0.008460
0.000000
0.000310
0.000000
0.011013
0.000000
0.000000
0.000000
0.012188
0.00000
0.00000
0.00000
Kuzin, A.P.
Sun, T.
Jorczak-Baillass, J.
Healy, V.L.
Walsh, C.T.
Knox, J.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
92.10
90.00
118.200
90.800
82.100
C10 H15 N5 O10 P2
427.201
n
ADENOSINE-5'-DIPHOSPHATE
non-polymer
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
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C6 H15 N O7 P2
275.133
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
non-polymer
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
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
S
P
N
6
N
O
N
7
N
O
N
8
N
O
N
9
N
O
N
10
N
C
N
11
R
C
N
12
N
O
N
13
S
C
N
14
N
O
N
15
R
C
N
16
N
O
N
17
R
C
Y
18
N
N
Y
19
N
C
Y
20
N
N
Y
21
N
C
Y
22
N
C
N
23
N
N
Y
24
N
N
Y
25
N
C
Y
26
N
N
Y
27
N
C
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
H
N
42
N
H
N
43
N
N
N
44
S
C
N
45
N
C
N
46
N
O
N
47
N
C
N
48
N
O
N
49
N
H
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
N
N
57
S
C
N
58
N
C
N
59
N
O
N
60
N
C
N
61
N
C
N
62
N
C
N
63
N
N
N
64
N
C
N
65
N
N
N
66
N
N
N
67
N
O
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
N
N
84
S
C
N
85
N
C
N
86
N
O
N
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
O
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
H
N
99
N
H
N
100
N
N
N
101
S
C
N
102
N
C
N
103
N
O
N
104
N
C
N
105
N
C
N
106
N
O
N
107
N
O
N
108
N
O
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
N
N
117
S
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
C
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
O
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
N
N
137
S
C
N
138
N
C
N
139
N
O
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
O
N
144
N
O
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
N
N
156
N
C
N
157
N
C
N
158
N
O
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
N
N
166
S
C
N
167
N
C
N
168
N
O
N
169
N
C
Y
170
N
C
Y
171
N
N
Y
172
N
C
Y
173
N
C
Y
174
N
N
N
175
N
O
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
O
N
187
N
H
N
188
N
H
N
189
N
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
S
C
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
O
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
N
N
212
S
C
N
213
N
C
N
214
N
O
N
215
N
C
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
O
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
N
N
234
S
C
N
235
N
C
N
236
N
O
N
237
N
C
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
N
N
242
N
O
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
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
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
S
N
265
N
C
N
266
N
O
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
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
MG
N
279
N
N
N
280
S
C
N
281
N
C
N
282
N
O
N
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
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
H
N
301
N
H
N
302
S
C
N
303
N
C
N
304
N
C
N
305
R
C
N
306
N
C
N
307
N
C
N
308
N
O
N
309
N
O
N
310
N
N
N
311
R
P
N
312
N
O
N
313
N
O
N
314
N
P
N
315
N
O
N
316
N
O
N
317
N
O
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
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
H
N
332
N
H
N
333
N
N
N
334
S
C
N
335
N
C
N
336
N
O
N
337
N
C
N
338
N
C
N
339
N
C
N
340
N
O
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
H
N
350
N
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
N
C
N
355
N
O
N
356
N
O
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
N
N
365
S
C
N
366
N
C
N
367
N
O
N
368
R
C
N
369
N
O
N
370
N
C
N
371
N
O
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
N
N
382
S
C
N
383
N
C
N
384
N
O
N
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
N
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
N
395
N
O
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
N
N
409
S
C
N
410
N
C
N
411
N
O
N
412
N
C
Y
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
N
419
N
O
N
420
N
O
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
N
437
N
C
N
438
N
C
N
439
N
O
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
1
N
doub
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
sing
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
Y
30
N
sing
Y
31
N
sing
Y
32
N
doub
N
33
N
sing
Y
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
doub
N
39
N
sing
N
40
N
sing
Y
41
N
sing
Y
42
N
doub
N
43
N
sing
Y
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
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
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
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
doub
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
doub
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
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
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
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
doub
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
Y
171
N
sing
Y
172
N
doub
Y
173
N
doub
N
174
N
sing
Y
175
N
sing
N
176
N
sing
Y
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
sing
N
189
N
doub
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
doub
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
doub
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
