0.008679
0.000000
0.000000
0.000000
0.007533
0.000000
0.000000
0.000000
0.016857
0.00000
0.00000
0.00000
Lee, J.H.
Na, Y.
Eom, S.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
115.216
132.744
59.324
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
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
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
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
N
312
N
H
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
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
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
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
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
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
Proteins
PSFGEY
0867
0887-3585
64
1078
1082
10.1002/prot.20927
16779845
Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes
2006
10.2210/pdb2fb9/pdb
pdb_00002fb9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
CCD
2004-11-24
ADSC QUANTUM 4
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
BL-6B
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-6B
35107.293
D-alanine:D-alanine ligase
6.3.2.4
1
man
polymer
18.015
water
115
nat
water
no
no
MEFMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVV
FPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANT
GSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELL
IPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELA
LT
MEFMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVV
FPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANT
GSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELL
IPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELA
LT
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
Thermus
Escherichia
sample
272
Thermus caldophilus
562
Escherichia coli
plasmid
pKK223-3
1
3.23
61.89
VAPOR DIFFUSION, HANGING DROP
8.5
29%(w/v) PEG MME 2000, 0.1M Tris-HCl, 0.2M Sodium Acetate, 0.2M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
294
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Data collection
Database references
1
0
2006-08-29
1
1
2008-05-01
1
2
2011-07-13
1
3
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
PDBJ
2005-12-08
REL
REL
HOH
water
TIP
1
2
HOH
HOH
323
A
TIP
2
2
HOH
HOH
324
A
TIP
3
2
HOH
HOH
325
A
TIP
4
2
HOH
HOH
326
A
TIP
5
2
HOH
HOH
327
A
TIP
6
2
HOH
HOH
328
A
TIP
7
2
HOH
HOH
329
A
TIP
8
2
HOH
HOH
330
A
TIP
9
2
HOH
HOH
331
A
TIP
10
2
HOH
HOH
332
A
TIP
11
2
HOH
HOH
333
A
TIP
12
2
HOH
HOH
334
A
TIP
13
2
HOH
