0.021596
0.000000
0.000000
0.000000
0.018488
0.000000
0.000000
0.000000
0.009194
0.00000
0.00000
0.00000
Fonze, E.
Charlier, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
46.305
54.090
108.769
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
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
Na 1
22.990
SODIUM ION
non-polymer
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
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
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
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
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
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
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
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
H
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
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
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
H
N
250
N
NA
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
N
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
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
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
N
360
N
O
N
361
N
O
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
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
O
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
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
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
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
sing
N
364
N
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
42
2895
2906
10.1021/bi027256x
12627955
Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.
2003
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
274
21853
21860
10.1074/jbc.274.31.21853
The Crystal Structure of a Penicilloyl-Serine Transferase of Intermediate Penicillin Sensitivity
1999
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
241
295
297
10.1006/jmbi.1994.1504
Crystallization and X-Ray Diffraction Study of the Streptomyces K15 Penicillin-Binding Dd-Transpeptidase
1994
10.2210/pdb1es3/pdb
pdb_00001es3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
AREA DETECTOR
1996-06-24
SIEMENS X1000
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
27476.254
DD-TRANSPEPTIDASE
3.4.16.4
C98A
1
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
130
nat
water
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, DD-PEPTIDASE
no
no
VTKPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANNASQAHLIVG
DKVTVRQLLYGLMLPSGADAAYALADKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKI
ASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVL
ASTSIPARESDATKIMNYGFAL
VTKPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANNASQAHLIVG
DKVTVRQLLYGLMLPSGADAAYALADKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKI
ASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVL
ASTSIPARESDATKIMNYGFAL
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
Streptomyces
K15
Streptomyces
Streptomyces lividans
sample
1958
Streptomyces sp.
457428
Streptomyces lividans TK24
TK24
1
2.48
50.38
VAPOR DIFFUSION, HANGING DROP
6.0
Mes 0.1M, PEG 6K 25%, NaCl 0.5M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
Database references
Derived calculations
Data collection
1
0
2000-05-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-11-03
1
4
2024-02-07
_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
1SKF contains the wild type protein.
K38H MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
S96A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
C98N MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
S216A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
R248L MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
RCSB
Y
RCSB
2000-04-07
REL
REL
NA
SODIUM ION
HOH
water
SOD
600
2
NA
NA
600
A
WAT
300
3
HOH
HOH
300
A
WAT
301
3
HOH
HOH
301
A
WAT
302
3
HOH
HOH
302
A
WAT
303
3
HOH
HOH
303
A
WAT
304
3
HOH
HOH
304
A
WAT
306
3
HOH
HOH
306
A
WAT
307
3
HOH
HOH
307
A
WAT
308
3
HOH
HOH
308
A
WAT
309
3
HOH
HOH
309
A
WAT
310
3
HOH
HOH
310
A
WAT
312
3
HOH
HOH
312
A
WAT
313
3
HOH
HOH
313
A
WAT
314
3
HOH
HOH
314
A
WAT
315
3
HOH
HOH
315
A
WAT
316
3
HOH
HOH
316
A
WAT
317
3
HOH
HOH
317
A
WAT
318
3
HOH
HOH
318
A
WAT
319
3
HOH
HOH
319
A
WAT
320
3
HOH
HOH
320
A
WAT
321
3
HOH
HOH
321
A
WAT
322
3
HOH
HOH
322
A
WAT
323
3
HOH
HOH
323
A
WAT
324
3
HOH
HOH
324
A
WAT
325
3
HOH
HOH
325
A
WAT
326
3
HOH
HOH
326
A
WAT
327
3
HOH
HOH
327
A
WAT
328
3
HOH
HOH
328
A
WAT
329
3
HOH
HOH
329
A
WAT
330
3
HOH
HOH
330
A
WAT
331
3
HOH
HOH
331
A
WAT
332
3
HOH
HOH
332
A
WAT
333
3
HOH
HOH
333
A
WAT
334
3
HOH
HOH
334
A
WAT
335
3
HOH
HOH
335
A
WAT
336
3
HOH
HOH
336
A
WAT
337
3
HOH
HOH
337
A
WAT
338
3
HOH
HOH
338
A
WAT
339
3
HOH
HOH
339
A
WAT
341
3
HOH
HOH
341
A
WAT
342
3
HOH
HOH
342
A
WAT
343
3
HOH
HOH
343
A
WAT
344
3
HOH
HOH
344
A
WAT
345
3
HOH
HOH
345
A
WAT
346
3
HOH
HOH
346
A
WAT
348
3
HOH
HOH
348
A
WAT
349
3
HOH
HOH
349
A
WAT
350
3
HOH
HOH
350
A
WAT
351
3
HOH
HOH
351
A
WAT
352
3
HOH
HOH
352
A
WAT
353
3
HOH
HOH
353
A
WAT
354
3
HOH
HOH
354
A
WAT
356
3
HOH
HOH
356
A
WAT
357
3
HOH
HOH
357
A
WAT
358
3
HOH
HOH
358
A
WAT
359
3
HOH
HOH
359
A
WAT
360
3
HOH
HOH
360
A
WAT
361
3
HOH
HOH
361
A
WAT
363
3
HOH
HOH
363
A
WAT
364
3
HOH
HOH
364
A
WAT
365
3
HOH
HOH
365
A
WAT
366
3
HOH
HOH
366
A
WAT
367
3
HOH
HOH
367
A
WAT
368
3
HOH
HOH
368
A
WAT
369
3
HOH
HOH
369
A
WAT
370
3
HOH
HOH
370
A
WAT
371