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
doub
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
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
doub
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
Y
279
N
doub
Y
280
N
sing
Y
281
N
sing
N
282
N
sing
Y
283
N
doub
N
284
N
sing
Y
285
N
doub
N
286
N
sing
Y
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
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
doub
N
314
N
sing
N
315
N
sing
N
316
N
doub
N
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
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
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
doub
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
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
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
doub
Y
383
N
sing
Y
384
N
sing
N
385
N
sing
Y
386
N
sing
Y
387
N
doub
N
388
N
sing
Y
389
N
doub
N
390
N
sing
Y
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
doub
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
Y
406
N
doub
Y
407
N
sing
Y
408
N
sing
N
409
N
sing
Y
410
N
doub
N
411
N
sing
Y
412
N
doub
N
413
N
sing
Y
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
doub
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
8
463
470
10.1016/S0969-2126(00)00129-5
10801495
Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
2000
US
Science
SCIEAS
0038
0036-8075
266
439
443
Vancomycin Resistance: Structure of D-alanine:D-alanine Ligase at 2.3 A Resolution
1994
US
Biochemistry
BICHAW
0033
0006-2960
36
2531
2538
10.1021/bi962431t
D-alanine:D-alanine ligase: Phosphonate and Phosphinate Intermediates with Wild-type and the Y216F Mutant
1997
10.2210/pdb1ehi/pdb
pdb_00001ehi
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
1997-08-15
ADSC
MAD
M
x-ray
1
0.908
1.0
A1
CHESS
0.908
SYNCHROTRON
CHESS BEAMLINE A1
41866.883
D-ALANINE:D-LACTATE LIGASE
6.3.2.4
2
man
polymer
Made by Prof. Paul A. Bartlett, Dept. of Chem., UC Berkeley
24.305
MAGNESIUM ION
2
syn
non-polymer
427.201
ADENOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
275.133
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
1
syn
non-polymer
18.015
water
213
nat
water
LMDDL2
no
no
MTKKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSKKILALEDEQPIVDAFMKTVDASD
PLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGHAVSFDKALTKELLTVNGIRNTKYIVVDPES
ANNWSWDKIVAELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSFQYDYKVLIEEAVNGARELEVGVIGNDQPLVSEI
GAHTVPNQGSGDGWYDYNNKFVDNSAVHFQIPAQLSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNVPYLGEPNTL
PGFTNMSLFKRLWDYSDINNAKLVDMLIDYGFEDFAQNKKLSYSFVSLGEEKIGKFN
MTKKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSKKILALEDEQPIVDAFMKTVDASD
PLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGHAVSFDKALTKELLTVNGIRNTKYIVVDPES
ANNWSWDKIVAELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSFQYDYKVLIEEAVNGARELEVGVIGNDQPLVSEI
GAHTVPNQGSGDGWYDYNNKFVDNSAVHFQIPAQLSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNVPYLGEPNTL
PGFTNMSLFKRLWDYSDINNAKLVDMLIDYGFEDFAQNKKLSYSFVSLGEEKIGKFN
A,B
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
Leuconostoc
Escherichia
sample
8293
1245
Leuconostoc mesenteroides
562
Escherichia coli
DH5A AND BL21(DE3)
PLMDDL2
1
2.6
53.20
VAPOR DIFFUSION, SITTING DROP
6.5
PEG8000 15%, 0.1 M ammonium sulfate, 50mM NaCl, 2.4mM DTT, 1mM MgCl2, 3mM ATP, 3mM phosphinic acid, 50mM MES buffer., pH 6.5, VAPOR DIFFUSION, SITTING DROP
293-295
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
entity
pdbx_entity_src_syn
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Source and taxonomy
Structure summary
1
0
2000-05-23
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2024-02-07
1
5
2024-03-13
_software.name
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_entity.details
D-alanine:D-alanine ligase (DdlB) of E. coli complexed with phosphinate and ADP
DdlB ligase with phosphonate and ADP
DdlB Y215F mutant with phosphinate and ADP
RCSB
Y
RCSB
2000-02-21
REL
MG
MAGNESIUM ION
ADP
ADENOSINE-5'-DIPHOSPHATE
PHY
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
HOH
water
MG
783
2
MG
MG
783
A
MG
784
2
MG
MG
784
A
ADP
781
3
ADP
ADP
781
A
PHY
782
4
PHY
PHY
782
A
WAT
801
5
HOH
HOH
801
A
WAT
803
5
HOH
HOH
803
A
WAT
804
5
HOH
HOH
804
A
WAT
807
5
HOH
HOH
807
A
WAT
809
5
HOH
HOH
809
A
WAT
810
5
HOH
HOH
810
A
WAT
811
5
HOH
HOH
811
A
WAT
812
5
HOH
HOH
812
A
WAT
815
5
HOH
HOH
815
A
WAT
817
5
HOH
HOH
817
A
WAT
818
5
HOH
HOH
818
A
WAT
819
5
HOH
HOH
819
A
WAT
824
5
HOH
HOH
824
A
WAT
825
5
HOH
HOH
825
A
WAT
826
5
HOH
HOH
826
A
WAT
827
5
HOH
HOH
827
A
WAT
828
5
HOH
HOH
828
A
WAT
829
5
HOH
HOH
829
A
WAT
832
5
HOH
HOH
832
A
WAT
833
5
HOH
HOH
833
A
WAT
834
5
HOH
HOH
834
A
WAT
835
5
HOH
HOH
835
A
WAT
837
5
HOH
HOH
837
A
WAT
838
5
HOH
HOH
838
A
WAT
840
5
HOH
HOH
840
A
WAT
841
5
HOH
HOH
841
A
WAT
842
5
HOH
HOH
842
A
WAT
843
5
HOH
HOH
843
A
WAT
844
5
HOH
HOH
844
A
WAT
846
5
HOH
HOH
846
A
WAT
847
5
HOH
HOH
847
A
WAT
848
5
HOH
HOH
848
A
WAT
849
5
HOH
HOH
849
A
WAT
850
5
HOH
HOH
850
A
WAT
852
5
HOH
HOH
852
A
WAT
853
5
HOH
HOH
853
A
WAT
854
5
HOH
HOH
854
A
WAT
855
5
HOH
HOH
855
A
WAT
858
5
HOH
HOH
858
A
WAT
859
5
HOH
HOH
859
A
WAT
861
5
HOH
HOH
861
A
WAT
862
5
HOH
HOH
862
A
WAT
863
5
HOH
HOH
863
A
WAT
864
5
HOH
HOH
864
A
WAT
866