HOH
335
A
TIP
14
2
HOH
HOH
336
A
TIP
15
2
HOH
HOH
337
A
TIP
16
2
HOH
HOH
338
A
TIP
17
2
HOH
HOH
339
A
TIP
18
2
HOH
HOH
340
A
TIP
19
2
HOH
HOH
341
A
TIP
20
2
HOH
HOH
342
A
TIP
21
2
HOH
HOH
343
A
TIP
22
2
HOH
HOH
344
A
TIP
23
2
HOH
HOH
345
A
TIP
24
2
HOH
HOH
346
A
TIP
25
2
HOH
HOH
347
A
TIP
26
2
HOH
HOH
348
A
TIP
27
2
HOH
HOH
349
A
TIP
28
2
HOH
HOH
350
A
TIP
29
2
HOH
HOH
351
A
TIP
30
2
HOH
HOH
352
A
TIP
31
2
HOH
HOH
353
A
TIP
32
2
HOH
HOH
354
A
TIP
33
2
HOH
HOH
355
A
TIP
34
2
HOH
HOH
356
A
TIP
35
2
HOH
HOH
357
A
TIP
36
2
HOH
HOH
358
A
TIP
37
2
HOH
HOH
359
A
TIP
38
2
HOH
HOH
360
A
TIP
39
2
HOH
HOH
361
A
TIP
40
2
HOH
HOH
362
A
TIP
41
2
HOH
HOH
363
A
TIP
42
2
HOH
HOH
364
A
TIP
43
2
HOH
HOH
365
A
TIP
44
2
HOH
HOH
366
A
TIP
45
2
HOH
HOH
367
A
TIP
46
2
HOH
HOH
368
A
TIP
47
2
HOH
HOH
369
A
TIP
48
2
HOH
HOH
370
A
TIP
49
2
HOH
HOH
371
A
TIP
50
2
HOH
HOH
372
A
TIP
51
2
HOH
HOH
373
A
TIP
52
2
HOH
HOH
374
A
TIP
53
2
HOH
HOH
375
A
TIP
54
2
HOH
HOH
376
A
TIP
55
2
HOH
HOH
377
A
TIP
56
2
HOH
HOH
378
A
TIP
57
2
HOH
HOH
379
A
TIP
58
2
HOH
HOH
380
A
TIP
59
2
HOH
HOH
381
A
TIP
60
2
HOH
HOH
382
A
TIP
61
2
HOH
HOH
383
A
TIP
62
2
HOH
HOH
384
A
TIP
63
2
HOH
HOH
385
A
TIP
64
2
HOH
HOH
386
A
TIP
65
2
HOH
HOH
387
A
TIP
66
2
HOH
HOH
388
A
TIP
67
2
HOH
HOH
389
A
TIP
68
2
HOH
HOH
390
A
TIP
69
2
HOH
HOH
391
A
TIP
70
2
HOH
HOH
392
A
TIP
71
2
HOH
HOH
393
A
TIP
72
2
HOH
HOH
394
A
TIP
73
2
HOH
HOH
395
A
TIP
74
2
HOH
HOH
396
A
TIP
75
2
HOH
HOH
397
A
TIP
76
2
HOH
HOH
398
A
TIP
77
2
HOH
HOH
399
A
TIP
78
2
HOH
HOH
400
A
TIP
79
2
HOH
HOH
401
A
TIP
80
2
HOH
HOH
402
A
TIP
81
2
HOH
HOH
403
A
TIP
82
2
HOH
HOH
404
A
TIP
83
2
HOH
HOH
405
A
TIP
84
2
HOH
HOH
406
A
TIP
85
2
HOH
HOH
407
A
TIP
86
2
HOH
HOH
408
A
TIP
87
2
HOH
HOH
409
A
TIP
88
2
HOH
HOH
410
A
TIP
89
2
HOH
HOH
411
A
TIP
90
2
HOH
HOH
412
A
TIP
91
2
HOH
HOH
413
A
TIP
92
2
HOH
HOH
414
A
TIP
93
2
HOH
HOH
415
A
TIP
94
2
HOH
HOH
416
A
TIP
95
2
HOH
HOH
417
A
TIP
96
2
HOH
HOH
418
A
TIP
97
2
HOH
HOH
419
A
TIP
98
2
HOH
HOH
420
A
TIP
99
2
HOH
HOH
421
A
TIP
100
2
HOH
HOH
422
A
TIP
101
2
HOH
HOH
423
A
TIP
102
2
HOH
HOH
424
A
TIP
103
2
HOH
HOH
425
A
TIP
104
2
HOH
HOH
426
A
TIP
105
2
HOH
HOH
427
A
TIP
106
2
HOH
HOH
428
A
TIP
107
2
HOH
HOH
429
A
TIP
108
2
HOH
HOH
430
A
TIP
109
2
HOH
HOH
431
A
TIP
110
2
HOH
HOH
432
A
TIP
111
2
HOH
HOH
433
A
TIP
112
2
HOH
HOH
434
A
TIP
113
2
HOH
HOH
435
A
TIP
114
2
HOH
HOH
436
A
TIP
115
2
HOH
HOH
437
A
MET
1
n
1
MET
1
A
GLU
2
n
2
GLU
2
A
PHE
3
n
3
PHE
3
A
MET
4
n
4
MET
4
A
ARG
5
n
5
ARG
5
A
VAL
6
n
6
VAL
6
A
LEU
7
n
7
LEU
7
A
LEU
8
n
8
LEU
8
