
GLY
131
A
LEU
132
n
132
LEU
132
A
MET
133
n
133
MET
133
A
ASN
134
n
134
ASN
134
A
SER
135
n
135
SER
135
A
TYR
136
n
136
TYR
136
A
VAL
137
n
137
VAL
137
A
ASN
138
n
138
ASN
138
A
ALA
139
n
139
ALA
139
A
LEU
140
n
140
LEU
140
A
GLY
141
n
141
GLY
141
A
LEU
142
n
142
LEU
142
A
LYS
143
n
143
LYS
143
A
ASN
144
n
144
ASN
144
A
THR
145
n
145
THR
145
A
HIS
146
n
146
HIS
146
A
PHE
147
n
147
PHE
147
A
GLN
148
n
148
GLN
148
A
THR
149
n
149
THR
149
A
VAL
150
n
150
VAL
150
A
HIS
151
n
151
HIS
151
A
GLY
152
n
152
GLY
152
A
LEU
153
n
153
LEU
153
A
ASP
154
n
154
ASP
154
A
ALA
155
n
155
ALA
155
A
ASP
156
n
156
ASP
156
A
GLY
157
n
157
GLY
157
A
GLN
158
n
158
GLN
158
A
TYR
159
n
159
TYR
159
A
SER
160
n
160
SER
160
A
SER
161
n
161
SER
161
A
ALA
162
n
162
ALA
162
A
ARG
163
n
163
ARG
163
A
ASP
164
n
164
ASP
164
A
MET
165
n
165
MET
165
A
ALA
166
n
166
ALA
166
A
LEU
167
n
167
LEU
167
A
ILE
168
n
168
ILE
168
A
GLY
169
n
169
GLY
169
A
GLN
170
n
170
GLN
170
A
ALA
171
n
171
ALA
171
A
LEU
172
n
172
LEU
172
A
ILE
173
n
173
ILE
173
A
ARG
174
n
174
ARG
174
A
ASP
175
n
175
ASP
175
A
VAL
176
n
176
VAL
176
A
PRO
177
n
177
PRO
177
A
ASN
178
n
178
ASN
178
A
GLU
179
n
179
GLU
179
A
TYR
180
n
180
TYR
180
A
SER
181
n
181
SER
181
A
ILE
182
n
182
ILE
182
A
TYR
183
n
183
TYR
183
A
LYS
184
n
184
LYS
184
A
GLU
185
n
185
GLU
185
A
LYS
186
n
186
LYS
186
A
GLU
187
n
187
GLU
187
A
PHE
188
n
188
PHE
188
A
THR
189
n
189
THR
189
A
PHE
190
n
190
PHE
190
A
ASN
191
n
191
ASN
191
A
GLY
192
n
192
GLY
192
A
ILE
193
n
193
ILE
193
A
ARG
194
n
194
ARG
194
A
GLN
195
n
195
GLN
195
A
LEU
196
n
196
LEU
196
A
ASN
197
n
197
ASN
197
A
ARG
198
n
198
ARG
198
A
ASN
199
n
199
ASN
199
A
GLY
200
n
200
GLY
200
A
LEU
201
n
201
LEU
201
A
LEU
202
n
202
LEU
202
A
TRP
203
n
203
TRP
203
A
ASP
204
n
204
ASP
204
A
ASN
205
n
205
ASN
205
A
SER
206
n
206
SER
206
A
LEU
207
n
207
LEU
207
A
ASN
208
n
208
ASN
208
A
VAL
209
n
209
VAL
209
A
ASP
210
n
210
ASP
210
A
GLY
211
n
211
GLY
211
A
ILE
212
n
212
ILE
212
A
LYS
213
n
213
LYS
213
A
THR
214
n
214
THR
214
A
GLY
215
n
215
GLY
215
A
HIS
216
n
216
HIS
216
A
THR
217
n
217
THR
217
A
ASP
218
n
218
ASP
218
A
LYS
219
n
219
LYS
219
A
ALA
220
n
220
ALA
220
A
GLY
221
n
221
GLY
221
A
TYR
222
n
222
TYR
222
A
ASN
223
n
223
ASN
223
A
LEU
224
n
224
LEU
224
A
VAL
225
n
225
VAL
225
A
ALA
226
n
226
ALA
226
A
SER
227
n
227
SER
227
A
ALA
228
n
228
ALA
228
A
THR
229
n
229
THR
229
A
GLU
230
n
230
GLU
230
A
GLY
231
n
231
GLY
231
A
GLN
232
n
232
GLN
232
A
MET
233
n
233
MET
233
A
ARG
234
n
234
ARG
234
A
LEU
235
n
235
LEU
235
A
ILE
236
n
236
ILE
236
A
SER
237
n
237
SER
237
A
ALA
238
n
238
ALA
238
A
VAL
239
n
239
VAL
239
A
MET
240
n
240
MET
240
A
GLY
241