5
HOH
HOH
866
A
WAT
867
5
HOH
HOH
867
A
WAT
868
5
HOH
HOH
868
A
WAT
870
5
HOH
HOH
870
A
WAT
873
5
HOH
HOH
873
A
WAT
876
5
HOH
HOH
876
A
WAT
877
5
HOH
HOH
877
A
WAT
878
5
HOH
HOH
878
A
WAT
882
5
HOH
HOH
882
A
WAT
884
5
HOH
HOH
884
A
WAT
886
5
HOH
HOH
886
A
WAT
888
5
HOH
HOH
888
A
WAT
889
5
HOH
HOH
889
A
WAT
894
5
HOH
HOH
894
A
WAT
895
5
HOH
HOH
895
A
WAT
896
5
HOH
HOH
896
A
WAT
897
5
HOH
HOH
897
A
WAT
900
5
HOH
HOH
900
A
WAT
903
5
HOH
HOH
903
A
WAT
904
5
HOH
HOH
904
A
WAT
908
5
HOH
HOH
908
A
WAT
909
5
HOH
HOH
909
A
WAT
910
5
HOH
HOH
910
A
WAT
911
5
HOH
HOH
911
A
WAT
915
5
HOH
HOH
915
A
WAT
916
5
HOH
HOH
916
A
WAT
917
5
HOH
HOH
917
A
WAT
920
5
HOH
HOH
920
A
WAT
923
5
HOH
HOH
923
A
WAT
924
5
HOH
HOH
924
A
WAT
925
5
HOH
HOH
925
A
WAT
926
5
HOH
HOH
926
A
WAT
927
5
HOH
HOH
927
A
WAT
928
5
HOH
HOH
928
A
WAT
930
5
HOH
HOH
930
A
WAT
932
5
HOH
HOH
932
A
WAT
933
5
HOH
HOH
933
A
WAT
935
5
HOH
HOH
935
A
WAT
936
5
HOH
HOH
936
A
WAT
937
5
HOH
HOH
937
A
WAT
938
5
HOH
HOH
938
A
WAT
939
5
HOH
HOH
939
A
WAT
942
5
HOH
HOH
942
A
WAT
944
5
HOH
HOH
944
A
WAT
951
5
HOH
HOH
951
A
WAT
953
5
HOH
HOH
953
A
WAT
954
5
HOH
HOH
954
A
WAT
959
5
HOH
HOH
959
A
WAT
962
5
HOH
HOH
962
A
WAT
964
5
HOH
HOH
964
A
WAT
967
5
HOH
HOH
967
A
WAT
968
5
HOH
HOH
968
A
WAT
969
5
HOH
HOH
969
A
WAT
970
5
HOH
HOH
970
A
WAT
971
5
HOH
HOH
971
A
WAT
973
5
HOH
HOH
973
A
WAT
974
5
HOH
HOH
974
A
WAT
975
5
HOH
HOH
975
A
WAT
977
5
HOH
HOH
977
A
WAT
978
5
HOH
HOH
978
A
WAT
980
5
HOH
HOH
980
A
WAT
981
5
HOH
HOH
981
A
WAT
982
5
HOH
HOH
982
A
WAT
983
5
HOH
HOH
983
A
WAT
984
5
HOH
HOH
984
A
WAT
986
5
HOH
HOH
986
A
WAT
987
5
HOH
HOH
987
A
WAT
989
5
HOH
HOH
989
A
WAT
991
5
HOH
HOH
991
A
WAT
993
5
HOH
HOH
993
A
WAT
997
5
HOH
HOH
997
A
WAT
1001
5
HOH
HOH
1001
A
WAT
1002
5
HOH
HOH
1002
A
WAT
1003
5
HOH
HOH
1003
A
WAT
1005
5
HOH
HOH
1005
A
WAT
1008
5
HOH
HOH
1008
A
WAT
1009
5
HOH
HOH
1009
A
WAT
1010
5
HOH
HOH
1010
A
WAT
802
5
HOH
HOH
802
B
WAT
805
5
HOH
HOH
805
B
WAT
806
5
HOH
HOH
806
B
WAT
808
5
HOH
HOH
808
B
WAT
813
5
HOH
HOH
813
B
WAT
814
5
HOH
HOH
814
B
WAT
816
5
HOH
HOH
816
B
WAT
820
5
HOH
HOH
820
B
WAT
821
5
HOH
HOH
821
B
WAT
822
5
HOH
HOH
822
B
WAT
823
5
HOH
HOH
823
B
WAT
830
5
HOH
HOH
830
B
WAT
831
5
HOH
HOH
831
B
WAT
836
5
HOH
HOH
836
B
WAT
839
5
HOH
HOH
839
B
WAT
845
5
HOH
HOH
845
B
WAT
851
5
HOH
HOH
851
B
WAT
856
5
HOH
HOH
856
B
WAT
857
5
HOH
HOH
857
B
WAT
860
5
HOH
HOH
860
B
WAT
865
5
HOH
HOH
865
B
WAT
869
5
HOH
HOH
869
B
WAT
871
5
HOH
HOH
871
B
WAT
872
5
HOH
HOH
872
B
WAT
874
5
HOH
HOH
874
B
WAT
875
5
HOH
HOH
875
B
WAT
879
5
HOH
HOH
879
B
WAT
880
5
HOH
HOH
880
B
WAT
881
5
HOH
HOH
881
B
WAT
883
5
HOH
HOH
883
B
WAT
885
5
HOH
HOH
885
B
WAT
887
5
HOH
HOH
887
B
WAT
890
5
HOH
HOH
890
B
WAT
891
5
HOH
HOH
891
B
WAT
892
5
HOH
HOH
892
B
WAT
893
5
HOH
HOH
893
B
WAT
898
5
HOH
HOH
898
B
WAT
899
5
HOH
HOH
899
B
WAT
901
5
HOH
HOH
901
B
WAT
902
5
HOH
HOH
902
B
WAT
905
5
HOH
HOH
905
B
WAT
906
5
HOH
HOH
906
B
WAT
907
5
HOH
HOH
907
B
WAT
912
5
HOH
HOH
912
B
WAT
913
5
HOH
HOH
913
B
WAT
914
5
HOH
HOH
914
B
WAT
918
5
HOH
HOH
918
B
WAT
919
5
HOH
HOH
919
B
WAT
921
5
HOH
HOH
921
B
WAT
922
5
HOH
HOH
922
B
WAT
929
5
HOH
HOH
929
B
WAT
931
5
HOH
HOH
931
B
WAT
934
5
HOH
HOH
934
B
WAT
940
5
HOH
HOH
940
B
WAT
941
5
HOH
HOH
941
B
WAT
943
5
HOH
HOH
943
B
WAT
945
5
HOH
HOH
945
B
WAT
946
5
HOH
HOH
946
B
WAT
947
5
HOH
HOH
947
B
WAT
948
5
HOH
HOH
948
B
WAT
949
5
HOH
HOH
949
B
WAT
950
5
HOH
HOH
950
B
WAT
952
5
HOH
HOH
952
B
WAT
955
5
HOH
HOH
955
B
WAT
956
5
HOH
HOH
956
B
WAT
957
5
HOH
HOH
957
B
WAT
958
5
HOH
HOH
958
B
WAT
960
5
HOH
HOH
960
B
WAT
961
5
HOH
HOH
961
B
WAT
963
5
HOH
HOH
963
B
WAT
965
5
HOH
HOH
965
B
WAT
966
5
HOH
HOH
966
B
WAT
972
5
HOH
HOH
972
B
WAT
976
5
HOH
HOH
976
B
WAT
979
5
HOH
HOH
979
B
WAT
985
5
HOH
HOH
985
B
WAT
988
5
HOH
HOH
988
B
WAT
990
5
HOH
HOH
990
B
WAT
992
5
HOH
HOH
992
B
WAT
994
5
HOH
HOH
994
B
WAT
995
5
HOH
HOH
995
B
WAT
996
5
HOH
HOH
996
B
WAT
998
5
HOH
HOH
998
B
WAT
999
5
HOH
HOH
999
B
WAT
1000
5
HOH
HOH
1000
B
WAT
1004
5
HOH
HOH
1004
B
WAT
1006
5
HOH
HOH
1006
B
WAT
1007
5
HOH
HOH
1007
B
WAT
1011
5
HOH
HOH
1011
B
WAT
1012
5
HOH
HOH
1012
B
WAT
1013
5
HOH
HOH
1013
B
n
1
1
A
n
2
2
A
LYS
3
n
3
LYS
3
A
LYS
4
n
4
LYS
4
A
ARG
5
n
5
ARG
5
A
VAL
6
n
6
VAL
6
A
ALA
7
n
7
ALA
7
A
LEU
8
n
8
LEU
8
A
ILE
9
n
9
ILE
9
A
PHE
10
n
10
PHE
10
A
GLY
11
n
11
GLY
11
A
GLY
12
n
12
GLY
12
A
ASN
13
n
13
ASN
13
A
SER
14
n
14
SER
14
A
SER
15
n
15
SER
15
A
GLU
16
n
16
GLU
16
A
HIS
17
n
17
HIS
17
A
ASP
18
n
18
ASP
18
A
VAL
19
n
19
VAL
19
A
SER
20
n
20
SER
20
A
LYS
21
n
21
LYS
21
A
ARG
22
n
22
ARG
22
A
SER
23
n
23
SER
23
A
ALA
24
n
24
ALA
24
A
GLN
25
n
25
GLN
25
A
ASN
26
n
26
ASN
26
A
PHE
27
n
27
PHE
27
A
TYR
28
n
28
TYR
28
A
ASN
29
n
29
ASN
29
A
ALA
30
n
30
ALA
30
A
ILE
31
n
31
ILE
31
A
GLU
32
n
32
GLU
32
A
ALA
33
n
33
ALA
33
A
THR
34
n
34
THR
34
A
GLY
35
n
35
GLY
35
A
LYS
36
n
36
LYS
36
A
TYR
37
n
37
TYR
37
A
GLU
38
n
38
GLU
38
A
ILE
39
n
39
ILE
39
A
ILE
40
n
40
ILE
40
A
VAL
41
n
41
VAL
41
A
PHE
42
n
42
PHE
42
A
ALA
43
n
43
ALA
43
A
ILE
44
n
44
ILE
44
A
ALA
45
n
45
ALA
45
A
GLN
46
n
46
GLN
46
A
ASN
47
n
47
ASN
47
A
GLY
48
n
48
GLY
48
A
PHE
49
n
49
PHE
49
A
PHE
50
n
50
PHE
50
A
LEU
51
n
51
LEU
51
A
ASP
52
n
52
ASP
52
A
THR
53
n
53
THR
53
A
GLU
54
n
54
GLU
54
A
SER
55
n
55
SER
55
A
SER
56
n
56
SER
56
A
LYS
57
n
57
LYS
57
A
LYS
58
n
58
LYS
58
A
ILE
59
n
