0.005157
0.000000
0.002124
0.000000
0.019382
0.000000
0.000000
0.000000
0.008905
0.00000
0.00000
0.00000
Contreras-Martel, C.
Dahout-Gonzalez, C.
Dos-Santos-Martins, A.
Kotnik, M.
Dessen, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
112.38
90.00
193.897
51.593
121.440
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
Cl -1
35.453
CHLORIDE ION
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
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
CL
N
75
N
N
N
76
S
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
C
N
81
N
C
N
82
N
O
N
83
N
N
N
84
N
O
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
O
N
104
N
O
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
N
N
115
N
C
N
116
N
C
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
Y
129
N
C
Y
130
N
N
Y
131
N
C
Y
132
N
C
Y
133
N
N
N
134
N
O
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
N
N
149
S
C
N
150
N
C
N
151
N
O
N
152
S
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
O
N
157
N
H
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
H
N
169
N
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
O
N
179
N
H
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
N
N
193
S
C
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
N
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
H
N
216
N
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
S
N
224
N
C
N
225
N
O
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
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
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
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
O
N
283
N
O
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
R
C
N
296
N
O
N
297
N
C
N
298
N
O
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
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
N
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
N
322
N
O
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
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
N
346
N
O
N
347
N
O
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
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
O
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
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
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
doub
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
doub
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
doub
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
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
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
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
doub
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
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
doub
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
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
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
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
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
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
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
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
doub
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
387
899
10.1016/J.JMB.2009.02.024
19233207
Pbp Active Site Flexibility as the Key Mechanism for Beta-Lactam Resistance in Pneumococci
2009
US
Antimicrob.Agents Chemother.
AMACCQ
0788
0066-4804
48
1848
10.1128/AAC.48.5.1848-1855.2004
15105143
Biochemical Characterization of Streptococcus Pneumoniae Penicillin-Binding Protein 2B and its Implication in Beta-Lactam Resistance
2004
10.2210/pdb2waf/pdb
pdb_00002waf
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
1999-07-09
ADSC CCD
SINGLE WAVELENGTH
M
x-ray
1
0.9312
1.0
ID14-4
ESRF
0.9312
SYNCHROTRON
ESRF BEAMLINE ID14-4
74210.742
PENICILLIN-BINDING PROTEIN 2B