A
ILE
9
n
9
ILE
9
A
ALA
10
n
10
ALA
10
A
GLY
11
n
11
GLY
11
A
GLY
12
n
12
GLY
12
A
VAL
13
n
13
VAL
13
A
SER
14
n
14
SER
14
A
PRO
15
n
15
PRO
15
A
GLU
16
n
16
GLU
16
A
HIS
17
n
17
HIS
17
A
GLU
18
n
18
GLU
18
A
VAL
19
n
19
VAL
19
A
SER
20
n
20
SER
20
A
LEU
21
n
21
LEU
21
A
LEU
22
n
22
LEU
22
A
SER
23
n
23
SER
23
A
ALA
24
n
24
ALA
24
A
GLU
25
n
25
GLU
25
A
GLY
26
n
26
GLY
26
A
VAL
27
n
27
VAL
27
A
LEU
28
n
28
LEU
28
A
ARG
29
n
29
ARG
29
A
HIS
30
n
30
HIS
30
A
ILE
31
n
31
ILE
31
A
PRO
32
n
32
PRO
32
A
PHE
33
n
33
PHE
33
A
PRO
34
n
34
PRO
34
A
THR
35
n
35
THR
35
A
ASP
36
n
36
ASP
36
A
LEU
37
n
37
LEU
37
A
ALA
38
n
38
ALA
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
ALA
41
n
41
ALA
41
A
GLN
42
n
42
GLN
42
A
ASP
43
n
43
ASP
43
A
GLY
44
n
44
GLY
44
A
ARG
45
n
45
ARG
45
A
TRP
46
n
46
TRP
46
A
LEU
47
n
47
LEU
47
A
LEU
48
n
48
LEU
48
A
GLY
49
n
49
GLY
49
A
GLU
50
n
50
GLU
50
A
LYS
51
n
51
LYS
51
A
ALA
52
n
52
ALA
52
A
LEU
53
n
53
LEU
53
A
THR
54
n
54
THR
54
A
ALA
55
n
55
ALA
55
A
LEU
56
n
56
LEU
56
A
GLU
57
n
57
GLU
57
A
ALA
58
n
58
ALA
58
A
LYS
59
n
59
LYS
59
A
ALA
60
n
60
ALA
60
A
ALA
61
n
61
ALA
61
A
PRO
62
n
62
PRO
62
A
GLU
63
n
63
GLU
63
A
GLY
64
n
64
GLY
64
A
GLU
65
n
65
GLU
65
A
HIS
66
n
66
HIS
66
A
PRO
67
n
67
PRO
67
A
PHE
68
n
68
PHE
68
A
PRO
69
n
69
PRO
69
A
PRO
70
n
70
PRO
70
A
PRO
71
n
71
PRO
71
A
LEU
72
n
72
LEU
72
A
SER
73
n
73
SER
73
A
TRP
74
n
74
TRP
74
A
GLU
75
n
75
GLU
75
A
ARG
76
n
76
ARG
76
A
TYR
77
n
77
TYR
77
A
ASP
78
n
78
ASP
78
A
VAL
79
n
79
VAL
79
A
VAL
80
n
80
VAL
80
A
PHE
81
n
81
PHE
81
A
PRO
82
n
82
PRO
82
A
LEU
83
n
83
LEU
83
A
LEU
84
n
84
LEU
84
A
HIS
85
n
85
HIS
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
PHE
88
n
88
PHE
88
A
GLY
89
n
89
GLY
89
A
GLU
90
n
90
GLU
90
A
ASP
91
n
91
ASP
91
A
GLY
92
n
92
GLY
92
A
THR
93
n
93
THR
93
A
VAL
94
n
94
VAL
94
A
GLN
95
n
95
GLN
95
A
GLY
96
n
96
GLY
96
A
PHE
97
n
97
PHE
97
A
LEU
98
n
98
LEU
98
A
GLU
99
n
99
GLU
99
A
LEU
100
n
100
LEU
100
A
LEU
101
n
101
LEU
101
A
GLY
102
n
102
GLY
102
A
LYS
103
n
103
LYS
103
A
PRO
104
n
104
PRO
104
A
TYR
105
n
105
TYR
105
A
VAL
106
n
106
VAL
106
A
GLY
107
n
107
GLY
107
A
ALA
108
n
108
ALA
108
A
GLY
109
n
109
GLY
109
A
VAL
110
n
110
VAL
110
A
ALA
111
n
111
ALA
111
A
ALA
112
n
112
ALA
112
A
SER
113
n
113
SER
113
A
ALA
114
n
114
ALA
114
A
LEU
115
n
115
LEU
115
A
CYS
116
n
116
CYS
116
A
MET
117
n
117
MET
117
A
ASP
118
n
118
ASP
118
A
LYS
119
n
119
LYS
119
A
ASP
120
n
120
ASP
120
A
LEU
121
n
121
LEU
121
A
SER
122
n
122
SER
122
A
LYS
123
n
123
LYS
123
A
ARG
124
n