59
ILE
59
A
LEU
60
n
60
LEU
60
A
ALA
61
n
61
ALA
61
A
LEU
62
n
62
LEU
62
A
GLU
63
n
63
GLU
63
A
ASP
64
n
64
ASP
64
A
GLU
65
n
65
GLU
65
A
GLN
66
n
66
GLN
66
A
PRO
67
n
67
PRO
67
A
ILE
68
n
68
ILE
68
A
VAL
69
n
69
VAL
69
A
ASP
70
n
70
ASP
70
A
ALA
71
n
71
ALA
71
A
PHE
72
n
72
PHE
72
A
MET
73
n
73
MET
73
A
LYS
74
n
74
LYS
74
A
THR
75
n
75
THR
75
A
VAL
76
n
76
VAL
76
A
ASP
77
n
77
ASP
77
A
ALA
78
n
78
ALA
78
A
SER
79
n
79
SER
79
A
ASP
80
n
80
ASP
80
A
PRO
81
n
81
PRO
81
A
LEU
82
n
82
LEU
82
A
ALA
83
n
83
ALA
83
A
ARG
84
n
84
ARG
84
A
ILE
85
n
85
ILE
85
A
HIS
86
n
86
HIS
86
A
ALA
87
n
87
ALA
87
A
LEU
88
n
88
LEU
88
A
LYS
89
n
89
LYS
89
A
SER
90
n
90
SER
90
A
ALA
91
n
91
ALA
91
A
GLY
92
n
92
GLY
92
A
ASP
93
n
93
ASP
93
A
PHE
94
n
94
PHE
94
A
ASP
95
n
95
ASP
95
A
ILE
96
n
96
ILE
96
A
PHE
97
n
97
PHE
97
A
PHE
98
n
98
PHE
98
A
PRO
99
n
99
PRO
99
A
VAL
100
n
100
VAL
100
A
VAL
101
n
101
VAL
101
A
HIS
102
n
102
HIS
102
A
GLY
103
n
103
GLY
103
A
ASN
104
n
104
ASN
104
A
LEU
105
n
105
LEU
105
A
GLY
106
n
106
GLY
106
A
GLU
107
n
107
GLU
107
A
ASP
108
n
108
ASP
108
A
GLY
109
n
109
GLY
109
A
THR
110
n
110
THR
110
A
LEU
111
n
111
LEU
111
A
GLN
112
n
112
GLN
112
A
GLY
113
n
113
GLY
113
A
LEU
114
n
114
LEU
114
A
PHE
115
n
115
PHE
115
A
LYS
116
n
116
LYS
116
A
LEU
117
n
117
LEU
117
A
LEU
118
n
118
LEU
118
A
ASP
119
n
119
ASP
119
A
LYS
120
n
120
LYS
120
A
PRO
121
n
121
PRO
121
A
TYR
122
n
122
TYR
122
A
VAL
123
n
123
VAL
123
A
GLY
124
n
124
GLY
124
A
ALA
125
n
125
ALA
125
A
PRO
126
n
126
PRO
126
A
LEU
127
n
127
LEU
127
A
ARG
128
n
128
ARG
128
A
GLY
129
n
129
GLY
129
A
HIS
130
n
130
HIS
130
A
ALA
131
n
131
ALA
131
A
VAL
132
n
132
VAL
132
A
SER
133
n
133
SER
133
A
PHE
134
n
134
PHE
134
A
ASP
135
n
135
ASP
135
A
LYS
136
n
136
LYS
136
A
ALA
137
n
137
ALA
137
A
LEU
138
n
138
LEU
138
A
THR
139
n
139
THR
139
A
LYS
140
n
140
LYS
140
A
GLU
141
n
141
GLU
141
A
LEU
142
n
142
LEU
142
A
LEU
143
n
143
LEU
143
A
THR
144
n
144
THR
144
A
VAL
145
n
145
VAL
145
A
ASN
146
n
146
ASN
146
A
GLY
147
n
147
GLY
147
A
ILE
148
n
148
ILE
148
A
ARG
149
n
149
ARG
149
A
ASN
150
n
150
ASN
150
A
THR
151
n
151
THR
151
A
LYS
152
n
152
LYS
152
A
TYR
153
n
153
TYR
153
A
ILE
154
n
154
ILE
154
A
VAL
155
n
155
VAL
155
A
VAL
156
n
156
VAL
156
A
ASP
157
n
157
ASP
157
A
PRO
158
n
158
PRO
158
A
GLU
159
n
159
GLU
159
A
SER
160
n
160
SER
160
A
ALA
161
n
161
ALA
161
A
ASN
162
n
162
ASN
162
A
ASN
163
n
163
ASN
163
A
TRP
164
n
164
TRP
164
A
SER
165
n
165
SER
165
A
TRP
166
n
166
TRP
166
A
ASP
167
n
167
ASP
167
A
LYS
168
n
168
LYS
168
A
ILE
169
n
169
ILE
169
A
VAL
170
n
170
VAL
170
A
ALA
171
n
171
ALA
171
A
GLU
172
n
172
GLU
172
A
LEU
173
n
173
LEU
173
A
GLY
174
n
174
GLY
174
A
ASN
175
n
175
ASN
175
A
ILE
176
n
176
ILE
176
A
VAL
177
n
177
VAL
177
A
PHE
178
n
178
PHE
178
A
VAL
179
n
179
VAL
179
A
LYS
180
n
180
LYS
180
A
ALA
181
n
181
ALA
181
A
ALA
182
n
182
ALA
182
A
ASN
183
n
183
ASN
183
A
GLN
184
n
184
GLN
184
A
GLY
185
n
185
GLY
185
A
SER
186
n
186
SER
186
A
SER
187
n
187
SER
187
A
VAL
188
n
188
VAL
188
A
GLY
189
n
189
GLY
189
A
ILE
190
n
190
ILE
190
A
SER
191
n
191
SER
191
A
ARG
192
n
192
ARG
192
A
VAL
193
n
193
VAL
193
A
THR
194
n
194
THR
194
A
ASN
195
n
195
ASN
195
A
ALA
196
n
196
ALA
196
A
GLU
197
n
197
GLU
197
A
GLU
198
n
198
GLU
198
A
TYR
199
n
199
TYR
199
A
THR
200
n
200
THR
200
A
GLU
201
n
201
GLU
201
A
ALA
202
n
202
ALA
202
A
LEU
203
n
203
LEU
203
A
SER
204
n
204
SER
204
A
ASP
205
n
205
ASP
205
A
SER
206
n
206
SER
206
A
PHE
207
n
207
PHE
207
A
GLN
208
n
208
GLN
208
A
TYR
209
n
209
TYR
209
A
ASP
210
n
210
ASP
210
A
TYR
211
n
211
TYR
211
A
LYS
212
n
212
LYS
212
A
VAL
213
n
213
VAL
213
A
LEU
214
n
214
LEU
214
A
ILE
215
n
215
ILE
215
A
GLU
216
n
216
GLU
216
A
GLU
217
n
217
GLU
217
A
ALA
218
n
218
ALA
218
A
VAL
219
n
219
VAL
219
A
ASN
220
n
220
ASN
220
A
GLY
221
n
221
GLY
221
A
ALA
222
n
222
ALA
222
A
ARG
223
n
223
ARG
223
A
GLU
224
n
224
GLU
224
A
LEU
225
n
225
LEU
225
A
GLU
226
n
226
GLU
226
A
VAL
227
n
227
VAL
227
A
GLY
228
n
228
GLY
228
A
VAL
229
n
229
VAL
229
A
ILE
230
n
230
ILE
230
A
GLY
231
n
231
GLY
231
A
ASN
232
n
232
ASN
232
A
ASP
233
n
233
ASP
233
A
GLN
234
n
234
GLN
234
A
PRO
235
n
235
PRO
235
A
LEU
236
n
236
LEU
236
A
VAL
237
n
237
VAL
237
A
SER
238
n
238
SER
238
A
GLU
239
n
239
GLU
239
A
ILE
240
n
240
ILE
240
A
GLY
241
n
241
GLY
241
A
ALA
242
n
242
ALA
242
A
HIS
243
n
243
HIS
243
A
THR
244
n
244
THR
244
A
VAL
245
n
245
VAL
245
A
PRO
246
n
246
PRO
246
A
ASN
247
n
247
ASN
247
A
GLN
248
n
248
GLN
248
A
GLY
249
n
249
GLY
249
A
SER
250
n
250
SER
250
A
GLY
251
n
251
GLY
251
A
ASP
252
n
252
ASP
252
A
GLY
253
n
253
GLY
253
A
TRP
254
n
254
TRP
254
A
TYR
255
n
255
TYR
255
A
ASP
256
n
256
ASP
256
A
TYR
257
n
257
TYR
257
A
ASN
258
n
258
ASN
258
A
ASN
259
n
259
ASN
259
A
LYS
260
n
260
LYS
260
A
PHE
261
n
261
PHE
261
A
VAL
262
n
262
VAL
262
A
ASP
263
n
263
ASP
263
A
ASN
264
n
264
ASN
264
A
SER
265
n
265
SER
265
A
ALA
266
n
266
ALA
266
A
VAL
267
n
267
VAL
267
A
HIS
268
n
268
HIS
268
A
PHE
269
n
269
PHE
269
A
GLN
270
n
270
GLN
270
A
ILE
271
n
271
ILE
271
A
PRO
272
n
272
PRO
272
A
ALA
273
n
273
ALA
273
A
GLN
274
n
274
GLN
274
A
LEU
275
n
275
LEU
275
A
SER
276
n
276
SER
276
A
PRO
277
n
277
PRO
277
A
GLU
278
n
278
GLU
278
A
VAL
279
n
279
VAL
279
A
THR
280
n
280
THR
280
A
LYS
281
n
281
LYS
281
A
GLU
282
n
282
GLU
282
A
VAL
283
n
283