n
241
GLY
241
A
GLY
242
n
242
GLY
242
A
ARG
243
n
243
ARG
243
A
THR
244
n
244
THR
244
A
PHE
245
n
245
PHE
245
A
LYS
246
n
246
LYS
246
A
GLY
247
n
247
GLY
247
A
ARG
248
n
248
ARG
248
A
GLU
249
n
249
GLU
249
A
ALA
250
n
250
ALA
250
A
GLU
251
n
251
GLU
251
A
SER
252
n
252
SER
252
A
LYS
253
n
253
LYS
253
A
LYS
254
n
254
LYS
254
A
LEU
255
n
255
LEU
255
A
LEU
256
n
256
LEU
256
A
THR
257
n
257
THR
257
A
TRP
258
n
258
TRP
258
A
GLY
259
n
259
GLY
259
A
PHE
260
n
260
PHE
260
A
ARG
261
n
261
ARG
261
A
PHE
262
n
262
PHE
262
A
PHE
263
n
263
PHE
263
A
GLU
264
n
264
GLU
264
A
THR
265
n
265
THR
265
A
VAL
266
n
266
VAL
266
A
ASN
267
n
267
ASN
267
A
PRO
268
n
268
PRO
268
A
LEU
269
n
269
LEU
269
A
LYS
270
n
270
LYS
270
A
VAL
271
n
271
VAL
271
A
GLY
272
n
272
GLY
272
A
LYS
273
n
273
LYS
273
A
GLU
274
n
274
GLU
274
A
PHE
275
n
275
PHE
275
A
ALA
276
n
276
ALA
276
A
SER
277
n
277
SER
277
A
GLU
278
n
278
GLU
278
A
PRO
279
n
279
PRO
279
A
VAL
280
n
280
VAL
280
A
TRP
281
n
281
TRP
281
A
PHE
282
n
282
PHE
282
A
GLY
283
n
283
GLY
283
A
ASP
284
n
284
ASP
284
A
SER
285
n
285
SER
285
A
ASP
286
n
286
ASP
286
A
ARG
287
n
287
ARG
287
A
ALA
288
n
288
ALA
288
A
SER
289
n
289
SER
289
A
LEU
290
n
290
LEU
290
A
GLY
291
n
291
GLY
291
A
VAL
292
n
292
VAL
292
A
ASP
293
n
293
ASP
293
A
LYS
294
n
294
LYS
294
A
ASP
295
n
295
ASP
295
A
VAL
296
n
296
VAL
296
A
TYR
297
n
297
TYR
297
A
LEU
298
n
298
LEU
298
A
THR
299
n
299
THR
299
A
ILE
300
n
300
ILE
300
A
PRO
301
n
301
PRO
301
A
ARG
302
n
302
ARG
302
A
GLY
303
n
303
GLY
303
A
ARG
304
n
304
ARG
304
A
MET
305
n
305
MET
305
A
LYS
306
n
306
LYS
306
A
ASP
307
n
307
ASP
307
A
LEU
308
n
308
LEU
308
A
LYS
309
n
309
LYS
309
A
ALA
310
n
310
ALA
310
A
SER
311
n
311
SER
311
A
TYR
312
n
312
TYR
312
A
VAL
313
n
313
VAL
313
A
LEU
314
n
314
LEU
314
A
ASN
315
n
315
ASN
315
A
SER
316
n
316
SER
316
A
SER
317
n
317
SER
317
A
GLU
318
n
318
GLU
318
A
LEU
319
n
319
LEU
319
A
HIS
320
n
320
HIS
320
A
ALA
321
n
321
ALA
321
A
PRO
322
n
322
PRO
322
A
LEU
323
n
323
LEU
323
A
GLN
324
n
324
GLN
324
A
LYS
325
n
325
LYS
325
A
ASN
326
n
326
ASN
326
A
GLN
327
n
327
GLN
327
A
VAL
328
n
328
VAL
328
A
VAL
329
n
329
VAL
329
A
GLY
330
n
330
GLY
330
A
THR
331
n
331
THR
331
A
ILE
332
n
332
ILE
332
A
ASN
333
n
333
ASN
333
A
PHE
334
n
334
PHE
334
A
GLN
335
n
335
GLN
335
A
LEU
336
n
336
LEU
336
A
ASP
337
n
337
ASP
337
A
GLY
338
n
338
GLY
338
A
LYS
339
n
339
LYS
339
A
THR
340
n
340
THR
340
A
ILE
341
n
341
ILE
341
A
GLU
342
n
342
GLU
342
A
GLN
343
n
343
GLN
343
A
ARG
344
n
344
ARG
344
A
PRO
345
n
345
PRO
345
A
LEU
346
n
346
LEU
346
A
VAL
347
n
347
VAL
347
A
VAL
348
n
348
VAL
348
A
LEU
349
n
349
LEU
349
A
GLN
350
n
350
GLN
350
A