3.4.-.-
1
nat
polymer
35.453
CHLORIDE ION
2
syn
non-polymer
18.015
water
11
nat
water
no
no
MRKFNSHSIPIRLNLLFSIVILLFMTIIGRLLYMQVLNKDFYEKKLASASQTKITSSSARGEIYDASGKPLVENTLKQVV
SFTRSNKMTATDLKETAKKLLTYVSISSPNLTERQLADYYLADPEIYKKIVEALPSEKRLDSDGNRLSESELYNNAVDSV
QTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKVLETSLSSIVGSVSSE
KAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSV
DALLKSYFNSELENGGAKYSEGVYAVALNPKTGAVLSMSGIKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENG
VLSGNQTLTDQSIVFQGSAPINSWYTQAYGSFPITAVQALEYSSNTYMVQTALGLMGQTYQPNMFVGTSNLESAMEKLRS
TFGEYGLGTATGIDLPDESTGFVPKEYSFANYITNAFGQFDNYTPMQLAQYVATIANNGVRVAPRIVEGIYGNNDKGGLG
DLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGLTTGRAFSNGALVSISGKTGTAESYVADGQQATNTNAVAYAPS
DNPQIAVAVVFPHNTNLTNGVGPSIARDIINLYQKYHPMNHH
MRKFNSHSIPIRLNLLFSIVILLFMTIIGRLLYMQVLNKDFYEKKLASASQTKITSSSARGEIYDASGKPLVENTLKQVV
SFTRSNKMTATDLKETAKKLLTYVSISSPNLTERQLADYYLADPEIYKKIVEALPSEKRLDSDGNRLSESELYNNAVDSV
QTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKVLETSLSSIVGSVSSE
KAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSV
DALLKSYFNSELENGGAKYSEGVYAVALNPKTGAVLSMSGIKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENG
VLSGNQTLTDQSIVFQGSAPINSWYTQAYGSFPITAVQALEYSSNTYMVQTALGLMGQTYQPNMFVGTSNLESAMEKLRS
TFGEYGLGTATGIDLPDESTGFVPKEYSFANYITNAFGQFDNYTPMQLAQYVATIANNGVRVAPRIVEGIYGNNDKGGLG
DLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGLTTGRAFSNGALVSISGKTGTAESYVADGQQATNTNAVAYAPS
DNPQIAVAVVFPHNTNLTNGVGPSIARDIINLYQKYHPMNHH
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
171101
STREPTOCOCCUS PNEUMONIAE
R6
1
3.8
67.65
NONE
8
1.4M (NH4)2SO4, pH 8
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_site
repository
Initial release
Advisory
Version format compliance
Database references
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2009-02-24
1
1
2011-07-13
1
2
2014-02-19
1
3
2023-12-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
PDBE
Y
PDBE
2009-02-05
REL
REL
CL
CHLORIDE ION
HOH
water
2WAD
PDB ENTRY 2WAD
PDB
experimental model
CL
700
2
CL
CL
700
A
CL
701
2
CL
CL
701
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
n
9
9
A
n
10
10
A
n
11
11
A
n
12
12
A
n
13
13
A
n
14
14
A
n
15
15
A
n
16
16
A
n
17
17
A
n
18
18
A
n
19
19
A
n
20
20
A
n
21
21
A
n
22
22
A
n
23
23
A
n
24
24
A
n
25
25
A
n
26
26
A
n
27
27
A
n
28
28
A
n
29
29
A
n
30
30
A
n
31
31
A
n
32
32
A
n
33
33
A
n
34
34
A
n
35
35
A
n
36
36
A
n
37
37
A
n
38
38
A
n
39
39
A
n
40
40
A
n
41
41
A
n
42
42
A
n
43
43
A
n
44
44
A
n
45
45
A
n
46
46
A
n
47
47
A
n
48
48
A
n
49
49
A
n
50
50
A
n
51
51
A
THR
52
n
52
THR
52
A
LYS
53
n
53
LYS
53
A
ILE
54
n
54
ILE
54
A
THR
55
n
55
THR
55
A
SER
56
n
56
SER
56
A
SER
57
n
57
SER
57
A
SER
58
n
58
SER
58
A
ALA
59
n
59
ALA
59
A
ARG
60
n
60
ARG
60
A
GLY
61
n
61
GLY
61
A
GLU
62
n
62
GLU
62
A
ILE
63
n
63
ILE
63
A
TYR
64
n
64
TYR
64
A
ASP
65
n
65
ASP
65
A
ALA
66
n
66
ALA
66
A
SER
67
n
67
SER
67
A
GLY
68
n
68
GLY
68
A
LYS
69
n
69
LYS
69
A
PRO
70
n
70
PRO
70
A
LEU
71
n
71
LEU
71
A
VAL
72
n
72
VAL
72
A
GLU
73
n
73
GLU
73
A
ASN
74
n
74
ASN
74
A
THR
75
n
75
THR
75
A
LEU
76
n
76
LEU
76
A
LYS
77
n
77
LYS
77
A
GLN
78
n
78
GLN
78
A
VAL
79
n
79
VAL
79
A
VAL
80
n
80
VAL
80
A
SER
81
n
81
SER
81
A
PHE
82
n
82
PHE
82
A
THR
83
n
83
THR
83
A
ARG
84
n
84
ARG
84
A
SER
85
n
85
SER
85
A
ASN
86
n
86
ASN
86
A
LYS
87
n
87
LYS
87
A
MET
88
n
88
MET
88
A
THR
89
n
89
THR
89
A
ALA
90
n
90
ALA
90
A
THR
91
n
91
THR
91
A
ASP
92
n
92
ASP
92
A
LEU
93
n
93
LEU
93
A
LYS
94
n
94
LYS
94
A
GLU
95
n
95
GLU
95
A
THR
96
n
96
THR
96
A
ALA
97
n
97
ALA
97
A
LYS
98
n
98
LYS
98
A
LYS
99
n
99
LYS
99
A
LEU
100
n
100
LEU
100
A
LEU
101
n
101
LEU
101
A
THR
102
n
102
THR
102
A
TYR
103
n
103
TYR
103
A
VAL
104
n
104
VAL
104
A
SER
105
n
105
SER
105
A
ILE
106
n
106
ILE
106
A
SER
107
n
107
SER
107
A
SER
108
n
108
SER
108
A
PRO
109
n
109
PRO
109
A
ASN
110
n
110
ASN
110
A
LEU
111
n
111
LEU
111
A