VAL
283
A
LYS
284
n
284
LYS
284
A
GLN
285
n
285
GLN
285
A
MET
286
n
286
MET
286
A
ALA
287
n
287
ALA
287
A
LEU
288
n
288
LEU
288
A
ASP
289
n
289
ASP
289
A
ALA
290
n
290
ALA
290
A
TYR
291
n
291
TYR
291
A
LYS
292
n
292
LYS
292
A
VAL
293
n
293
VAL
293
A
LEU
294
n
294
LEU
294
A
ASN
295
n
295
ASN
295
A
LEU
296
n
296
LEU
296
A
ARG
297
n
297
ARG
297
A
GLY
298
n
298
GLY
298
A
GLU
299
n
299
GLU
299
A
ALA
300
n
300
ALA
300
A
ARG
301
n
301
ARG
301
A
MET
302
n
302
MET
302
A
ASP
303
n
303
ASP
303
A
PHE
304
n
304
PHE
304
A
LEU
305
n
305
LEU
305
A
LEU
306
n
306
LEU
306
A
ASP
307
n
307
ASP
307
A
GLU
308
n
308
GLU
308
A
ASN
309
n
309
ASN
309
A
ASN
310
n
310
ASN
310
A
VAL
311
n
311
VAL
311
A
PRO
312
n
312
PRO
312
A
TYR
313
n
313
TYR
313
A
LEU
314
n
314
LEU
314
A
GLY
315
n
315
GLY
315
A
GLU
316
n
316
GLU
316
A
PRO
317
n
317
PRO
317
A
ASN
318
n
318
ASN
318
A
THR
319
n
319
THR
319
A
LEU
320
n
320
LEU
320
A
PRO
321
n
321
PRO
321
A
GLY
322
n
322
GLY
322
A
PHE
323
n
323
PHE
323
A
THR
324
n
324
THR
324
A
ASN
325
n
325
ASN
325
A
MET
326
n
326
MET
326
A
SER
327
n
327
SER
327
A
LEU
328
n
328
LEU
328
A
PHE
329
n
329
PHE
329
A
LYS
330
n
330
LYS
330
A
ARG
331
n
331
ARG
331
A
LEU
332
n
332
LEU
332
A
TRP
333
n
333
TRP
333
A
ASP
334
n
334
ASP
334
A
TYR
335
n
335
TYR
335
A
SER
336
n
336
SER
336
A
ASP
337
n
337
ASP
337
A
ILE
338
n
338
ILE
338
A
ASN
339
n
339
ASN
339
A
ASN
340
n
340
ASN
340
A
ALA
341
n
341
ALA
341
A
LYS
342
n
342
LYS
342
A
LEU
343
n
343
LEU
343
A
VAL
344
n
344
VAL
344
A
ASP
345
n
345
ASP
345
A
MET
346
n
346
MET
346
A
LEU
347
n
347
LEU
347
A
ILE
348
n
348
ILE
348
A
ASP
349
n
349
ASP
349
A
TYR
350
n
350
TYR
350
A
GLY
351
n
351
GLY
351
A
PHE
352
n
352
PHE
352
A
GLU
353
n
353
GLU
353
A
ASP
354
n
354
ASP
354
A
PHE
355
n
355
PHE
355
A
ALA
356
n
356
ALA
356
A
GLN
357
n
357
GLN
357
A
ASN
358
n
358
ASN
358
A
LYS
359
n
359
LYS
359
A
LYS
360
n
360
LYS
360
A
LEU
361
n
361
LEU
361
A
SER
362
n
362
SER
362
A
n
363
363
A
n
364
364
A
n
365
365
A
n
366
366
A
n
367
367
A
n
368
368
A
n
369
369
A
n
370
370
A
n
371
371
A
n
372
372
A
n
373
373
A
n
374
374
A
n
375
375
A
n
376
376
A
n
377
377
A
n
1
401
B
THR
402
n
2
THR
402
B
LYS
403
n
3
LYS
403
B
LYS
404
n
4
LYS
404
B
ARG
405
n
5
ARG
405
B
VAL
406
n
6
VAL
406
B
ALA
407
n
7
ALA
407
B
LEU
408
n
8
LEU
408
B
ILE
409
n
9
ILE
409
B
PHE
410
n
10
PHE
410
B
GLY
411
n
11
GLY
411
B
GLY
412
n
12
GLY
412
B
ASN
413
n
13
ASN
413
B
SER
414
n
14
SER
414
B
SER
415
n
15
SER
415
B
GLU
416
n
16
GLU
416
B
HIS
417
n
17
HIS
417
B
ASP
418
n
18
ASP
418
B
VAL
419
n
19
VAL
419
B
SER
420
n
20
SER
420
B
LYS
421
n
21
LYS
421
B
ARG
422
n
22
ARG
422
B
SER
423
n
23
SER
423
B
ALA
424
n
24
ALA
424
B
GLN
425
n
25
GLN
425
B
ASN
426
n
26
ASN
426
B
PHE
427
n
27
PHE
427
B
TYR
428
n
28
TYR
428
B
ASN
429
n
29
ASN
429
B
ALA
430
n
30
ALA
430
B
ILE
431
n
31
ILE
431
B
GLU
432
n
32
GLU
432
B
ALA
433
n
33
ALA
433
B
THR
434
n
34
THR
434
B
GLY
435
n
35
GLY
435
B
LYS
436
n
36
LYS
436
B
TYR
437
n
37
TYR
437
B
GLU
438
n
38
GLU
438
B
ILE
439
n
39
ILE
439
B
ILE
440
n
40
ILE
440
B
VAL
441
n
41
VAL
441
B
PHE
442
n
42
PHE
442
B
ALA
443
n
43
ALA
443
B
ILE
444
n
44
ILE
444
B
ALA
445
n
45
ALA
445
B
GLN
446
n
46
GLN
446
B
ASN
447
n
47
ASN
447
B
GLY
448
n
48
GLY
448
B
PHE
449
n
49
PHE
449
B
PHE
450
n
50
PHE
450
B
LEU
451
n
51
LEU
451
B
ASP
452
n
52
ASP
452
B
THR
453
n
53
THR
453
B
GLU
454
n
54
GLU
454
B
SER
455
n
55
SER
455
B
SER
456
n
56
SER
456
B
LYS
457
n
57
LYS
457
B
LYS
458
n
58
LYS
458
B
ILE
459
n
59
ILE
459
B
LEU
460
n
60
LEU
460
B
ALA
461
n
61
ALA
461
B
LEU
462
n
62
LEU
462
B
GLU
463
n
63
GLU
463
B
ASP
464
n
64
ASP
464
B
GLU
465
n
65
GLU
465
B
GLN
466
n
66
GLN
466
B
PRO
467
n
67
PRO
467
B
ILE
468
n
68
ILE
468
B
VAL
469
n
69
VAL
469
B
ASP
470
n
70
ASP
470
B
ALA
471
n
71
ALA
471
B
PHE
472
n
72
PHE
472
B
MET
473
n
73
MET
473
B
LYS
474
n
74
LYS
474
B
THR
475
n
75
THR
475
B
VAL
476
n
76
VAL
476
B
ASP
477
n
77
ASP
477
B
ALA
478
n
78
ALA
478
B
SER
479
n
79
SER
479
B
ASP
480
n
80
ASP
480
B
PRO
481
n
81
PRO
481
B
LEU
482
n
82
LEU
482
B
ALA
483
n
83
ALA
483
B
ARG
484
n
84
ARG
484
B
ILE
485
n
85
ILE
485
B
HIS
486
n
86
HIS
486
B
ALA
487
n
87
ALA
487
B
LEU
488
n
88
LEU
488
B
LYS
489
n
89
LYS
489
B
SER
490
n
90
SER
490
B
ALA
491
n
91
ALA
491
B
GLY
492
n
92
GLY
492
B
ASP
493
n
93
ASP
493
B
PHE
494
n
94
PHE
494
B
ASP
495
n
95
ASP
495
B
ILE
496
n
96
ILE
496
B
PHE
497
n
97
PHE
497
B
PHE
498
n
98
PHE
498
B
PRO
499
n
99
PRO
499
B
VAL
500
n
100
VAL
500
B
VAL
501
n
101
VAL
501
B
HIS
502
n
102
HIS
502
B
GLY
503
n
103
GLY
503
B
ASN
504
n
104
ASN
504
B
LEU
505
n
105
LEU
505
B
GLY
506
n
106
GLY
506
B
GLU
507
n
107
GLU
507
B
ASP
508
n
108
ASP
508
B
GLY
509
n
109
GLY
509
B
THR
510
n
110
THR
510
B
LEU
511
n
111
LEU
511
B
GLN
512
n
112
GLN
512
B
GLY
513
n
113
GLY
513
B
LEU
514
n
114
LEU
514
B
PHE
515
n
115
PHE
515
B
LYS
516
n
116
LYS
516
B
LEU
517
n
117
LEU
517
B
LEU
518
n
118
LEU
518
B
ASP
519
n
119
ASP
519
B
LYS
520
n
120
LYS
520
B
PRO
521
n
121
PRO
521
B
TYR
522
n
122
TYR
522
B
VAL
523
n
123
VAL
523
B
GLY
524
n
124
GLY
524
B
ALA
525
n
125
ALA
525
B
PRO
526
n
126
PRO
526
B
LEU
527
n
127
LEU
527
B
ARG
528
n
128
ARG
528
B
GLY
529
n
129
GLY
529
B
HIS
530
n
130
HIS
530
B
ALA
531
n
131
ALA
531
B
VAL
532
n
132
VAL
532
B
SER
533
n
133
SER
533
B
PHE
534
n
134
PHE
534
B
ASP
535
n
135
ASP
535
B
LYS
536
n
136
LYS
536
B
ALA
537
n
137
ALA
537
B
LEU