3
HOH
HOH
371
A
WAT
372
3
HOH
HOH
372
A
WAT
379
3
HOH
HOH
379
A
WAT
380
3
HOH
HOH
380
A
WAT
384
3
HOH
HOH
384
A
WAT
385
3
HOH
HOH
385
A
WAT
386
3
HOH
HOH
386
A
WAT
387
3
HOH
HOH
387
A
WAT
388
3
HOH
HOH
388
A
WAT
390
3
HOH
HOH
390
A
WAT
391
3
HOH
HOH
391
A
WAT
392
3
HOH
HOH
392
A
WAT
393
3
HOH
HOH
393
A
WAT
394
3
HOH
HOH
394
A
WAT
395
3
HOH
HOH
395
A
WAT
396
3
HOH
HOH
396
A
WAT
397
3
HOH
HOH
397
A
WAT
398
3
HOH
HOH
398
A
WAT
400
3
HOH
HOH
400
A
WAT
401
3
HOH
HOH
401
A
WAT
403
3
HOH
HOH
403
A
WAT
405
3
HOH
HOH
405
A
WAT
406
3
HOH
HOH
406
A
WAT
407
3
HOH
HOH
407
A
WAT
408
3
HOH
HOH
408
A
WAT
409
3
HOH
HOH
409
A
WAT
411
3
HOH
HOH
411
A
WAT
412
3
HOH
HOH
412
A
WAT
413
3
HOH
HOH
413
A
WAT
414
3
HOH
HOH
414
A
WAT
415
3
HOH
HOH
415
A
WAT
416
3
HOH
HOH
416
A
WAT
417
3
HOH
HOH
417
A
WAT
418
3
HOH
HOH
418
A
WAT
419
3
HOH
HOH
419
A
WAT
420
3
HOH
HOH
420
A
WAT
421
3
HOH
HOH
421
A
WAT
422
3
HOH
HOH
422
A
WAT
423
3
HOH
HOH
423
A
WAT
425
3
HOH
HOH
425
A
WAT
426
3
HOH
HOH
426
A
WAT
427
3
HOH
HOH
427
A
WAT
429
3
HOH
HOH
429
A
WAT
430
3
HOH
HOH
430
A
WAT
432
3
HOH
HOH
432
A
WAT
433
3
HOH
HOH
433
A
WAT
436
3
HOH
HOH
436
A
WAT
437
3
HOH
HOH
437
A
WAT
438
3
HOH
HOH
438
A
WAT
439
3
HOH
HOH
439
A
WAT
440
3
HOH
HOH
440
A
WAT
441
3
HOH
HOH
441
A
WAT
443
3
HOH
HOH
443
A
WAT
444
3
HOH
HOH
444
A
WAT
449
3
HOH
HOH
449
A
WAT
450
3
HOH
HOH
450
A
WAT
451
3
HOH
HOH
451
A
WAT
452
3
HOH
HOH
452
A
WAT
453
3
HOH
HOH
453
A
WAT
454
3
HOH
HOH
454
A
WAT
455
3
HOH
HOH
455
A
WAT
456
3
HOH
HOH
456
A
WAT
457
3
HOH
HOH
457
A
WAT
458
3
HOH
HOH
458
A
WAT
459
3
HOH
HOH
459
A
n
1
1
A
n
2
2
A
LYS
3
n
3
LYS
3
A
PRO
4
n
4
PRO
4
A
THR
5
n
5
THR
5
A
ILE
6
n
6
ILE
6
A
ALA
7
n
7
ALA
7
A
ALA
8
n
8
ALA
8
A
VAL
9
n
9
VAL
9
A
GLY
10
n
10
GLY
10
A
GLY
11
n
11
GLY
11
A
TYR
12
n
12
TYR
12
A
ALA
13
n
13
ALA
13
A
MET
14
n
14
MET
14
A
ASN
15
n
15
ASN
15
A
ASN
16
n
16
ASN
16
A
GLY
17
n
17
GLY
17
A
THR
18
n
18
THR
18
A
GLY
19
n
19
GLY
19
A
THR
20
n
20
THR
20
A
THR
21
n
21
THR
21
A
LEU
22
n
22
LEU
22
A
TYR
23
n
23
TYR
23
A
THR
24
n
24
THR
24
A
LYS
25
n
25
LYS
25
A
ALA
26
n
26
ALA
26
A
ALA
27
n
27
ALA
27
A
ASP
28
n
28
ASP
28
A
THR
29
n
29
THR
29
A
ARG
30
n
30
ARG
30
A
ARG
31
n
31
ARG
31
A
SER
32
n
32
SER
32
A
THR
33
n
33
THR
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
THR
36
n
36
THR
36
A
THR
37
n
37
THR
37
A
LYS
38
n
38
LYS
38
A
ILE
39
n
39
ILE
39
A
MET
40
n
40
MET
40
A
THR
41
n
41
THR
41
A
ALA
42
n
42
ALA
42
A
LYS
43
n
43
LYS
43
A
VAL
44
n
44
VAL
44
A
VAL
45
n
45
VAL
45
A
LEU
46
n
46
LEU
46
A
ALA
47
n
47
ALA
47
A
GLN
48
n
48
GLN
48
A
SER
49
n
49
SER
49
A
ASN
50
n
50
ASN
50
A
LEU
51
n
51
LEU
51
A
ASN
52
n
52
ASN
52
A
LEU
53
n
53
LEU
53
A
ASP
54
n
54
ASP
54
A
ALA
55
n
55
ALA
55
A
LYS
56
n
56
LYS
56
A
VAL
57