THR
112
n
112
THR
112
A
GLU
113
n
113
GLU
113
A
ARG
114
n
114
ARG
114
A
GLN
115
n
115
GLN
115
A
LEU
116
n
116
LEU
116
A
ALA
117
n
117
ALA
117
A
ASP
118
n
118
ASP
118
A
TYR
119
n
119
TYR
119
A
TYR
120
n
120
TYR
120
A
LEU
121
n
121
LEU
121
A
ALA
122
n
122
ALA
122
A
ASP
123
n
123
ASP
123
A
PRO
124
n
124
PRO
124
A
GLU
125
n
125
GLU
125
A
ILE
126
n
126
ILE
126
A
TYR
127
n
127
TYR
127
A
LYS
128
n
128
LYS
128
A
LYS
129
n
129
LYS
129
A
ILE
130
n
130
ILE
130
A
VAL
131
n
131
VAL
131
A
GLU
132
n
132
GLU
132
A
ALA
133
n
133
ALA
133
A
LEU
134
n
134
LEU
134
A
PRO
135
n
135
PRO
135
A
SER
136
n
136
SER
136
A
n
137
137
A
n
138
138
A
n
139
139
A
n
140
140
A
n
141
141
A
n
142
142
A
n
143
143
A
n
144
144
A
n
145
145
A
n
146
146
A
n
147
147
A
n
148
148
A
GLU
149
n
149
GLU
149
A
SER
150
n
150
SER
150
A
GLU
151
n
151
GLU
151
A
LEU
152
n
152
LEU
152
A
TYR
153
n
153
TYR
153
A
ASN
154
n
154
ASN
154
A
ASN
155
n
155
ASN
155
A
ALA
156
n
156
ALA
156
A
VAL
157
n
157
VAL
157
A
ASP
158
n
158
ASP
158
A
SER
159
n
159
SER
159
A
VAL
160
n
160
VAL
160
A
GLN
161
n
161
GLN
161
A
THR
162
n
162
THR
162
A
SER
163
n
163
SER
163
A
GLN
164
n
164
GLN
164
A
LEU
165
n
165
LEU
165
A
ASN
166
n
166
ASN
166
A
TYR
167
n
167
TYR
167
A
THR
168
n
168
THR
168
A
GLU
169
n
169
GLU
169
A
ASP
170
n
170
ASP
170
A
GLU
171
n
171
GLU
171
A
LYS
172
n
172
LYS
172
A
LYS
173
n
173
LYS
173
A
GLU
174
n
174
GLU
174
A
ILE
175
n
175
ILE
175
A
TYR
176
n
176
TYR
176
A
LEU
177
n
177
LEU
177
A
PHE
178
n
178
PHE
178
A
SER
179
n
179
SER
179
A
GLN
180
n
180
GLN
180
A
LEU
181
n
181
LEU
181
A
ASN
182
n
182
ASN
182
A
ALA
183
n
183
ALA
183
A
VAL
184
n
184
VAL
184
A
GLY
185
n
185
GLY
185
A
ASN
186
n
186
ASN
186
A
PHE
187
n
187
PHE
187
A
ALA
188
n
188
ALA
188
A
THR
189
n
189
THR
189
A
GLY
190
n
190
GLY
190
A
THR
191
n
191
THR
191
A
ILE
192
n
192
ILE
192
A
ALA
193
n
193
ALA
193
A
THR
194
n
194
THR
194
A
ASP
195
n
195
ASP
195
A
PRO
196
n
196
PRO
196
A
LEU
197
n
197
LEU
197
A
ASN
198
n
198
ASN
198
A
ASP
199
n
199
ASP
199
A
SER
200
n
200
SER
200
A
GLN
201
n
201
GLN
201
A
VAL
202
n
202
VAL
202
A
ALA
203
n
203
ALA
203
A
VAL
204
n
204
VAL
204
A
ILE
205
n
205
ILE
205
A
ALA
206
n
206
ALA
206
A
SER
207
n
207
SER
207
A
ILE
208
n
208
ILE
208
A
SER
209
n
209
SER
209
A
LYS
210
n
210
LYS
210
A
GLU
211
n
211
GLU
211
A
MET
212
n
212
MET
212
A
PRO
213
n
213
PRO
213
A
GLY
214
n
214
GLY
214
A
ILE
215
n
215
ILE
215
A
SER
216
n
216
SER
216
A
ILE
217
n
217
ILE
217
A
SER
218
n
218
SER
218
A
THR
219
n
219
THR
219
A
SER
220
n
220
SER
220
A
TRP
221
n
221
TRP
221
A
ASP
222
n
222
ASP
222
A
ARG
223
n
223
ARG
223
A
LYS
224
n
224
LYS
224
A
VAL
225
n
225
VAL
225
A
LEU
226
n
226
LEU
226
A
GLU
227
n
227
GLU
227
A
THR
228
n
228
THR
228
A
SER
229
n
229
SER
229
A
LEU
230
n
230
LEU
230
A
SER
231
n
231
SER
231
A
SER
232
n
232
SER
232
A
ILE
233
n
233
ILE
233
A
VAL
234
n
234
VAL
234
A
GLY
235
n
235
GLY
235
A
SER
236
n
236
SER
236
A
VAL
237
n
237
VAL
237
A
SER
238
n
238
SER
238
A
SER
239
n
239
SER
239
A
GLU
240
n
240
GLU
240
A
LYS
241
n
241
LYS
241
A
ALA
242
n
242
ALA
242
A
GLY
243
n
243
GLY
243
A
LEU
244
n
244
LEU
244
A
PRO
245
n
245
PRO
245
A
ALA
246
n
246
ALA
246
A
GLU
247
n
247
GLU
247
A
GLU
248
n
248
GLU
248
A
ALA
249
n
249
ALA
249
A
GLU
250
n
250
GLU
250
A
ALA
251
n
251
ALA
251
A
TYR
252
n
252
TYR
252
A
LEU
253
n
253
LEU
253
A
LYS
254
n
254
LYS
254
A
LYS
255
n
255
LYS
255
A
GLY
256
n
256
GLY
256
A
TYR
257
n
257
TYR
257
A
SER
258
n
258
SER
258
A
LEU
259
n
259
LEU
259
A
ASN
260
n
260
ASN
260
A
ASP
261
n
261
ASP
261
A
ARG
262
n
262
ARG
262
A
VAL
263
n
263
VAL
263
A
GLY
264
n
264
GLY
264
A
THR
265
n
265
THR
265
A
SER
266
n
266
SER
266
A
TYR
267
n
267
TYR
267
A
LEU
268
n
268
LEU
268
A
GLU
269
n
269
GLU
269
A
LYS
270
n
270
LYS
270
A
GLN
271
n
271
GLN
271
A
TYR
272
n
272
TYR
272
A
GLU
273
n
273
GLU
273
A
GLU
274
n
274
GLU
274
A
THR
275
n
275
THR
275
A
LEU
276
n
276
LEU
276
A
GLN
277
n
277
GLN
277