538
n
138
LEU
538
B
THR
539
n
139
THR
539
B
LYS
540
n
140
LYS
540
B
GLU
541
n
141
GLU
541
B
LEU
542
n
142
LEU
542
B
LEU
543
n
143
LEU
543
B
THR
544
n
144
THR
544
B
VAL
545
n
145
VAL
545
B
ASN
546
n
146
ASN
546
B
GLY
547
n
147
GLY
547
B
ILE
548
n
148
ILE
548
B
ARG
549
n
149
ARG
549
B
ASN
550
n
150
ASN
550
B
THR
551
n
151
THR
551
B
LYS
552
n
152
LYS
552
B
TYR
553
n
153
TYR
553
B
ILE
554
n
154
ILE
554
B
VAL
555
n
155
VAL
555
B
VAL
556
n
156
VAL
556
B
ASP
557
n
157
ASP
557
B
PRO
558
n
158
PRO
558
B
GLU
559
n
159
GLU
559
B
SER
560
n
160
SER
560
B
ALA
561
n
161
ALA
561
B
ASN
562
n
162
ASN
562
B
ASN
563
n
163
ASN
563
B
TRP
564
n
164
TRP
564
B
SER
565
n
165
SER
565
B
TRP
566
n
166
TRP
566
B
ASP
567
n
167
ASP
567
B
LYS
568
n
168
LYS
568
B
ILE
569
n
169
ILE
569
B
VAL
570
n
170
VAL
570
B
ALA
571
n
171
ALA
571
B
GLU
572
n
172
GLU
572
B
LEU
573
n
173
LEU
573
B
GLY
574
n
174
GLY
574
B
ASN
575
n
175
ASN
575
B
ILE
576
n
176
ILE
576
B
VAL
577
n
177
VAL
577
B
PHE
578
n
178
PHE
578
B
VAL
579
n
179
VAL
579
B
LYS
580
n
180
LYS
580
B
ALA
581
n
181
ALA
581
B
ALA
582
n
182
ALA
582
B
ASN
583
n
183
ASN
583
B
GLN
584
n
184
GLN
584
B
GLY
585
n
185
GLY
585
B
SER
586
n
186
SER
586
B
SER
587
n
187
SER
587
B
VAL
588
n
188
VAL
588
B
GLY
589
n
189
GLY
589
B
ILE
590
n
190
ILE
590
B
SER
591
n
191
SER
591
B
ARG
592
n
192
ARG
592
B
VAL
593
n
193
VAL
593
B
THR
594
n
194
THR
594
B
ASN
595
n
195
ASN
595
B
ALA
596
n
196
ALA
596
B
GLU
597
n
197
GLU
597
B
GLU
598
n
198
GLU
598
B
TYR
599
n
199
TYR
599
B
THR
600
n
200
THR
600
B
GLU
601
n
201
GLU
601
B
ALA
602
n
202
ALA
602
B
LEU
603
n
203
LEU
603
B
SER
604
n
204
SER
604
B
ASP
605
n
205
ASP
605
B
SER
606
n
206
SER
606
B
PHE
607
n
207
PHE
607
B
GLN
608
n
208
GLN
608
B
TYR
609
n
209
TYR
609
B
ASP
610
n
210
ASP
610
B
TYR
611
n
211
TYR
611
B
LYS
612
n
212
LYS
612
B
VAL
613
n
213
VAL
613
B
LEU
614
n
214
LEU
614
B
ILE
615
n
215
ILE
615
B
GLU
616
n
216
GLU
616
B
GLU
617
n
217
GLU
617
B
ALA
618
n
218
ALA
618
B
VAL
619
n
219
VAL
619
B
ASN
620
n
220
ASN
620
B
GLY
621
n
221
GLY
621
B
ALA
622
n
222
ALA
622
B
ARG
623
n
223
ARG
623
B
GLU
624
n
224
GLU
624
B
LEU
625
n
225
LEU
625
B
GLU
626
n
226
GLU
626
B
VAL
627
n
227
VAL
627
B
GLY
628
n
228
GLY
628
B
VAL
629
n
229
VAL
629
B
ILE
630
n
230
ILE
630
B
GLY
631
n
231
GLY
631
B
ASN
632
n
232
ASN
632
B
ASP
633
n
233
ASP
633
B
GLN
634
n
234
GLN
634
B
PRO
635
n
235
PRO
635
B
LEU
636
n
236
LEU
636
B
VAL
637
n
237
VAL
637
B
SER
638
n
238
SER
638
B
GLU
639
n
239
GLU
639
B
ILE
640
n
240
ILE
640
B
GLY
641
n
241
GLY
641
B
ALA
642
n
242
ALA
642
B
HIS
643
n
243
HIS
643
B
THR
644
n
244
THR
644
B
n
245
645
B
n
246
646
B
n
247
647
B
n
248
648
B
n
249
649
B
n
250
650
B
n
251
651
B
n
252
652
B
n
253
653
B
n
254
654
B
n
255
655
B
n
256
656
B
n
257
657
B
n
258
658
B
n
259
659
B
n
260
660
B
n
261
661
B
n
262
662
B
n
263
663
B
n
264
664
B
n
265
665
B
n
266
666
B
VAL
667
n
267
VAL
667
B
HIS
668
n
268
HIS
668
B
PHE
669
n
269
PHE
669
B
GLN
670
n
270
GLN
670
B
ILE
671
n
271
ILE
671
B
PRO
672
n
272
PRO
672
B
ALA
673
n
273
ALA
673
B
GLN
674
n
274
GLN
674
B
LEU
675
n
275
LEU
675
B
SER
676
n
276
SER
676
B
PRO
677
n
277
PRO
677
B
GLU
678
n
278
GLU
678
B
VAL
679
n
279
VAL
679
B
THR
680
n
280
THR
680
B
LYS
681
n
281
LYS
681
B
GLU
682
n
282
GLU
682
B
VAL
683
n
283
VAL
683
B
LYS
684
n
284
LYS
684
B
GLN
685
n
285
GLN
685
B
MET
686
n
286
MET
686
B
ALA
687
n
287
ALA
687
B
LEU
688
n
288
LEU
688
B
ASP
689
n
289
ASP
689
B
ALA
690
n
290
ALA
690
B
TYR
691
n
291
TYR
691
B
LYS
692
n
292
LYS
692
B
VAL
693
n
293
VAL
693
B
LEU
694
n
294
LEU
694
B
ASN
695
n
295
ASN
695
B
LEU
696
n
296
LEU
696
B
ARG
697
n
297
ARG
697
B
GLY
698
n
298
GLY
698
B
GLU
699
n
299
GLU
699
B
ALA
700
n
300
ALA
700
B
ARG
701
n
301
ARG
701
B
MET
702
n
302
MET
702
B
ASP
703
n
303
ASP
703
B
PHE
704
n
304
PHE
704
B
LEU
705
n
305
LEU
705
B
LEU
706
n
306
LEU
706
B
ASP
707
n
307
ASP
707
B
GLU
708
n
308
GLU
708
B
ASN
709
n
309
ASN
709
B
ASN
710
n
310
ASN
710
B
VAL
711
n
311
VAL
711
B
PRO
712
n
312
PRO
712
B
TYR
713
n
313
TYR
713
B
LEU
714
n
314
LEU
714
B
GLY
715
n
315
GLY
715
B
GLU
716
n
316
GLU
716
B
PRO
717
n
317
PRO
717
B
ASN
718
n
318
ASN
718
B
THR
719
n
319
THR
719
B
LEU
720
n
320
LEU
720
B
PRO
721
n
321
PRO
721
B
GLY
722
n
322
GLY
722
B
PHE
723
n
323
PHE
723
B
THR
724
n
324
THR
724
B
ASN
725
n
325
ASN
725
B
MET
726
n
326
MET
726
B
SER
727
n
327
SER
727
B
LEU
728
n
328
LEU
728
B
PHE
729
n
329
PHE
729
B
LYS
730
n
330
LYS
730
B
ARG
731
n
331
ARG
731
B
LEU
732
n
332
LEU
732
B
TRP
733
n
333
TRP
733
B
ASP
734
n
334
ASP
734
B
TYR
735
n
335
TYR
735
B
SER
736
n
336
SER
736
B
ASP
737
n
337
ASP
737
B
ILE
738
n
338
ILE
738
B
ASN
739
n
339
ASN
739
B
ASN
740
n
340
ASN
740
B
ALA
741
n
341
ALA
741
B
LYS
742
n
342
LYS
742
B
LEU
743
n
343
LEU
743
B
VAL
744
n
344
VAL
744
B
ASP
745
n
345
ASP
745
B
MET
746
n
346
MET
746
B
LEU
747
n
347
LEU
747
B
ILE
748
n
348
ILE
748
B
ASP
749
n
349
ASP
749
B
TYR
750
n
350
TYR
750
B
GLY
751
n
351
GLY
751
B
PHE
752
n
352
PHE
752
B
GLU
753
n
353
GLU
753
B
ASP
754
n
354
ASP
754
B
PHE
755
n
355
PHE
755
B
ALA
756
n
356
ALA
756
B
GLN
757
n
357
GLN
757
B
ASN
758
n
358
ASN
758
B
LYS
759
n
359
LYS
759
B
LYS
760
n
360
LYS
760
B
LEU
761
n
361
LEU
761
B
SER
762
n
362
SER
762
B
TYR
763
n
363
TYR
763
B
SER
764
n
364
SER
764
B
PHE
765
n
365
PHE
765
B
VAL
766
n
366
VAL
766
B
SER
767
n
367
SER
767
B
LEU
768