n
57
VAL
57
A
THR
58
n
58
THR
58
A
ILE
59
n
59
ILE
59
A
GLN
60
n
60
GLN
60
A
LYS
61
n
61
LYS
61
A
ALA
62
n
62
ALA
62
A
TYR
63
n
63
TYR
63
A
SER
64
n
64
SER
64
A
ASP
65
n
65
ASP
65
A
TYR
66
n
66
TYR
66
A
VAL
67
n
67
VAL
67
A
VAL
68
n
68
VAL
68
A
ALA
69
n
69
ALA
69
A
ASN
70
n
70
ASN
70
A
ASN
71
n
71
ASN
71
A
ALA
72
n
72
ALA
72
A
SER
73
n
73
SER
73
A
GLN
74
n
74
GLN
74
A
ALA
75
n
75
ALA
75
A
HIS
76
n
76
HIS
76
A
LEU
77
n
77
LEU
77
A
ILE
78
n
78
ILE
78
A
VAL
79
n
79
VAL
79
A
GLY
80
n
80
GLY
80
A
ASP
81
n
81
ASP
81
A
LYS
82
n
82
LYS
82
A
VAL
83
n
83
VAL
83
A
THR
84
n
84
THR
84
A
VAL
85
n
85
VAL
85
A
ARG
86
n
86
ARG
86
A
GLN
87
n
87
GLN
87
A
LEU
88
n
88
LEU
88
A
LEU
89
n
89
LEU
89
A
TYR
90
n
90
TYR
90
A
GLY
91
n
91
GLY
91
A
LEU
92
n
92
LEU
92
A
MET
93
n
93
MET
93
A
LEU
94
n
94
LEU
94
A
PRO
95
n
95
PRO
95
A
SER
96
n
96
SER
96
A
GLY
97
n
97
GLY
97
A
ALA
98
n
98
ALA
98
A
ASP
99
n
99
ASP
99
A
ALA
100
n
100
ALA
100
A
ALA
101
n
101
ALA
101
A
TYR
102
n
102
TYR
102
A
ALA
103
n
103
ALA
103
A
LEU
104
n
104
LEU
104
A
ALA
105
n
105
ALA
105
A
ASP
106
n
106
ASP
106
A
LYS
107
n
107
LYS
107
A
TYR
108
n
108
TYR
108
A
GLY
109
n
109
GLY
109
A
SER
110
n
110
SER
110
A
GLY
111
n
111
GLY
111
A
SER
112
n
112
SER
112
A
THR
113
n
113
THR
113
A
ARG
114
n
114
ARG
114
A
ALA
115
n
115
ALA
115
A
ALA
116
n
116
ALA
116
A
ARG
117
n
117
ARG
117
A
VAL
118
n
118
VAL
118
A
LYS
119
n
119
LYS
119
A
SER
120
n
120
SER
120
A
PHE
121
n
121
PHE
121
A
ILE
122
n
122
ILE
122
A
GLY
123
n
123
GLY
123
A
LYS
124
n
124
LYS
124
A
MET
125
n
125
MET
125
A
ASN
126
n
126
ASN
126
A
THR
127
n
127
THR
127
A
ALA
128
n
128
ALA
128
A
ALA
129
n
129
ALA
129
A
THR
130
n
130
THR
130
A
ASN
131
n
131
ASN
131
A
LEU
132
n
132
LEU
132
A
GLY
133
n
133
GLY
133
A
LEU
134
n
134
LEU
134
A
HIS
135
n
135
HIS
135
A
ASN
136
n
136
ASN
136
A
THR
137
n
137
THR
137
A
HIS
138
n
138
HIS
138
A
PHE
139
n
139
PHE
139
A
ASP
140
n
140
ASP
140
A
SER
141
n
141
SER
141
A
PHE
142
n
142
PHE
142
A
ASP
143
n
143
ASP
143
A
GLY
144
n
144
GLY
144
A
ILE
145
n
145
ILE
145
A
GLY
146
n
146
GLY
146
A
ASN
147
n
147
ASN
147
A
GLY
148
n
148
GLY
148
A
ALA
149
n
149
ALA
149
A
ASN
150
n
150
ASN
150
A
TYR
151
n
151
TYR
151
A
SER
152
n
152
SER
152
A
THR
153
n
153
THR
153
A
PRO
154
n
154
PRO
154
A
ARG
155
n
155
ARG
155
A
ASP
156
n
156
ASP
156
A
LEU
157
n
157
LEU
157
A
THR
158
n
158
THR
158
A
LYS
159
n
159
LYS
159
A
ILE
160
n
160
ILE
160
A
ALA
161
n
161
ALA
161
A
SER
162
n
162
SER
162
A
SER
163
n
163
SER
163
A
ALA
164
n
164
ALA
164
A
MET
165
n
165
MET
165
A
LYS
166
n
166
LYS
166
A
ASN
167
n
167
ASN
167
A
SER
168
n
168
SER
168
A
THR
169
n
169
THR
169
A
PHE
170
n
170
PHE
170
A
ARG
171
n
171
ARG
171
A
THR
172
n
172
THR
172
A
VAL
173
n
173
VAL
173
A
VAL
174
n
174
VAL
174
A
LYS