A
GLY
278
n
278
GLY
278
A
LYS
279
n
279
LYS
279
A
ARG
280
n
280
ARG
280
A
SER
281
n
281
SER
281
A
VAL
282
n
282
VAL
282
A
LYS
283
n
283
LYS
283
A
GLU
284
n
284
GLU
284
A
ILE
285
n
285
ILE
285
A
HIS
286
n
286
HIS
286
A
LEU
287
n
287
LEU
287
A
ASP
288
n
288
ASP
288
A
LYS
289
n
289
LYS
289
A
TYR
290
n
290
TYR
290
A
GLY
291
n
291
GLY
291
A
ASN
292
n
292
ASN
292
A
MET
293
n
293
MET
293
A
GLU
294
n
294
GLU
294
A
SER
295
n
295
SER
295
A
VAL
296
n
296
VAL
296
A
ASP
297
n
297
ASP
297
A
THR
298
n
298
THR
298
A
ILE
299
n
299
ILE
299
A
GLU
300
n
300
GLU
300
A
GLU
301
n
301
GLU
301
A
GLY
302
n
302
GLY
302
A
SER
303
n
303
SER
303
A
LYS
304
n
304
LYS
304
A
GLY
305
n
305
GLY
305
A
ASN
306
n
306
ASN
306
A
ASN
307
n
307
ASN
307
A
ILE
308
n
308
ILE
308
A
LYS
309
n
309
LYS
309
A
LEU
310
n
310
LEU
310
A
THR
311
n
311
THR
311
A
ILE
312
n
312
ILE
312
A
ASP
313
n
313
ASP
313
A
LEU
314
n
314
LEU
314
A
ALA
315
n
315
ALA
315
A
PHE
316
n
316
PHE
316
A
GLN
317
n
317
GLN
317
A
ASP
318
n
318
ASP
318
A
SER
319
n
319
SER
319
A
VAL
320
n
320
VAL
320
A
ASP
321
n
321
ASP
321
A
ALA
322
n
322
ALA
322
A
LEU
323
n
323
LEU
323
A
LEU
324
n
324
LEU
324
A
LYS
325
n
325
LYS
325
A
SER
326
n
326
SER
326
A
TYR
327
n
327
TYR
327
A
PHE
328
n
328
PHE
328
A
ASN
329
n
329
ASN
329
A
SER
330
n
330
SER
330
A
GLU
331
n
331
GLU
331
A
LEU
332
n
332
LEU
332
A
GLU
333
n
333
GLU
333
A
ASN
334
n
334
ASN
334
A
GLY
335
n
335
GLY
335
A
GLY
336
n
336
GLY
336
A
ALA
337
n
337
ALA
337
A
LYS
338
n
338
LYS
338
A
TYR
339
n
339
TYR
339
A
SER
340
n
340
SER
340
A
GLU
341
n
341
GLU
341
A
GLY
342
n
342
GLY
342
A
VAL
343
n
343
VAL
343
A
TYR
344
n
344
TYR
344
A
ALA
345
n
345
ALA
345
A
VAL
346
n
346
VAL
346
A
ALA
347
n
347
ALA
347
A
LEU
348
n
348
LEU
348
A
ASN
349
n
349
ASN
349
A
PRO
350
n
350
PRO
350
A
LYS
351
n
351
LYS
351
A
THR
352
n
352
THR
352
A
GLY
353
n
353
GLY
353
A
ALA
354
n
354
ALA
354
A
VAL
355
n
355
VAL
355
A
LEU
356
n
356
LEU
356
A
SER
357
n
357
SER
357
A
MET
358
n
358
MET
358
A
SER
359
n
359
SER
359
A
GLY
360
n
360
GLY
360
A
ILE
361
n
361
ILE
361
A
LYS
362
n
362
LYS
362
A
HIS
363
n
363
HIS
363
A
ASP
364
n
364
ASP
364
A
LEU
365
n
365
LEU
365
A
LYS
366
n
366
LYS
366
A
THR
367
n
367
THR
367
A
GLY
368
n
368
GLY
368
A
GLU
369
n
369
GLU
369
A
LEU
370
n
370
LEU
370
A
THR
371
n
371
THR
371
A
PRO
372
n
372
PRO
372
A
ASP
373
n
373
ASP
373
A
SER
374
n
374
SER
374
A
LEU
375
n
375
LEU
375
A
GLY
376
n
376
GLY
376
A
THR
377
n
377
THR
377
A
VAL
378
n
378
VAL
378
A
THR
379
n
379
THR
379
A
ASN
380
n
380
ASN
380
A
VAL
381
n
381
VAL
381
A
PHE
382
n
382
PHE
382
A
VAL
383
n
383
VAL
383
A
PRO
384
n
384
PRO
384
A
GLY
385
n
385
GLY
385
A
SER
386
n
386
SER
386
A
VAL
387
n
387
VAL
387
A
VAL
388
n
388
VAL
388
A
LYS
389
n
389
LYS
389
A
ALA
390
n
390
ALA
390
A
ALA
391
n
391
ALA
391
A
THR
392
n
392
THR
392
A
ILE
393
n
393
ILE
393
A
SER
394
n
394
SER
394
A
SER
395
n
395
SER
395
A
GLY
396
n
396
GLY
396
A
TRP
397
n
397
TRP
397
A
GLU
398
n
398
GLU
398
A
ASN
399
n
399
ASN
399
A
GLY
400
n
400
GLY
400
A
VAL
401
n
401
VAL
401
A
LEU
402
n
402
LEU
402
A
SER
403
n
403
SER
403
A
GLY
404
n
404
GLY
404
A
ASN
405
n
405
ASN
405
A
GLN
406
n
406
GLN
406
A
THR
407
n
407
THR
407
A
LEU
408
n
408
LEU
408
A
THR
409
n
409
THR
409
A
ASP
410
n
410
ASP
410
A
GLN
411
n
411
GLN
411
A
SER
412
n
412
SER
412
A
ILE
413
n
413
ILE
413
A
VAL
414
n
414
VAL
414
A
PHE
415
n
415
PHE
415
A
GLN
416
n
416
GLN
416
A
GLY
417
n
417
GLY
417
A
SER
418
n
418
SER
418
A
ALA
419
n
419
ALA
419
A
PRO
420
n
420
PRO
420
A
ILE
421
n
421
ILE
421
A
ASN
422
n
422
ASN
422
A
SER
423
n
423
SER
423
A
TRP
424
n
424
TRP
424
A
TYR
425
n
425
TYR
425
A
THR
426
n
426
THR
426
A
GLN
427
n
427
GLN
427
A
ALA
428
n
428
ALA
428
A
TYR
429
n
429
TYR
429
A
GLY
430
n
430
GLY
430
A
SER
431
n
431
SER
431
A
PHE
432
n
432
PHE
432
A
PRO
433
n
433
PRO
433
A
ILE
434
n
434
ILE
434
A
THR
435
n
435
THR
435
A
ALA
436
n
436
ALA
436
A
VAL
437
n
437
VAL