n
368
LEU
768
B
GLY
769
n
369
GLY
769
B
ALA
770
n
370
GLU
770
B
n
371
771
B
n
372
772
B
n
373
773
B
n
374
774
B
n
375
775
B
n
376
776
B
n
377
777
B
author_and_software_defined_assembly
PISA
2
dimeric
6820
-62
27050
A
GLU
316
A
OE1
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
GLU
316
A
OE2
GLU
316
1_555
49.4
A
GLU
316
A
OE1
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
ASN
318
A
OD1
ASN
318
1_555
109.1
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
ASN
318
A
OD1
ASN
318
1_555
76.3
A
GLU
316
A
OE1
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
ADP
781
E
O3B
ADP
1_555
64.9
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
ADP
781
E
O3B
ADP
1_555
92.0
A
ASN
318
A
OD1
ASN
318
1_555
A
MG
783
C
MG
MG
1_555
A
ADP
781
E
O3B
ADP
1_555
167.4
A
GLU
316
A
OE1
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
PHY
782
F
O5P
PHY
1_555
145.1
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
A
PHY
782
F
O5P
PHY
1_555
100.6
A
ASN
318
A
OD1
ASN
318
1_555
A
MG
783
C
MG
MG
1_555
A
PHY
782
F
O5P
PHY
1_555
73.0
A
ADP
781
E
O3B
ADP
1_555
A
MG
783
C
MG
MG
1_555
A
PHY
782
F
O5P
PHY
1_555
105.4
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
784
D
MG
MG
1_555
A
ADP
781
E
O2B
ADP
1_555
81.0
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
784
D
MG
MG
1_555
A
ADP
781
E
O2A
ADP
1_555
61.4
A
ADP
781
E
O2B
ADP
1_555
A
MG
784
D
MG
MG
1_555
A
ADP
781
E
O2A
ADP
1_555
76.4
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
784
D
MG
MG
1_555
A
PHY
782
F
O4P
PHY
1_555
80.7
A
ADP
781
E
O2B
ADP
1_555
A
MG
784
D
MG
MG
1_555
A
PHY
782
F
O4P
PHY
1_555
69.1
A
ADP
781
E
O2A
ADP
1_555
A
MG
784
D
MG
MG
1_555
A
PHY
782
F
O4P
PHY
1_555
132.0
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
GLU
38
A
N
GLU
38
A
O
LYS
4
A
O
LYS
4
A
N
ALA
7
A
N
ALA
7
A
O
ILE
96
A
O
ILE
96
A
O
VAL
156
A
O
VAL
156
A
N
VAL
213
A
N
VAL
213
A
O
GLU
216
A
O
GLU
216
A
N
PHE
178
A
N
PHE
178
A
O
VAL
179
A
O
VAL
179
A
N
SER
191
A
N
SER
191
A
O
GLN
270
A
O
GLN
270
A
N
ALA
242
A
N
ALA
242
A
O
HIS
243
A
O
HIS
243
A
N
GLU
224
A
N
GLU
224
A
N
GLY
231
A
N
GLY
231
A
O
GLY
298
A
O
GLY
298
A
O
LEU
305
A
O
LEU
305
A
N
TYR
313
A
N
TYR
313
B
N
LEU
451
B
N
LEU
51
B
O
ALA
443
B
O
ALA
43
B
N
GLU
438
B
N
GLU
38
B
O
LYS
404
B
O
LYS
4
B
N
ALA
407
B
N
ALA
7
B
O
ILE
496
B
O
ILE
96
B
N
VAL
556
B
N
VAL
156
B
O
VAL
613
B
O
VAL
213
B
O
GLU
616
B
O
GLU
216
B
N
PHE
578
B
N
PHE
178
B
O
VAL
579
B
O
VAL
179
B
N
SER
591
B
N
SER
191
B
N
GLN
670
B
N
GLN
270
B
O
ALA
642
B
O
ALA
242
B
N
HIS
643
B
N
HIS
243
B
O
GLU
624
B
O
GLU
224
B
O
GLY
631
B
O
GLY
231
B
N
GLY
698
B
N
GLY
298
B
O
LEU
705
B
O
LEU
305
B
N
TYR
713
B
N
TYR
313
1
B
CG
GLU
770
B
CG
GLU
370
1
Y
1
B
CD
GLU
770
B
CD
GLU
370
1
Y
1
B
OE1
GLU
770
B
OE1
GLU
370
1
Y
1
B
OE2
GLU
770
B
OE2
GLU
370
1
Y
1
A
MET
1
A
MET
1
1
Y
1
A
THR
2
A
THR
2
1
Y
1
A
TYR
363
A
TYR
363
1
Y
1
A
SER
364
A
SER
364
1
Y
1
A
PHE
365
A
PHE
365
1
Y
1
A
VAL
366
A
VAL
366
1
Y
1
A
SER
367
A
SER
367
1
Y
1
A
LEU
368
A
LEU
368
1
Y
1
A
GLY
369
A
GLY
369
1
Y
1
A
GLU
370
A
GLU
370
1
Y
1
A
GLU
371
A
GLU
371
1
Y
1
A
LYS
372
A
LYS
372
1
Y
1
A
ILE
373
A
ILE
373
1
Y
1
A
GLY
374
A
GLY
374
1
Y
1
A
LYS
375
A
LYS
375
1
Y
1
A
PHE
376
A
PHE
376
1
Y
1
A
ASN
377
A
ASN
377
1
Y
1
B
MET
401
B
MET
1
1
Y
1
B
VAL
645
B
VAL
245
1
Y
1
B
PRO
646
B
PRO
246
1
Y
1
B
ASN
647
B
ASN
247
1
Y
1
B
GLN
648
B
GLN
248
1
Y
1
B
GLY
649
B
GLY
249
1
Y
1
B
SER
650
B
SER
250
1
Y
1
B
GLY
651
B
GLY
251
1
Y
1
B
ASP
652
B
ASP
252
1
Y
1
B
GLY
653
B
GLY
253
1
Y
1
B
TRP
654
B
TRP
254
1
Y
1
B
TYR
655
B
TYR
255
1
Y
1
B
ASP
656
B
ASP
256
1
Y
1
B
TYR
657
B
TYR
257
1
Y
1
B
ASN
658
B
ASN
258
1
Y
1
B
ASN
659
B
ASN
259
1
Y
1
B
LYS
660
B
LYS
260
1
Y
1
B
PHE
661
B
PHE
261
1
Y
1
B
VAL
662
B
VAL
262
1
Y
1
B
ASP
663
B
ASP
263
1
Y
1
B
ASN
664
B
ASN
264
1
Y
1
B
SER
665
B
SER
265
1
Y
1
B
ALA
666
B
ALA
266
1
Y
1
B
GLU
771
B
GLU
371
1
Y
1
B
LYS
772
B
LYS
372
1
Y
1
B
ILE
773
B
ILE
373
1
Y
1
B
GLY
774
B
GLY
374
1
Y
1
B
LYS
775
B
LYS
375
1
Y
1
B
PHE
776
B
PHE
376
1
Y
1
B
ASN
777
B
ASN
377
1
Y
1
A
ALA
61
-65.16
11.93
1
A
LEU
82
-99.89
30.33
1
A
SER
90
-63.80
16.46
1
A
ALA
91
-153.80
7.76
1
A
SER
186
57.43
15.43
1
A
PHE
207
-64.49
7.04
1
A
ASN
232
-111.02
-98.03
1
A
SER
250
-86.56
43.95
1
A
SER
265
-69.59
10.33
1
A
PHE
323
-144.16
36.85
1
A
LEU
361
-66.45
30.25
1
B
LYS
403
-157.31
-64.30
1
B
ASN
413
-82.68
46.82
1
B
GLU
416
-98.75
34.92
1
B
LEU
462
85.05
21.34
1
B
VAL
500
-145.72
39.45
1
B
ASN
504
-73.75
22.76
1
B
LEU
505
-136.76
-37.44
1
B
GLN
584
179.28
153.19
1
B
SER
586
66.13
-29.22
1
B
SER
587
-158.93
-74.35
1
B
ALA
622
-113.71
67.66
1
B
ASN
632
-120.15
-105.04
1
B
SER
638
-69.24
-178.74
bulk solvent correction. A 3-wavelength MAD method was used to determine structure of the selenomet-protein. A native data set (A1 at CHESS) was used to refine structure.
0.257
0.184
0.184
0.184
2.38
100
951
28899
27948
82
random
1
0
0
3-wavelength MAD near Se edge (x12c at BNL)
Engh & Huber
2.38
100
213
5789
45
0
5531
0.008
1.4
1.2
2.38
100
1EHI
30564
30564
0
0
0.072
1
11.0
3.1
82
0.210
2.38
2.48
3.8
1738
2.5
47
phasing
SOLVE
refinement
X-PLOR
3.851
data reduction
DENZO
(DENZO)
data scaling
SCALEPACK
(DENZO)
D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
The ligase is a dimer formed of chain A and B.
However, part of chain B is missing in the crystallographic model.