175
n
175
LYS
175
A
THR
176
n
176
THR
176
A
LYS
177
n
177
LYS
177
A
ALA
178
n
178
ALA
178
A
TYR
179
n
179
TYR
179
A
THR
180
n
180
THR
180
A
ALA
181
n
181
ALA
181
A
LYS
182
n
182
LYS
182
A
THR
183
n
183
THR
183
A
VAL
184
n
184
VAL
184
A
THR
185
n
185
THR
185
A
LYS
186
n
186
LYS
186
A
THR
187
n
187
THR
187
A
GLY
188
n
188
GLY
188
A
SER
189
n
189
SER
189
A
ILE
190
n
190
ILE
190
A
ARG
191
n
191
ARG
191
A
THR
192
n
192
THR
192
A
MET
193
n
193
MET
193
A
ASP
194
n
194
ASP
194
A
THR
195
n
195
THR
195
A
TRP
196
n
196
TRP
196
A
LYS
197
n
197
LYS
197
A
ASN
198
n
198
ASN
198
A
THR
199
n
199
THR
199
A
ASN
200
n
200
ASN
200
A
GLY
201
n
201
GLY
201
A
LEU
202
n
202
LEU
202
A
LEU
203
n
203
LEU
203
A
SER
204
n
204
SER
204
A
SER
205
n
205
SER
205
A
TYR
206
n
206
TYR
206
A
SER
207
n
207
SER
207
A
GLY
208
n
208
GLY
208
A
ALA
209
n
209
ALA
209
A
ILE
210
n
210
ILE
210
A
GLY
211
n
211
GLY
211
A
VAL
212
n
212
VAL
212
A
LYS
213
n
213
LYS
213
A
THR
214
n
214
THR
214
A
GLY
215
n
215
GLY
215
A
SER
216
n
216
SER
216
A
GLY
217
n
217
GLY
217
A
PRO
218
n
218
PRO
218
A
GLU
219
n
219
GLU
219
A
ALA
220
n
220
ALA
220
A
LYS
221
n
221
LYS
221
A
TYR
222
n
222
TYR
222
A
CYS
223
n
223
CYS
223
A
LEU
224
n
224
LEU
224
A
VAL
225
n
225
VAL
225
A
PHE
226
n
226
PHE
226
A
ALA
227
n
227
ALA
227
A
ALA
228
n
228
ALA
228
A
THR
229
n
229
THR
229
A
ARG
230
n
230
ARG
230
A
GLY
231
n
231
GLY
231
A
GLY
232
n
232
GLY
232
A
LYS
233
n
233
LYS
233
A
THR
234
n
234
THR
234
A
VAL
235
n
235
VAL
235
A
ILE
236
n
236
ILE
236
A
GLY
237
n
237
GLY
237
A
THR
238
n
238
THR
238
A
VAL
239
n
239
VAL
239
A
LEU
240
n
240
LEU
240
A
ALA
241
n
241
ALA
241
A
SER
242
n
242
SER
242
A
THR
243
n
243
THR
243
A
SER
244
n
244
SER
244
A
ILE
245
n
245
ILE
245
A
PRO
246
n
246
PRO
246
A
ALA
247
n
247
ALA
247
A
ARG
248
n
248
ARG
248
A
GLU
249
n
249
GLU
249
A
SER
250
n
250
SER
250
A
ASP
251
n
251
ASP
251
A
ALA
252
n
252
ALA
252
A
THR
253
n
253
THR
253
A
LYS
254
n
254
LYS
254
A
ILE
255
n
255
ILE
255
A
MET
256
n
256
MET
256
A
ASN
257
n
257
ASN
257
A
TYR
258
n
258
TYR
258
A
GLY
259
n
259
GLY
259
A
PHE
260
n
260
PHE
260
A
ALA
261
n
261
ALA
261
A
LEU
262
n
262
LEU
262
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
LYS
25
A
O
LYS
25
A
N
GLY
11
A
N
GLY
11
A
N
MET
14
A
N
MET
14
A
O
ILE
236
A
O
ILE
236
A
N
SER
242
A
N
SER
242
A
O
TYR
222
A
O
TYR
222
A
O
ALA
227
A
O
ALA
227
A
N
ILE
210
A
N
ILE
210
A
N
ARG
31
A
N
ARG
31
A
O
SER
152
A
O
SER
152
A
O
VAL
57
A
O
VAL
57
A
N
VAL
83
A
N
VAL
83
A
O
TYR
179
A
O
TYR
179
A
N
TRP
196
A
N
TRP
196
A
O
THR
183
A
O
THR
183
A
N
ARG
191
A
N
ARG
191
1
A
VAL
1
A
VAL
1
1
Y
1
A
THR
2
A
THR
2
1
Y
1
A
A
O
O
HOH
HOH
317
343
2.19
1_555
4_456
1
A
ASN
50
-96.82
32.64
1
A
ILE
145
-101.21
56.13
1
A
ASN
147
65.10
164.64
1
A
SER