437
A
GLN
438
n
438
GLN
438
A
ALA
439
n
439
ALA
439
A
LEU
440
n
440
LEU
440
A
GLU
441
n
441
GLU
441
A
TYR
442
n
442
TYR
442
A
SER
443
n
443
SER
443
A
SER
444
n
444
SER
444
A
ASN
445
n
445
ASN
445
A
THR
446
n
446
THR
446
A
TYR
447
n
447
TYR
447
A
MET
448
n
448
MET
448
A
VAL
449
n
449
VAL
449
A
GLN
450
n
450
GLN
450
A
THR
451
n
451
THR
451
A
ALA
452
n
452
ALA
452
A
LEU
453
n
453
LEU
453
A
GLY
454
n
454
GLY
454
A
LEU
455
n
455
LEU
455
A
MET
456
n
456
MET
456
A
GLY
457
n
457
GLY
457
A
GLN
458
n
458
GLN
458
A
THR
459
n
459
THR
459
A
TYR
460
n
460
TYR
460
A
GLN
461
n
461
GLN
461
A
PRO
462
n
462
PRO
462
A
ASN
463
n
463
ASN
463
A
MET
464
n
464
MET
464
A
PHE
465
n
465
PHE
465
A
VAL
466
n
466
VAL
466
A
GLY
467
n
467
GLY
467
A
THR
468
n
468
THR
468
A
SER
469
n
469
SER
469
A
ASN
470
n
470
ASN
470
A
LEU
471
n
471
LEU
471
A
GLU
472
n
472
GLU
472
A
SER
473
n
473
SER
473
A
ALA
474
n
474
ALA
474
A
MET
475
n
475
MET
475
A
GLU
476
n
476
GLU
476
A
LYS
477
n
477
LYS
477
A
LEU
478
n
478
LEU
478
A
ARG
479
n
479
ARG
479
A
SER
480
n
480
SER
480
A
THR
481
n
481
THR
481
A
PHE
482
n
482
PHE
482
A
GLY
483
n
483
GLY
483
A
GLU
484
n
484
GLU
484
A
TYR
485
n
485
TYR
485
A
GLY
486
n
486
GLY
486
A
LEU
487
n
487
LEU
487
A
GLY
488
n
488
GLY
488
A
THR
489
n
489
THR
489
A
ALA
490
n
490
ALA
490
A
THR
491
n
491
THR
491
A
GLY
492
n
492
GLY
492
A
ILE
493
n
493
ILE
493
A
ASP
494
n
494
ASP
494
A
LEU
495
n
495
LEU
495
A
PRO
496
n
496
PRO
496
A
ASP
497
n
497
ASP
497
A
GLU
498
n
498
GLU
498
A
SER
499
n
499
SER
499
A
THR
500
n
500
THR
500
A
GLY
501
n
501
GLY
501
A
PHE
502
n
502
PHE
502
A
VAL
503
n
503
VAL
503
A
PRO
504
n
504
PRO
504
A
LYS
505
n
505
LYS
505
A
GLU
506
n
506
GLU
506
A
TYR
507
n
507
TYR
507
A
SER
508
n
508
SER
508
A
PHE
509
n
509
PHE
509
A
ALA
510
n
510
ALA
510
A
ASN
511
n
511
ASN
511
A
TYR
512
n
512
TYR
512
A
ILE
513
n
513
ILE
513
A
THR
514
n
514
THR
514
A
ASN
515
n
515
ASN
515
A
ALA
516
n
516
ALA
516
A
PHE
517
n
517
PHE
517
A
GLY
518
n
518
GLY
518
A
GLN
519
n
519
GLN
519
A
PHE
520
n
520
PHE
520
A
ASP
521
n
521
ASP
521
A
ASN
522
n
522
ASN
522
A
TYR
523
n
523
TYR
523
A
THR
524
n
524
THR
524
A
PRO
525
n
525
PRO
525
A
MET
526
n
526
MET
526
A
GLN
527
n
527
GLN
527
A
LEU
528
n
528
LEU
528
A
ALA
529
n
529
ALA
529
A
GLN
530
n
530
GLN
530
A
TYR
531
n
531
TYR
531
A
VAL
532
n
532
VAL
532
A
ALA
533
n
533
ALA
533
A
THR
534
n
534
THR
534
A
ILE
535
n
535
ILE
535
A
ALA
536
n
536
ALA
536
A
ASN
537
n
537
ASN
537
A
ASN
538
n
538
ASN
538
A
GLY
539
n
539
GLY
539
A
VAL
540
n
540
VAL
540
A
ARG
541
n
541
ARG
541
A
VAL
542
n
542
VAL
542
A
ALA
543
n
543
ALA
543
A
PRO
544
n
544
PRO
544
A
ARG
545
n
545
ARG
545
A
ILE
546
n
546
ILE
546
A
VAL
547
n
547
VAL
547
A
GLU
548
n
548
GLU
548
A
GLY
549
n
549
GLY
549
A
ILE
550
n
550
ILE
550
A
TYR
551
n
551
TYR
551
A
GLY
552
n
552
GLY
552
A
ASN
553
n
553
ASN
553
A
ASN
554
n
554
ASN
554
A
ASP
555
n
555
ASP
555
A
LYS
556
n
556
LYS
556
A
GLY
557
n
557
GLY
557
A
GLY
558
n
558
GLY
558
A
LEU
559
n
559
LEU
559
A
GLY
560
n
560
GLY
560
A
ASP
561
n
561
ASP
561
A
LEU
562
n
562
LEU
562
A
ILE
563
n
563
ILE
563
A
GLN
564
n
564
GLN
564
A
GLN
565
n
565
GLN
565
A
LEU
566
n
566
LEU
566
A
GLN
567
n
567
GLN
567
A
PRO
568
n
568
PRO
568
A
THR
569
n
569
THR
569
A
GLU
570
n
570
GLU
570
A
MET
571
n
571
MET
571
A
ASN
572
n
572
ASN
572
A
LYS
573
n
573
LYS
573
A
VAL
574
n
574
VAL
574
A
ASN
575
n
575
ASN
575
A
ILE
576
n
576
ILE
576
A
SER
577
n
577
SER
577
A
ASP
578
n
578
ASP
578
A
SER
579
n
579
SER
579
A
ASP
580
n
580
ASP
580
A
MET
581
n
581
MET
581
A
SER
582
n
582
SER
582
A
ILE
583
n
583
ILE
583
A
LEU
584
n
584
LEU
584
A
HIS
585
n
585
HIS
585
A
GLN
586
n
586
GLN
586
A
GLY
587
n
587
GLY
587
A
PHE
588
n
588
PHE
588
A
TYR
589
n
589
TYR
589
A
GLN
590
n
590
GLN
590
A
VAL
591
n
591
VAL
591
A
ALA
592
n
592
ALA
592
A
HIS
593
n
593
HIS
593
A
GLY
594
n
594
GLY
594
A
THR
595
n
595
THR
595
A
SER
596
n
596
SER
596
A
GLY
597
n
597