GLU
351
n
351
GLU
351
A
ILE
352
n
352
ILE
352
A
PRO
353
n
353
PRO
353
A
GLU
354
n
354
GLU
354
A
GLY
355
n
355
GLY
355
A
n
356
356
A
n
357
357
A
n
358
358
A
n
359
359
A
n
360
360
A
n
361
361
A
n
362
362
A
n
363
363
A
author_defined_assembly
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
A
O
LEU
31
A
O
LEU
31
A
N
LEU
22
A
N
LEU
22
A
N
SER
19
A
N
SER
19
A
O
MET
240
A
O
MET
240
A
O
GLY
242
A
O
GLY
242
A
N
TYR
222
A
N
TYR
222
A
O
ASN
223
A
O
ASN
223
A
N
GLY
215
A
N
GLY
215
A
N
VAL
69
A
N
VAL
69
A
O
VAL
97
A
O
VAL
97
A
N
PHE
188
A
N
PHE
188
A
O
GLN
195
A
O
GLN
195
A
N
VAL
266
A
N
VAL
266
A
O
LEU
298
A
O
LEU
298
A
N
LYS
309
A
N
LYS
309
A
O
GLN
335
A
O
GLN
335
A
N
ILE
332
A
N
ILE
332
A
O
ARG
344
A
O
ARG
344
A
O
VAL
347
A
O
VAL
347
A
N
GLY
291
A
N
GLY
291
A
O
ALA
288
A
O
ALA
288
A
N
GLU
278
A
N
GLU
278
A
N
TRP
281
A
N
TRP
281
A
O
LEU
319
A
O
LEU
319
1
A
ASP
1
A
ASP
1
1
Y
1
A
ASP
2
A
ASP
2
1
Y
1
A
GLY
79
A
GLY
79
1
Y
1
A
ASN
80
A
ASN
80
1
Y
1
A
PRO
81
A
PRO
81
1
Y
1
A
VAL
82
A
VAL
82
1
Y
1
A
PHE
83
A
PHE
83
1
Y
1
A
LYS
84
A
LYS
84
1
Y
1
A
ASN
356
A
ASN
356
1
Y
1
A
PHE
357
A
PHE
357
1
Y
1
A
GLY
358
A
GLY
358
1
Y
1
A
ASP
359
A
ASP
359
1
Y
1
A
PRO
360
A
PRO
360
1
Y
1
A
VAL
361
A
VAL
361
1
Y
1
A
ILE
362
A
ILE
362
1
Y
1
A
ASP
363
A
ASP
363
1
Y
1
A
A
O
O
HOH
HOH
412
423
1.74
1
A
A
O
O
HOH
HOH
423
424
1.81
1
A
A
O
O
HOH
HOH
507
547
1.91
1
A
A
OD1
O
ASN
HOH
208
477
1.97
A
1
A
A
O
O
HOH
HOH
489
514
1.99
1
A
A
NH1
OD2
ARG
ASP
304
337
1.99
1
A
A
OE1
NH2
GLU
ARG
342
344
2.00
1
A
A
OE2
NH2
GLU
ARG
18
40
2.04
B
1
5.41
0.90
118.30
123.71
A
A
A
CB
CG
OD2
ASP
ASP
ASP
16
16
16
N
1
5.88
0.90
118.30
124.18
A
A
A
CB
CG
OD2
ASP
ASP
ASP
74
74
74
N
1
6.62
0.90
118.30
124.92
A
A
A
CB
CG
OD2
ASP
ASP
ASP
113
113
113
N
1
-13.20
2.00
110.40
97.20
A
A
A
CB
CA
C
ASP
ASP
ASP
154
154
154
N
1
A
ALA
43
56.09
-127.82
1
A
SER
110
-104.60
-111.30
1
A
ILE
212
-133.71
-60.02
32.775
0.01
0.01
0.00
0.01
0.00
-0.02
0.942
0.918
0.26617
0.21926
0.2241
0.2241
2.00
14.84
2650
26273
26273
10.1
99.9
6.190
0.171
RANDOM
1
isotropic
THROUGHOUT
0.0
0.220
0.192
0.80
0.80
1.40
PDB ENTRY 1HD8
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.00
14.84
174
2859
4
0
2681
0.009
0.022
2731
1.332
1.956
3684
3.506
3.000
345
19.047
15.000
501
0.095
0.200
410
0.004
0.020
2053
0.237
0.300
1271
0.207
0.500
266
0.218
0.300
41
0.139
0.500
5
0.591
1.500
1713
1.118
2.000
2745
1.659
3.000
1018
2.723
4.500
939
0.34
0.289
2.051
196
1698
1894
20
30.37
2.0
41.5
1NZU
26382
26382
0.0
0.0
0.065
1
6.1
2.8
99.9
0.308
2.00
2.07
2.0
2657
2.7
99.8
refinement
REFMAC
5.0
data reduction
CrystalClear
(MSC/RIGAKU)
data scaling
CrystalClear
(MSC/RIGAKU)
Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol
1
N
N
2
N
N
3
N
N
A
LEU
3
A
LEU
3
HELX_P
A
MET
8
A
MET
8
1
1
6
A
PRO
42
A
PRO
42
HELX_P
A
SER
44
A
SER
44
5
2
3
A
LEU
45
A
LEU
45
HELX_P
A
ALA
60
A
ALA
60
1
3
16
A
GLY
72
A
GLY
72
HELX_P
A
ALA
77
A
ALA
77
1
4
6
A
VAL
99
A
VAL
99
HELX_P
A
ARG
104
A
ARG
104
1
5
6
A
GLY
105
A
GLY
105
HELX_P
A
LEU
108
A
LEU
108
5
6
4
A
GLY
111
A
GLY
111
HELX_P
A
GLY
124
A
GLY
124
1
7
14
A
SER
125
A
SER
125
HELX_P
A
LEU
140
A
LEU
140
1
8
16
A
SER
161
A
SER
161
HELX_P
A
VAL
176
A
VAL
176
1
9
16
A
VAL
176
A
VAL
176
HELX_P
A
SER
181
A
SER
181
1
10
6
A
ILE
182
A
ILE
182
HELX_P
A
GLU
185
A
GLU
185
5
11
4
A
ASN
199
A
ASN
199
HELX_P
A
ASP
204
A
ASP
204
5
12
6
A
LYS
246
A
LYS
246
HELX_P
A
PHE
262
A
PHE
262
1
13
17
A
ARG
304
A
ARG
304
HELX_P
A
LEU
308
A
LEU
308
5
14
5
covale
2.020
none
A
CYS
115
A
SG
CYS
115
1_555
A
BME
400
B
S2
BME
1_555
HYDROLASE
PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, DD-CARBOXYPEPTIDASE, HYDROLASE
A
GLY
211
A
GLY
211
1
A
ILE
212
A
ILE
212
5.45
A
ALA
321
A
ALA
321
1
A
PRO
322
A
PRO
322
1.86
DACA_ECOLI
UNP
1
1
P04287
MNTIFSARIMKRLALTTALCTAFISAAHADDLNIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTS
YVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVG
LMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDG
IKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLG
VDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEGNF
30
386
1NZU
1
357
P04287
A
1
1
357
1
SEE REMARK 999
GLY
358
1NZU
A
P04287
UNP
358
1
SEE REMARK 999
ASP
359
1NZU
A
P04287
UNP
359
1
SEE REMARK 999
PRO
360
1NZU
A
P04287
UNP
360
1
SEE REMARK 999
VAL
361
1NZU
A
P04287
UNP
361
1
SEE REMARK 999
ILE
362
1NZU
A
P04287
UNP
362
1
SEE REMARK 999
ASP
363
1NZU
A
P04287
UNP
363
5
2
2
2
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
A
VAL
30
A
VAL
30
A
GLN
34
A
GLN
34
A
ALA
17
A
ALA
17
A
ASP
24
A
ASP
24
A
MET
233
A
MET
233
A
GLY
242
A
GLY
242
A
GLY
221
A
GLY
221
A
GLU
230
A
GLU
230
A
ASN
208
A
ASN
208
A
THR
217
A
THR
217
A
LEU
68
A
LEU
68
A
THR
70
A
THR
70
A
GLN
96
A
GLN
96
A
PRO
98
A
PRO
98
A
GLU
187
A
GLU
187
A
PHE
190
A
PHE
190
A
ILE
193
A
ILE
193
A
LEU
196
A
LEU
196
A
PHE
263
A
PHE
263
A
LEU
269
A
LEU
269
A
VAL
296
A
VAL
296
A
PRO
301
A
PRO
301
A
LYS
309
A
LYS
309
A
LEU
314
A
LEU
314
A
VAL
328
A
VAL
328
A
LEU
336
A
LEU
336
A
LYS
339
A
LYS
339
A
VAL
348
A
VAL
348
A
ARG
287
A
ARG
287
A
GLY
291
A
GLY
291
A
ALA
276
A
ALA
276
A
TRP
281
A
TRP
281
A
LEU
319
A
LEU
319
A
HIS
320
A
HIS
320
BINDING SITE FOR RESIDUE BME A 400
A
BME
400
Software
5
A
ILE
54
A
ILE
54
5
1_555
A
LEU
102
A
LEU
102
5
1_555
A
ILE
106
A
ILE
106
5
1_555
A
CYS
115
A
CYS
115
5
1_555
A
HOH
427
C
HOH
5
1_555
145
P 32