124
ARG
124
A
VAL
125
n
125
VAL
125
A
LEU
126
n
126
LEU
126
A
ALA
127
n
127
ALA
127
A
GLN
128
n
128
GLN
128
A
ALA
129
n
129
ALA
129
A
GLY
130
n
130
GLY
130
A
VAL
131
n
131
VAL
131
A
PRO
132
n
132
PRO
132
A
VAL
133
n
133
VAL
133
A
VAL
134
n
134
VAL
134
A
PRO
135
n
135
PRO
135
A
TRP
136
n
136
TRP
136
A
VAL
137
n
137
VAL
137
A
ALA
138
n
138
ALA
138
A
VAL
139
n
139
VAL
139
A
ARG
140
n
140
ARG
140
A
LYS
141
n
141
LYS
141
A
GLY
142
n
142
GLY
142
A
GLU
143
n
143
GLU
143
A
PRO
144
n
144
PRO
144
A
PRO
145
n
145
PRO
145
A
VAL
146
n
146
VAL
146
A
VAL
147
n
147
VAL
147
A
PRO
148
n
148
PRO
148
A
PHE
149
n
149
PHE
149
A
ASP
150
n
150
ASP
150
A
PRO
151
n
151
PRO
151
A
PRO
152
n
152
PRO
152
A
PHE
153
n
153
PHE
153
A
PHE
154
n
154
PHE
154
A
VAL
155
n
155
VAL
155
A
LYS
156
n
156
LYS
156
A
PRO
157
n
157
PRO
157
A
ALA
158
n
158
ALA
158
A
ASN
159
n
159
ASN
159
A
THR
160
n
160
THR
160
A
GLY
161
n
161
GLY
161
A
SER
162
n
162
SER
162
A
SER
163
n
163
SER
163
A
VAL
164
n
164
VAL
164
A
GLY
165
n
165
GLY
165
A
ILE
166
n
166
ILE
166
A
SER
167
n
167
SER
167
A
ARG
168
n
168
ARG
168
A
VAL
169
n
169
VAL
169
A
GLU
170
n
170
GLU
170
A
ARG
171
n
171
ARG
171
A
PHE
172
n
172
PHE
172
A
GLN
173
n
173
GLN
173
A
ASP
174
n
174
ASP
174
A
LEU
175
n
175
LEU
175
A
GLU
176
n
176
GLU
176
A
ALA
177
n
177
ALA
177
A
ALA
178
n
178
ALA
178
A
LEU
179
n
179
LEU
179
A
ALA
180
n
180
ALA
180
A
LEU
181
n
181
LEU
181
A
ALA
182
n
182
ALA
182
A
PHE
183
n
183
PHE
183
A
ARG
184
n
184
ARG
184
A
TYR
185
n
185
TYR
185
A
ASP
186
n
186
ASP
186
A
GLU
187
n
187
GLU
187
A
LYS
188
n
188
LYS
188
A
ALA
189
n
189
ALA
189
A
VAL
190
n
190
VAL
190
A
VAL
191
n
191
VAL
191
A
GLU
192
n
192
GLU
192
A
LYS
193
n
193
LYS
193
A
ALA
194
n
194
ALA
194
A
LEU
195
n
195
LEU
195
A
SER
196
n
196
SER
196
A
PRO
197
n
197
PRO
197
A
VAL
198
n
198
VAL
198
A
ARG
199
n
199
ARG
199
A
GLU
200
n
200
GLU
200
A
LEU
201
n
201
LEU
201
A
GLU
202
n
202
GLU
202
A
VAL
203
n
203
VAL
203
A
GLY
204
n
204
GLY
204
A
VAL
205
n
205
VAL
205
A
LEU
206
n
206
LEU
206
A
GLY
207
n
207
GLY
207
A
ASN
208
n
208
ASN
208
A
VAL
209
n
209
VAL
209
A
PHE
210
n
210
PHE
210
A
GLY
211
n
211
GLY
211
A
GLU
212
n
212
GLU
212
A
ALA
213
n
213
ALA
213
A
SER
214
n
214
SER
214
A
PRO
215
n
215
PRO
215
A
VAL
216
n
216
VAL
216
A
GLY
217
n
217
GLY
217
A
GLU
218
n
218
GLU
218
A
VAL
219
n
219
VAL
219
A
ARG
220
n
220
ARG
220
A
TYR
221
n
221
TYR
221
A
GLU
222
n
222
GLU
222
A
ALA
223
n
223
ALA
223
A
PRO
224
n
224
PRO
224
A
PHE
225
n
225
PHE
225
A
TYR
226
n
226
TYR
226
A
ASP
227
n
227
ASP
227
A
TYR
228
n
228
TYR
228
A
GLU