GLY
597
A
LEU
598
n
598
LEU
598
A
THR
599
n
599
THR
599
A
THR
600
n
600
THR
600
A
GLY
601
n
601
GLY
601
A
ARG
602
n
602
ARG
602
A
ALA
603
n
603
ALA
603
A
PHE
604
n
604
PHE
604
A
SER
605
n
605
SER
605
A
ASN
606
n
606
ASN
606
A
GLY
607
n
607
GLY
607
A
ALA
608
n
608
ALA
608
A
LEU
609
n
609
LEU
609
A
VAL
610
n
610
VAL
610
A
SER
611
n
611
SER
611
A
ILE
612
n
612
ILE
612
A
SER
613
n
613
SER
613
A
GLY
614
n
614
GLY
614
A
LYS
615
n
615
LYS
615
A
THR
616
n
616
THR
616
A
GLY
617
n
617
GLY
617
A
THR
618
n
618
THR
618
A
ALA
619
n
619
ALA
619
A
GLU
620
n
620
GLU
620
A
SER
621
n
621
SER
621
A
TYR
622
n
622
TYR
622
A
VAL
623
n
623
VAL
623
A
ALA
624
n
624
ALA
624
A
ASP
625
n
625
ASP
625
A
GLY
626
n
626
GLY
626
A
GLN
627
n
627
GLN
627
A
GLN
628
n
628
GLN
628
A
ALA
629
n
629
ALA
629
A
THR
630
n
630
THR
630
A
ASN
631
n
631
ASN
631
A
THR
632
n
632
THR
632
A
ASN
633
n
633
ASN
633
A
ALA
634
n
634
ALA
634
A
VAL
635
n
635
VAL
635
A
ALA
636
n
636
ALA
636
A
TYR
637
n
637
TYR
637
A
ALA
638
n
638
ALA
638
A
PRO
639
n
639
PRO
639
A
SER
640
n
640
SER
640
A
ASP
641
n
641
ASP
641
A
ASN
642
n
642
ASN
642
A
PRO
643
n
643
PRO
643
A
GLN
644
n
644
GLN
644
A
ILE
645
n
645
ILE
645
A
ALA
646
n
646
ALA
646
A
VAL
647
n
647
VAL
647
A
ALA
648
n
648
ALA
648
A
VAL
649
n
649
VAL
649
A
VAL
650
n
650
VAL
650
A
PHE
651
n
651
PHE
651
A
PRO
652
n
652
PRO
652
A
HIS
653
n
653
HIS
653
A
ASN
654
n
654
ASN
654
A
THR
655
n
655
THR
655
A
ASN
656
n
656
ASN
656
A
LEU
657
n
657
LEU
657
A
THR
658
n
658
THR
658
A
ASN
659
n
659
ASN
659
A
GLY
660
n
660
GLY
660
A
VAL
661
n
661
VAL
661
A
GLY
662
n
662
GLY
662
A
PRO
663
n
663
PRO
663
A
SER
664
n
664
SER
664
A
ILE
665
n
665
ILE
665
A
ALA
666
n
666
ALA
666
A
ARG
667
n
667
ARG
667
A
ASP
668
n
668
ASP
668
A
ILE
669
n
669
ILE
669
A
ILE
670
n
670
ILE
670
A
ASN
671
n
671
ASN
671
A
LEU
672
n
672
LEU
672
A
TYR
673
n
673
TYR
673
A
GLN
674
n
674
GLN
674
A
LYS
675
n
675
LYS
675
A
TYR
676
n
676
TYR
676
A
HIS
677
n
677
HIS
677
A
PRO
678
n
678
PRO
678
A
MET
679
n
679
MET
679
A
ASN
680
n
680
ASN
680
A
HIS
681
n
681
HIS
681
A
HIS
682
n
682
HIS
682
A
5.7758
3.7165
0.2679
9.8147
-1.9574
5.7870
-0.1840
0.6486
0.0543
-0.4826
-0.1728
-0.6567
-0.2666
0.1321
0.3568
0.0023
0.0149
0.1925
0.5369
-0.1430
-0.2120
refined
18.4994
-5.6885
-43.4724
X-RAY DIFFRACTION
10.1276
1.3193
-3.8873
0.4007
0.0384
2.7893
-0.4412
0.2978
-0.8039
-0.1814
0.1239
-0.0598
0.4606
0.2848
0.3172
-0.0009
-0.0076
0.0294
0.0490
-0.0860
0.0771
refined
-0.0363
-15.0495
-19.7435
X-RAY DIFFRACTION
6.0374
-0.9879
-0.6026
2.6440
1.1196
5.2117
-0.2301
-0.1120
0.5100
0.0743
0.2196
-0.2126
-0.5154
-0.0200
0.0105
-0.5965
-0.0487
-0.0618
-0.6228
0.1172
-0.3896
refined
-32.3311
0.8373
4.2958
X-RAY DIFFRACTION
A
86
A
185
X-RAY DIFFRACTION
1
A
196
A
213
X-RAY DIFFRACTION
1
A
52
A
85
X-RAY DIFFRACTION
2
A
186
A
195
X-RAY DIFFRACTION
2
A
214
A
310
X-RAY DIFFRACTION
2
A
548
A
566
X-RAY DIFFRACTION
2
A
311
A
547
X-RAY DIFFRACTION
3
A
567
A
682
X-RAY DIFFRACTION
3
author_and_software_defined_assembly
PQS
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
N
SER
58
A
N
SER
58
A
O
GLY
278
A
O
GLY
278
A
N
TYR
64
A
N
TYR
64
A
O
ILE
308
A
O
ILE
308
A
O
LYS
309
A
O
LYS
309
A
N
GLU
548
A
N
GLU
548
A
O
GLY
552
A
O
GLY
552
A
N
GLY
560
A
N
GLY
560
A
N
GLY
190
A
N
GLY
190
A
O
PHE
82
A
O
PHE
82
A
N
SER
81
A
N
SER
81
A
O
SER
216
A
O
SER
216
A
O
SER
236
A
O
SER
236
A
N
THR
265
A
N
THR
265
A
O
HIS
286
A
O
HIS
286
A
N
GLU
294
A
N
GLU
294
A
N
THR
371
A
N
THR
371
A
O
LYS
362
A
O
LYS
362
A
N
ILE
361
A
N
ILE
361
A
O
VAL
343
A
O
VAL
343
A
N
LEU
348
A
N
LEU
348
A
O
ALA
646
A
O
ALA
646
A
N
VAL
649
A
N
VAL
649
A
O
ALA
634
A
O
ALA
634
A
N
TYR
637
A
N
TYR
637
A
O
SER
613
A
O
SER
613
A
N
ASP
410
A
N
ASP
410
A
O
PHE
432
A
O
PHE
432
A
O
ARG
541
A
O
ARG
541
A
N
MET
571
A
N
MET
571
A
N
SER
621
A
N
SER
621
A
O
ALA
629
A
O
ALA
629
1
A
MET
1
A
MET
1
1
Y
1
A
ARG
2
A
ARG
2
1
Y
1
A
LYS
3
A
LYS