152
-165.89
-166.63
1
A
LYS
213
-176.42
134.41
1
A
LYS
221
63.40
-150.77
PROTEIN_REP.PARAM
TOPHCSDX.PRO
TIP3P.PARAMETER
TIP3P.TOPOLOGY
20.7
0.00
0.00
0.00
0.00
0.00
0.00
0.245
0.010
0.174
0.174
2.20
10.00
641
12742
5.0
89.3
RANDOM
100000.00
0.10
1
RESTRAINED
3.0
0.30
0.22
5.00
0.28
0.23
2.20
10.00
130
2043
1
0
1912
0.007
1.2
26.2
0.60
2.08
1.50
3.22
2.00
3.68
2.00
5.26
2.50
0.27
0.046
0.236
2.28
34
916
10
3.6
68.3
23.5
2.127
42.60
1ES3
14472
14472
0.0
0.0
0.044
1
4.21
3.47
90.6
0.183
2.127
2.203
730
1
3.47
46.8
data scaling
SAINT
data reduction
SAINT
phasing
AMoRE
refinement
X-PLOR
3.851
C98A mutant of streptomyces K15 DD-transpeptidase
1
N
N
2
N
N
3
N
N
The biological assembly is a monomer
A
GLY
34
A
GLY
34
HELX_P
A
THR
36
A
THR
36
5
1
3
A
THR
37
A
THR
37
HELX_P
A
ALA
47
A
ALA
47
1
2
11
A
GLN
60
A
GLN
60
HELX_P
A
ASN
71
A
ASN
71
1
3
12
A
VAL
85
A
VAL
85
HELX_P
A
LEU
94
A
LEU
94
1
4
10
A
GLY
97
A
GLY
97
HELX_P
A
GLY
109
A
GLY
109
1
5
13
A
THR
113
A
THR
113
HELX_P
A
LEU
132
A
LEU
132
1
6
20
A
THR
153
A
THR
153
HELX_P
A
MET
165
A
MET
165
1
7
13
A
ASN
167
A
ASN
167
HELX_P
A
LYS
175
A
LYS
175
1
8
9
A
GLY
201
A
GLY
201
HELX_P
A
TYR
206
A
TYR
206
1
9
6
A
SER
244
A
SER
244
HELX_P
A
LEU
262
A
LEU
262
1
10
19
HYDROLASE
PENICILLIN-BINDING, DD-TRANSPEPTIDASE, SERINE PEPTIDASE, BETA-LACTAMASE, HYDROLASE CARBOXYPEPTIDASE, HYDROLASE
A
GLY
211
A
GLY
211
1
A
VAL
212
A
VAL
212
2.19
DACX_STRSK
UNP
1
30
P39042
VTKPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANKPSQAHLIVG
DKVTVRQLLYGLMLPSGCDAAYALADKYGSGSQAAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRHLTKI
ASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVL
ASTSIPARESDATKIMNYGFAL
30
291
1ES3
1
262
P39042
A
1
1
262
1
LYS
conflict
ASN
71
1ES3
A
P39042
UNP
100
71
1
PRO
conflict
ALA
72
1ES3
A
P39042
UNP
101
72
1
CYS
engineered mutation
ALA
98
1ES3
A
P39042
UNP
127
98
1
GLN
conflict
THR
113
1ES3
A
P39042
UNP
142
113
1
ALA
conflict
ARG
114
1ES3
A
P39042
UNP
143
114
1
HIS
conflict
ASP
156
1ES3
A
P39042
UNP
185
156
5
2
2
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
21
A
THR
21
A
LYS
25
A
LYS
25
A
GLY
10
A
GLY
10
A
ASN
15
A
ASN
15
A
LYS
233
A
LYS
233
A
SER
242
A
SER
242
A
TYR
222
A
TYR
222
A
ARG
230
A
ARG
230
A
ALA
209
A
ALA
209
A
GLY
215
A
GLY
215
A
ARG
31
A
ARG
31
A
SER
32
A
SER
32
A
TYR
151
A
TYR
151
A
SER
152
A
SER
152
A
LYS
56
A
LYS
56
A
THR
58
A
THR
58
A
LYS
82
A
LYS
82
A
THR
84
A
THR
84
A
ALA
178
A
ALA
178
A
TYR
179
A
TYR
179
A
TRP
196
A
TRP
196
A
LYS
197
A
LYS
197
A
LYS
182
A
LYS
182
A
VAL
184
A
VAL
184
A
ILE
190
A
ILE
190
A
THR
192
A
THR
192
BINDING SITE FOR RESIDUE NA A 600
A
NA
600
Software
3
A
THR
214
A
THR
214
3
1_555
A
SER
216
A
SER
216
3
1_555
A
HOH
336
C
HOH
3
1_555
19
P 21 21 21