A
GLU
16
A
GLU
16
HELX_P
A
GLY
35
A
GLY
35
1
1
20
A
ASP
52
A
ASP
52
HELX_P
A
ALA
61
A
ALA
61
1
2
10
A
ASP
64
A
ASP
64
HELX_P
A
LYS
74
A
LYS
74
1
3
11
A
ILE
85
A
ILE
85
HELX_P
A
SER
90
A
SER
90
5
4
6
A
GLY
109
A
GLY
109
HELX_P
A
LEU
118
A
LEU
118
1
5
10
A
PRO
126
A
PRO
126
HELX_P
A
ASP
135
A
ASP
135
1
6
10
A
ASP
135
A
ASP
135
HELX_P
A
VAL
145
A
VAL
145
1
7
11
A
GLU
159
A
GLU
159
HELX_P
A
TRP
164
A
TRP
164
5
8
6
A
SER
165
A
SER
165
HELX_P
A
GLY
174
A
GLY
174
1
9
10
A
ASN
195
A
ASN
195
HELX_P
A
PHE
207
A
PHE
207
1
10
13
A
ASP
256
A
ASP
256
HELX_P
A
PHE
261
A
PHE
261
1
11
6
A
SER
276
A
SER
276
HELX_P
A
LEU
294
A
LEU
294
1
12
19
A
SER
327
A
SER
327
HELX_P
A
ARG
331
A
ARG
331
5
13
5
A
ARG
331
A
ARG
331
HELX_P
A
ASP
337
A
ASP
337
5
14
7
A
ASN
339
A
ASN
339
HELX_P
A
LEU
361
A
LEU
361
1
15
23
B
GLU
416
B
GLU
16
HELX_P
B
ALA
433
B
ALA
33
1
16
18
B
ASP
452
B
ASP
52
HELX_P
B
ALA
461
B
ALA
61
1
17
10
B
ASP
464
B
ASP
64
HELX_P
B
LYS
474
B
LYS
74
1
18
11
B
LEU
482
B
LEU
82
HELX_P
B
ALA
487
B
ALA
87
1
19
6
B
GLY
509
B
GLY
109
HELX_P
B
LEU
518
B
LEU
118
1
20
10
B
PRO
526
B
PRO
126
HELX_P
B
ASP
535
B
ASP
135
1
21
10
B
ASP
535
B
ASP
135
HELX_P
B
ASN
546
B
ASN
146
1
22
12
B
GLU
559
B
GLU
159
HELX_P
B
TRP
564
B
TRP
164
5
23
6
B
SER
565
B
SER
165
HELX_P
B
LEU
573
B
LEU
173
1
24
9
B
ASN
595
B
ASN
195
HELX_P
B
PHE
607
B
PHE
207
1
25
13
B
SER
676
B
SER
276
HELX_P
B
LEU
694
B
LEU
294
1
26
19
B
SER
727
B
SER
327
HELX_P
B
ARG
731
B
ARG
331
5
27
5
B
LEU
732
B
LEU
332
HELX_P
B
ASP
737
B
ASP
337
5
28
6
B
ASN
739
B
ASN
339
HELX_P
B
LYS
759
B
LYS
359
1
29
21
metalc
2.307
A
GLU
316
A
OE1
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
metalc
2.831
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
783
C
MG
MG
1_555
metalc
2.650
A
GLU
316
A
OE2
GLU
316
1_555
A
MG
784
D
MG
MG
1_555
metalc
2.542
A
ASN
318
A
OD1
ASN
318
1_555
A
MG
783
C
MG
MG
1_555
metalc
2.476
A
ADP
781
E
O3B
ADP
1_555
A
MG
783
C
MG
MG
1_555
metalc
2.513
A
ADP
781
E
O2B
ADP
1_555
A
MG
784
D
MG
MG
1_555
metalc
2.664
A
ADP
781
E
O2A
ADP
1_555
A
MG
784
D
MG
MG
1_555
metalc
2.200
A
PHY
782
F
O5P
PHY
1_555
A
MG
783
C
MG
MG
1_555
metalc
2.248
A
PHY
782
F
O4P
PHY
1_555
A
MG
784
D
MG
MG
1_555
LIGASE
ATP-binding. Grasp motif for ATP., LIGASE
A
ILE
271
A
ILE
271
1
A
PRO
272
A
PRO
272
-0.09
B
ILE
671
B
ILE
271
1
B
PRO
672
B
PRO
272
-0.01
P71454_LEUME
UNP
1
1
P71454
MTKKRVALIFGGNSSEHDVSKRSAQNFYNAIEATGKYEIIVFAIAQNGFFLDTESSKKILALEDEQPIVDAFMKTVDASD
PLARIHALKSAGDFDIFFPVVHGNLGEDGTLQGLFKLLDKPYVGAPLRGHAVSFDKALTKELLTVNGIRNTKYIVVDPES
ANNWSWDKIVAELGNIVFVKAANQGSSVGISRVTNAEEYTEALSDSFQYDYKVLIEEAVNGARELEVGVIGNDQPLVSEI
GAHTVPNQGSGDGWYDYNNKFVDNSAVHFEIPAQLSPEVTKEVKQMALDAYKVLNLRGEARMDFLLDENNVPYLGEPNTL
PGFTNMSLFKRLWDYSDINNAKLVDMLIDYGFEDFAQNKKLSYSFVSLGEEKIGKFN
1
377
1EHI
1
377
P71454
A
1
1
377
1
377
1EHI
401
777
P71454
B
1
1
377
1
GLU
conflict
GLN
270
1EHI
A
P71454
UNP
270
270
2
GLU
conflict
GLN
670
1EHI
B
P71454
UNP
270
270
3
4
5
4
4
5
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
37
A
TYR
37
A
ILE
44
A
ILE
44
A
LYS
4
A
LYS
4
A
GLY
11
A
GLY
11
A
ILE
96
A
ILE
96
A
VAL
100
A
VAL
100
A
TYR
153
A
TYR
153
A
VAL
156
A
VAL
156
A
VAL
213
A
VAL
213
A
GLU
217
A
GLU
217
A
VAL
177
A
VAL
177
A
ALA
181
A
ALA
181
A
ILE
190
A
ILE
190
A
VAL
193
A
VAL
193
A
HIS
268
A
HIS
268
A
GLN
270
A
GLN
270
A
LEU
236
A
LEU
236
A
THR
244
A
THR
244
A
GLU
224
A
GLU
224
A
GLY
231
A
GLY
231
A
GLY
298
A
GLY
298
A
LEU
306
A
LEU
306
A
PRO
312
A
PRO
312
A
ASN
318
A
ASN
318
B
PHE
450
B
PHE
50
B
LEU
451
B
LEU
51
B
TYR
437
B
TYR
37
B
ILE
444
B
ILE
44
B
LYS
404
B
LYS
4
B
GLY
411
B
GLY
11
B
ILE
496
B
ILE
96
B
PRO
499
B
PRO
99
B
TYR
553
B
TYR
153
B
VAL
556
B
VAL
156
B
VAL
613
B
VAL
213
B
GLU
617
B
GLU
217
B
VAL
577
B
VAL
177
B
ALA
581
B
ALA
181
B
SER
591
B
SER
191
B
VAL
593
B
VAL
193
B
PHE
669
B
PHE
269
B
GLN
670
B
GLN
270
B
LEU
636
B
LEU
236
B
HIS
643
B
HIS
243
B
ARG
623
B
ARG
223
B
GLY
631
B
GLY
231
B
GLY
698
B
GLY
298
B
LEU
706
B
LEU
306
B
PRO
712
B
PRO
312
B
ASN
718
B
ASN
318
BINDING SITE FOR RESIDUE MG A 783
A
MG
783
Software
4
BINDING SITE FOR RESIDUE MG A 784
A
MG
784
Software
4
BINDING SITE FOR RESIDUE ADP A 781
A
ADP
781
Software
22
BINDING SITE FOR RESIDUE PHY A 782
A
PHY
782
Software
17
A
GLU
316
A
GLU
316
4
1_555
A
ASN
318
A
ASN
318
4
1_555
A
ADP
781
E
ADP
4
1_555
A
PHY
782
F
PHY
4
1_555
A
ASP
303
A
ASP
303
4
1_555
A
GLU
316
A
GLU
316
4
1_555
A
ADP
781
E
ADP
4
1_555
A
PHY
782
F
PHY
4
1_555
A
THR
151
A
THR
151
22
1_555
A
PHE
178
A
PHE
178
22
1_555
A
LYS
180
A
LYS
180
22
1_555
A
GLN
184
A
GLN
184
22
1_555
A
GLY
185
A
GLY
185
22
1_555
A
SER
186
A
SER
186
22
1_555
A
SER
187
A
SER
187
22
1_555
A
ILE
190
A
ILE
190
22
1_555
A
GLU
216
A
GLU
216
22
1_555
A
GLU
217
A
GLU
217
22
1_555
A
ALA
218
A
ALA
218
22
1_555
A
VAL
219
A
VAL
219
22
1_555
A
GLU
224
A
GLU
224
22
1_555
A
TRP
254
A
TRP
254
22
1_555
A
TYR
255
A
TYR
255
22
1_555
A
LYS
260
A
LYS
260
22
1_555
A
LEU
305
A
LEU
305
22
1_555
A
GLU
316
A
GLU
316
22
1_555
A
PHY
782
F
PHY
22
1_555
A
MG
783
C
MG
22
1_555
A
MG
784
D
MG
22
1_555
A
HOH
847
G
HOH
22
1_555
A
GLU
16
A
GLU
16
17
1_555
A
SER
186
A
SER
186
17
1_555
A
LYS
260
A
LYS
260
17
1_555
A
PHE
261
A
PHE
261
17
1_555
A
ARG
301
A
ARG
301
17
1_555
A
ASP
303
A
ASP
303
17
1_555
A
GLU
316
A
GLU
316
17
1_555
A
ASN
318
A
ASN
318
17
1_555
A
GLY
322
A
GLY
322
17
1_555
A
MET
326
A
MET
326
17
1_555
A
SER
327
A
SER
327
17
1_555
A
ADP
781
E
ADP
17
1_555
A
MG
783
C
MG
17
1_555
A
MG
784
D
MG
17
1_555
A
HOH
824
G
HOH
17
1_555
A
HOH
834
G
HOH
17
1_555
A
HOH
924
G
HOH
17
1_555
5
C 1 2 1