3
1
Y
1
A
PHE
4
A
PHE
4
1
Y
1
A
ASN
5
A
ASN
5
1
Y
1
A
SER
6
A
SER
6
1
Y
1
A
HIS
7
A
HIS
7
1
Y
1
A
SER
8
A
SER
8
1
Y
1
A
ILE
9
A
ILE
9
1
Y
1
A
PRO
10
A
PRO
10
1
Y
1
A
ILE
11
A
ILE
11
1
Y
1
A
ARG
12
A
ARG
12
1
Y
1
A
LEU
13
A
LEU
13
1
Y
1
A
ASN
14
A
ASN
14
1
Y
1
A
LEU
15
A
LEU
15
1
Y
1
A
LEU
16
A
LEU
16
1
Y
1
A
PHE
17
A
PHE
17
1
Y
1
A
SER
18
A
SER
18
1
Y
1
A
ILE
19
A
ILE
19
1
Y
1
A
VAL
20
A
VAL
20
1
Y
1
A
ILE
21
A
ILE
21
1
Y
1
A
LEU
22
A
LEU
22
1
Y
1
A
LEU
23
A
LEU
23
1
Y
1
A
PHE
24
A
PHE
24
1
Y
1
A
MET
25
A
MET
25
1
Y
1
A
THR
26
A
THR
26
1
Y
1
A
ILE
27
A
ILE
27
1
Y
1
A
ILE
28
A
ILE
28
1
Y
1
A
GLY
29
A
GLY
29
1
Y
1
A
ARG
30
A
ARG
30
1
Y
1
A
LEU
31
A
LEU
31
1
Y
1
A
LEU
32
A
LEU
32
1
Y
1
A
TYR
33
A
TYR
33
1
Y
1
A
MET
34
A
MET
34
1
Y
1
A
GLN
35
A
GLN
35
1
Y
1
A
VAL
36
A
VAL
36
1
Y
1
A
LEU
37
A
LEU
37
1
Y
1
A
ASN
38
A
ASN
38
1
Y
1
A
LYS
39
A
LYS
39
1
Y
1
A
ASP
40
A
ASP
40
1
Y
1
A
PHE
41
A
PHE
41
1
Y
1
A
TYR
42
A
TYR
42
1
Y
1
A
GLU
43
A
GLU
43
1
Y
1
A
LYS
44
A
LYS
44
1
Y
1
A
LYS
45
A
LYS
45
1
Y
1
A
LEU
46
A
LEU
46
1
Y
1
A
ALA
47
A
ALA
47
1
Y
1
A
SER
48
A
SER
48
1
Y
1
A
ALA
49
A
ALA
49
1
Y
1
A
SER
50
A
SER
50
1
Y
1
A
GLN
51
A
GLN
51
1
Y
1
A
GLU
137
A
GLU
137
1
Y
1
A
LYS
138
A
LYS
138
1
Y
1
A
ARG
139
A
ARG
139
1
Y
1
A
LEU
140
A
LEU
140
1
Y
1
A
ASP
141
A
ASP
141
1
Y
1
A
SER
142
A
SER
142
1
Y
1
A
ASP
143
A
ASP
143
1
Y
1
A
GLY
144
A
GLY
144
1
Y
1
A
ASN
145
A
ASN
145
1
Y
1
A
ARG
146
A
ARG
146
1
Y
1
A
LEU
147
A
LEU
147
1
Y
1
A
SER
148
A
SER
148
1
Y
1
A
A
O
OD2
SER
ASP
105
195
1.65
1
A
A
OE2
CB
GLU
SER
113
163
1.74
1
A
A
OG
OD1
SER
ASN
258
260
1.85
1
A
A
OG
ND2
SER
ASN
412
422
1.95
1
A
A
NE2
O
GLN
ASN
416
463
1.96
1
A
A
O
CG1
VAL
VAL
157
160
1.98
1
A
A
CG2
CB
THR
SER
55
258
1.98
1
A
A
OG
O
SER
ILE
209
215
1.99
1
A
A
CG
O
LYS
ASP
283
297
2.01
1
A
A
O
CG2
LYS
THR
87
89
2.02
1
A
A
O
N
ALA
ALA
246
249
2.02
1
A
A
O
CB
THR
GLU
52
284
2.06
1
A
A
CG2
OG
THR
SER
55
258
2.07
1
A
A
O
N
VAL
SER
79
218
2.11
1
A
A
C
OD2
SER
ASP
105
195
2.12
1
A
A
O
CG
SER
ASP
105
195
2.14
1
A
A
NE1
NH2
TRP
ARG
221
262
2.14
1
A
A
O
N
GLU
LYS
171
173
2.15
1
A
A
CG1
CD1
VAL
ILE
80
217
2.15
1
A
A
N
O
ILE
LYS
54
283
2.16
1
A
A
OE2
NZ
GLU
LYS
169
172
2.17
1
A
A
OD2
OD1
ASP
ASN
288
292
2.18
1
A
A
O
CE
ILE
LYS
106
173
2.18
1
A
A
SER
TYR
621
622
148.77
1
9.18
1.50
119.30
128.48
A
A
A
C
N
CA
ASP
PRO
PRO
195
196
196
Y
1
11.47
1.50
119.30
130.77
A
A
A
C
N
CA
PHE
PRO
PRO
651
652
652
Y
1
A
SER
57
-42.59
154.81
1
A
ALA
59
-37.07
129.27
1
A
LYS
77
-171.76
112.07
1
A
ARG
84
-127.39
-149.51
1
A
SER
85
160.20
113.74
1
A
ASN
86
-50.38
4.67
1
A
LYS
87
-106.27
-64.84
1
A
MET
88
-48.11
156.17
1
A
ALA
90
-23.30
-68.81
1
A
PRO
109
-111.74
77.57
1
A
ARG
114
-34.86
-30.86
1
A
GLU
125
-29.70
-75.83
1
A
ILE
126
-22.46
-69.49
1
A
GLN
164
-66.75
93.48
1
A
GLU
171
-39.10
-76.78
1
A
LYS
172
-35.18
-4.85
1
A
TYR
176
-54.49
-79.87
1
A
LEU
177
-23.67
-62.96
1
A
PHE
187
75.86
-5.43
1
A
THR
191
-109.49
-154.07
1
A
ILE
192
-158.73
89.87
1
A
ALA
193
-50.11
101.07
1
A
THR
194
-125.77
-143.49
1
A
PRO
196
-21.52
147.20
1
A
ASN
198
-79.97
-143.88
1
A
LYS
210
-61.27
5.31
1
A
PRO
213
-18.14
97.61
1
A
SER
229
-39.20
-33.94
1
A
GLU
247
-4.02
-81.60
1
A
ALA
251
-29.95
-29.44
1
A
ASP
261
-59.49
-176.20
1
A
TYR
267
58.08
-153.87
1
A
TYR
272
-99.77
33.96
1
A
GLU
274
-30.54
-72.21
1
A
LEU
287
178.59
162.27
1
A
SER
295
142.51
142.02
1
A
SER
303
-105.24
-162.18
1
A
LEU
314
-44.43
-70.91
1
A
ALA
391
-29.79
-50.19
1
A
GLN
416
-33.93
116.18
1
A
ILE
434
-175.22
130.25
1
A
PHE
520
-135.63
-84.95
1
A
ASN
538
81.99
40.69
1
A
LEU
559
-39.20
107.43
1
A
ASN
572
173.01
162.60
1
A
SER
621
150.44
-154.20
1
A
TYR
622
-30.48
153.38
1
A
VAL
623
-177.40
89.84
1
A
ALA
624
42.94
-153.36
1
A
ASP
625
-62.81
94.64
1
A
GLN
627
111.90
117.04
1
A
ALA
638
174.69
162.39
1
A
HIS
653
31.80
57.61
1
A
LEU
657
61.40
-12.33
1
A
THR
658
-92.66
-72.48
1
A
HIS
677
-158.18
75.82
1
A
HIS
681
143.52
38.31