229
n
229
GLU
229
A
THR
230
n
230
THR
230
A
LYS
231
n
231
LYS
231
A
TYR
232
n
232
TYR
232
A
THR
233
n
233
THR
233
A
PRO
234
n
234
PRO
234
A
GLY
235
n
235
GLY
235
A
ARG
236
n
236
ARG
236
A
ALA
237
n
237
ALA
237
A
GLU
238
n
238
GLU
238
A
LEU
239
n
239
LEU
239
A
LEU
240
n
240
LEU
240
A
ILE
241
n
241
ILE
241
A
PRO
242
n
242
PRO
242
A
ALA
243
n
243
ALA
243
A
PRO
244
n
244
PRO
244
A
LEU
245
n
245
LEU
245
A
ASP
246
n
246
ASP
246
A
PRO
247
n
247
PRO
247
A
GLY
248
n
248
GLY
248
A
THR
249
n
249
THR
249
A
GLN
250
n
250
GLN
250
A
GLU
251
n
251
GLU
251
A
THR
252
n
252
THR
252
A
VAL
253
n
253
VAL
253
A
GLN
254
n
254
GLN
254
A
GLU
255
n
255
GLU
255
A
LEU
256
n
256
LEU
256
A
ALA
257
n
257
ALA
257
A
LEU
258
n
258
LEU
258
A
LYS
259
n
259
LYS
259
A
ALA
260
n
260
ALA
260
A
TYR
261
n
261
TYR
261
A
LYS
262
n
262
LYS
262
A
VAL
263
n
263
VAL
263
A
LEU
264
n
264
LEU
264
A
GLY
265
n
265
GLY
265
A
VAL
266
n
266
VAL
266
A
ARG
267
n
267
ARG
267
A
GLY
268
n
268
GLY
268
A
MET
269
n
269
MET
269
A
ALA
270
n
270
ALA
270
A
ARG
271
n
271
ARG
271
A
VAL
272
n
272
VAL
272
A
ASP
273
n
273
ASP
273
A
PHE
274
n
274
PHE
274
A
PHE
275
n
275
PHE
275
A
LEU
276
n
276
LEU
276
A
ALA
277
n
277
ALA
277
A
GLU
278
n
278
GLU
278
A
GLY
279
n
279
GLY
279
A
GLU
280
n
280
GLU
280
A
LEU
281
n
281
LEU
281
A
TYR
282
n
282
TYR
282
A
LEU
283
n
283
LEU
283
A
ASN
284
n
284
ASN
284
A
GLU
285
n
285
GLU
285
A
LEU
286
n
286
LEU
286
A
ASN
287
n
287
ASN
287
A
THR
288
n
288
THR
288
A
ILE
289
n
289
ILE
289
A
PRO
290
n
290
PRO
290
A
GLY
291
n
291
GLY
291
A
PHE
292
n
292
PHE
292
A
THR
293
n
293
THR
293
A
PRO
294
n
294
PRO
294
A
THR
295
n
295
THR
295
A
SER
296
n
296
SER
296
A
MET
297
n
297
MET
297
A
TYR
298
n
298
TYR
298
A
PRO
299
n
299
PRO
299
A
ARG
300
n
300
ARG
300
A
LEU
301
n
301
LEU
301
A
PHE
302
n
302
PHE
302
A
GLU
303
n
303
GLU
303
A
ALA
304
n
304
ALA
304
A
GLY
305
n
305
GLY
305
A
GLY
306
n
306
GLY
306
A
VAL
307
n
307
VAL
307
A
ALA
308
n
308
ALA
308
A
TYR
309
n
309
TYR
309
A
PRO
310
n
310
PRO
310
A
GLU
311
n
311
GLU
311
A
LEU
312
n
312
LEU
312
A
LEU
313
n
313
LEU
313
A
ARG
314
n
314
ARG
314
A
ARG
315
n
315
ARG
315
A
LEU
316
n
316
LEU
316
A
VAL
317
n
317
VAL
317
A
GLU
318
n
318
GLU
318
A
LEU
319
n
319
LEU
319
A
ALA
320
n
320
ALA
320
A
LEU
321
n
321
LEU
321
A
THR
322
n
322
THR
322
A
author_and_software_defined_assembly
PISA,PQS
2
dimeric
2740
-22
27930
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_755
-x+2,y,-z+1/2
crystal symmetry operation
230.4320000000
0.0000000000
29.6620000000
A
O
LEU
47
A
O
LEU
47
A
N
VAL
39
A
N
VAL
39
A
O