91.21
-2.67000
0.00000
2.57000
-0.08000
0.00000
4.71000
0.908
0.867
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.287
0.237
0.240
3.29
47.25
770
15012
4.900
100.0
78.151
0.532
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.538
0.80
0.80
1.20
PDB ENTRY 2WAD
MAXIMUM LIKELIHOOD
MASK
3.29
47.25
11
4714
2
0
4701
0.009
0.022
4785
1.287
1.958
6501
7.344
5.000
617
37.541
26.039
207
19.993
15.000
794
18.503
15.000
11
0.093
0.200
747
0.006
0.021
3612
0.906
1.500
3065
1.781
2.000
4941
2.570
3.000
1720
4.636
4.500
1560
0.4080
0.3560
3.38
30
747
20
100.00
69.16
3.29
47.25
2WAF
14291
3.0
0.10
1
11.20
3.4
82.5
3.29
3.49
2.82
0.44
1
3
54.9
refinement
REFMAC
5.4.0067
data reduction
XDS
data scaling
XSCALE
phasing
PHASER
PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6)
1
N
N
2
N
N
2
N
N
3
N
N
A
THR
89
A
THR
89
HELX_P
A
THR
102
A
THR
102
1
1
14
A
THR
112
A
THR
112
HELX_P
A
LEU
121
A
LEU
121
1
2
10
A
ASP
123
A
ASP
123
HELX_P
A
GLU
132
A
GLU
132
1
3
10
A
GLU
149
A
GLU
149
HELX_P
A
GLN
161
A
GLN
161
1
4
13
A
ASP
170
A
ASP
170
HELX_P
A
ALA
183
A
ALA
183
1
5
14
A
ASP
199
A
ASP
199
HELX_P
A
SER
209
A
SER
209
1
6
11
A
LYS
210
A
LYS
210
HELX_P
A
MET
212
A
MET
212
5
7
3
A
LEU
230
A
LEU
230
HELX_P
A
GLY
235
A
GLY
235
1
8
6
A
PRO
245
A
PRO
245
HELX_P
A
GLY
256
A
GLY
256
1
9
12
A
TYR
267
A
TYR
267
HELX_P
A
TYR
272
A
TYR
272
1
10
6
A
TYR
272
A
TYR
272
HELX_P
A
GLN
277
A
GLN
277
1
11
6
A
ASP
313
A
ASP
313
HELX_P
A
ASN
334
A
ASN
334
1
12
22
A
LEU
375
A
LEU
375
HELX_P
A
ASN
380
A
ASN
380
1
13
6
A
PRO
384
A
PRO
384
HELX_P
A
VAL
387
A
VAL
387
5
14
4
A
VAL
388
A
VAL
388
HELX_P
A
ASN
399
A
ASN
399
1
15
12
A
ALA
436
A
ALA
436
HELX_P
A
TYR
442
A
TYR
442
1
16
7
A
SER
444
A
SER
444
HELX_P
A
GLY
457
A
GLY
457
1
17
14
A
GLY
467
A
GLY
467
HELX_P
A
SER
469
A
SER
469
5
18
3
A
ASN
470
A
ASN
470
HELX_P
A
TYR
485
A
TYR
485
1
19
16
A
SER
508
A
SER
508
HELX_P
A
ALA
516
A
ALA
516
1
20
9
A
THR
524
A
THR
524
HELX_P
A
ASN
537
A
ASN
537
1
21
14
A
SER
577
A
SER
577
HELX_P
A
GLY
594
A
GLY
594
1
22
18
A
GLY
601
A
GLY
601
HELX_P
A
ASN
606
A
ASN
606
1
23
6
A
GLY
660
A
GLY
660
HELX_P
A
LYS
675
A
LYS
675
1
24
16
PEPTIDE BINDING PROTEIN
PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, TRANSMEMBRANE, ANTIBIOTIC RESISTANCE, CELL SHAPE, PEPTIDOGLYCAN, CELL MEMBRANE, CELL WALL BIOGENESIS/DEGRADATION, MEMBRANE, INFECTION, RESISTANCE, ANTIBIOTIC, PEPTIDE BINDING PROTEIN
A
GLY
626
A
GLY
626
1
A
GLN
627
A
GLN
627
11.78
A
ALA
638
A
ALA
638
1
A
PRO
639
A
PRO
639
-10.48
PBP2_STRR6
UNP
1
P0A3M6
2WAF
PDB
1
2WAF
1
680
2WAF
1
680
P0A3M6
A
1
1
680
681
682
2WAF
681
682
2WAF
A
2
681
682
2
4
3
2
2
6
2
2
2
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
53
A
LYS
53
A
SER
58
A
SER
58
A
GLY
278
A
GLY
278
A
GLU
284
A
GLU
284
A
ILE
63
A
ILE
63
A
TYR
64
A
TYR
64
A
ASN
307
A
ASN
307
A
LEU
310
A
LEU
310
A
VAL
547
A
VAL
547
A
ASN
553
A
ASN
553
A
LEU
559
A
LEU
559
A
GLN
565
A
GLN
565
A
THR
189
A
THR
189
A
GLY
190
A
GLY
190
A
VAL
72
A
VAL
72
A
THR
83
A
THR
83
A
SER
216
A
SER
216
A
VAL
225
A
VAL
225
A
SER
236
A
SER
236
A
VAL
237
A
VAL
237
A
GLY
264
A
GLY
264
A
SER
266
A
SER
266
A
HIS
286
A
HIS
286
A
LEU
287
A
LEU
287
A
MET
293
A
MET
293
A
SER
295
A
SER
295
A
LEU
370
A
LEU
370
A
PRO
372
A
PRO
372
A
VAL
355
A
VAL
355
A
HIS
363
A
HIS
363
A
GLY
342
A
GLY
342
A
LEU
348
A
LEU
348
A
ILE
645
A
ILE
645
A
VAL
650
A
VAL
650
A
ALA
634
A
ALA
634
A
ALA
638
A
ALA
638
A
SER
613
A
SER
613
A
THR
616
A
THR
616
A
THR
407
A
THR
407
A
ASP
410
A
ASP
410
A
PHE
432
A
PHE
432
A
THR
435
A
THR
435
A
VAL
540
A
VAL
540
A
VAL
542
A
VAL
542
A
GLU
570
A
GLU
570
A
LYS
573
A
LYS
573
A
ALA
619
A
ALA
619
A
SER
621
A
SER
621
A
ALA
629
A
ALA
629
A
ASN
631
A
ASN
631
BINDING SITE FOR RESIDUE CL A 700
A
CL
700
Software
2
BINDING SITE FOR RESIDUE CL A 701
A
CL
701
Software
1
A
ASN
656
A
ASN
656
2
1_555
A
THR
658
A
THR
658
2
1_555
A
ARG
667
A
ARG
667
1
1_555
5
C 1 2 1