ASP
36
A
O
ASP
36
A
N
LEU
8
A
N
LEU
8
A
N
LEU
7
A
N
LEU
7
A
O
PHE
81
A
O
PHE
81
A
N
VAL
139
A
N
VAL
139
A
O
ALA
189
A
O
ALA
189
A
O
GLU
192
A
O
GLU
192
A
N
PHE
154
A
N
PHE
154
A
N
VAL
155
A
N
VAL
155
A
O
SER
167
A
O
SER
167
A
O
GLU
238
A
O
GLU
238
A
N
ARG
220
A
N
ARG
220
A
O
GLY
217
A
O
GLY
217
A
N
GLU
202
A
N
GLU
202
A
N
LEU
201
A
N
LEU
201
A
O
PHE
274
A
O
PHE
274
A
N
ASP
273
A
N
ASP
273
A
O
GLU
285
A
O
GLU
285
A
N
ASP
227
A
N
ASP
227
A
O
LYS
231
A
O
LYS
231
1
A
PRO
32
-65.78
15.77
1
A
GLU
63
-50.39
-112.43
1
A
PHE
68
-9.17
-92.89
1
A
PRO
69
-49.34
90.54
1
A
TRP
74
58.81
-45.55
1
A
ASP
150
-41.73
157.35
1
A
VAL
198
64.70
141.33
1
A
VAL
209
67.65
-56.35
1
A
LYS
231
63.40
-141.11
1
A
ALA
270
-178.07
143.42
0.268
0.228
0.249
0.232
1.9
30
3379
33979
24867
RANDOM
1
2
MOLECULAR REPLACEMENT
Engh & Huber
1.9
30
115
2596
0
0
2481
1.9
50
2FB9
25640
2.0
2.0
1
85
1.9
1.96
1
97
data collection
HKL-2000
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
1.1
data reduction
HKL-2000
Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes
1
N
N
2
N
N
Biological unit is dimer
A
GLU
16
A
GLU
16
HELX_P
A
ILE
31
A
ILE
31
1
1
16
A
LEU
48
A
LEU
48
HELX_P
A
LEU
56
A
LEU
56
1
2
9
A
GLY
92
A
GLY
92
HELX_P
A
GLY
102
A
GLY
102
1
3
11
A
GLY
109
A
GLY
109
HELX_P
A
ASP
118
A
ASP
118
1
4
10
A
ASP
118
A
ASP
118
HELX_P
A
ALA
129
A
ALA
129
1
5
12
A
ARG
171
A
ARG
171
HELX_P
A
PHE
183
A
PHE
183
1
6
13
A
GLY
248
A
GLY
248
HELX_P
A
GLY
265
A
GLY
265
1
7
18
A
SER
296
A
SER
296
HELX_P
A
GLY
305
A
GLY
305
1
8
10
A
ALA
308
A
ALA
308
HELX_P
A
LEU
321
A
LEU
321
1
9
14
LIGASE
ligase
A
SER
196
A
SER
196
1
A
PRO
197
A
PRO
197
0.21
A
ILE
241
A
ILE
241
1
A
PRO
242
A
PRO
242
-0.06
Q3T920_THECA
UNP
1
1
Q3T920
1
319
2FB9
4
322
Q3T920
A
1
4
322
1
cloning artifact
MET
1
2FB9
A
Q3T920
UNP
1
1
cloning artifact
GLU
2
2FB9
A
Q3T920
UNP
2
1
cloning artifact
PHE
3
2FB9
A
Q3T920
UNP
3
4
4
5
2
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TRP
46
A
TRP
46
A
LEU
47
A
LEU
47
A
THR
35
A
THR
35
A
ILE
40
A
ILE
40
A
VAL
6
A
VAL
6
A
GLY
11
A
GLY
11
A
VAL
79
A
VAL
79
A
LEU
83
A
LEU
83
A
TRP
136
A
TRP
136
A
ARG
140
A
ARG
140
A
LYS
188
A
LYS
188
A
LYS
193
A
LYS
193
A
PHE
153
A
PHE
153
A
PRO
157
A
PRO
157
A
SER
167
A
SER
167
A
VAL
169
A
VAL
169
A
ARG
236
A
ARG
236
A
LEU
240
A
LEU
240
A
GLU
212
A
GLU
212
A
GLU
222
A
GLU
222
A
ARG
199
A
ARG
199
A
LEU
206
A
LEU
206
A
MET
269
A
MET
269
A
ALA
277
A
ALA
277
A
GLU
280
A
GLU
280
A
ASN
287
A
ASN
287
A
PHE
225
A
PHE
225
A
ASP
227
A
ASP
227
A
LYS
231
A
LYS
231
A
THR
233
A
THR
233
20
C 2 2 21