0.008443
0.000000
0.000000
0.000000
0.008443
0.000000
0.000000
0.000000
0.008443
0.00000
0.00000
0.00000
Vainer, R.
Belakhov, V.
Rabkin, E.
Baasov, T.
Adir, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90
90
90
118.441
118.441
118.441
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
C3 H5 O6 P
168.042
PHOSPHOENOLPYRUVATE
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
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
C
N
251
N
O
N
252
N
O
N
253
N
C
N
254
N
C
N
255
N
O
N
256
N
P
N
257
N
O
N
258
N
O
N
259
N
O
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
O
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
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
O
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
N
N
320
S
C
N
321
N
C
N
322
N
O
N
323
R
C
N
324
N
O
N
325
N
C
N
326
N
O
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
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
C
N
347
N
O
N
348
N
O
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
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
N
365
N
C
N
366
N
C
N
367
N
O
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
378
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
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
doub
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
sing
N
256
N
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
Y
262
N
doub
Y
263
N
sing
Y
264
N
sing
N
265
N
sing
Y
266
N
doub
N
267
N
sing
Y
268
N
doub
N
269
N
sing
Y
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
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
doub
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
doub
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
Y
331
N
doub
Y
332
N
sing
Y
333
N
sing
N
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
doub
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
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
351
641
652
10.1016/j.jmb.2005.06.021
16023668
Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility.
2005
10.2210/pdb1q3n/pdb
pdb_00001q3n
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
2003-04-23
MARRESEARCH
Bent mirror
SINGLE WAVELENGTH
M
x-ray
1
0.9797
1.0
BM30A
ESRF
0.9797
SYNCHROTRON
ESRF BEAMLINE BM30A
30870.676
2-dehydro-3-deoxyphosphooctonate aldolase
2.5.1.55
1
man
polymer
168.042
PHOSPHOENOLPYRUVATE
1
syn
non-polymer
18.015
water
69
nat
water
Phospho-2-dehydro-3-deoxyoctonate aldolase, 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase, KDO-8-phosphate synthetase, KDO 8-P synthase, KDOPS
no
no
MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKI
FQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGN
EKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEA
HPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK
MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKI
FQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGN
EKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEA
HPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK
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
Escherichia
Escherichia
sample
KDSA
562
Escherichia coli
562
Escherichia coli
1
2.24
45.15
VAPOR DIFFUSION, HANGING DROP
7.4
PEG 4000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2004-10-12
1
1
2008-04-29
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structures of kdo8p synthase in its binary complex with substrate phosphoenol pyruvate
Structure of e. Coli kdo8p synthase
CRYSTAL STRUCTURE OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE ANALOG E-FPEP
CRYSTAL STRUCTURE OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE ANALOG 1-DEOXY-A5P
Crystal structure of KDO8P synthase in its binary complex with substrate analog Z-FPEP
RCSB
Y
RCSB
2003-07-31
REL
REL
PEP
PHOSPHOENOLPYRUVATE
HOH
water
1D9E
PDB entry 1D9E
PDB
experimental model
PEP
300
2
PEP
PEP
300
A
HOH
1
3
HOH
HOH
301
A
HOH
2
3
HOH
HOH
302
A
HOH
3
3
HOH
HOH
303
A
HOH
4
3
HOH
HOH
304
A
HOH
5
3
HOH
HOH
305
A
HOH
6
3
HOH
HOH
306
A
HOH
7
3
HOH
HOH
307
A
HOH
8
3
HOH
HOH
308
A
HOH
9
3
HOH
HOH
309
A
HOH
10
3
HOH
HOH
310
A
HOH
11
3
HOH
HOH
311
A
HOH
12
3
HOH
HOH
312
A
HOH
13
3
HOH
HOH
313
A
HOH
14
3
HOH
HOH
314
A
HOH
15
3
HOH
HOH
315
A
HOH
16
3
HOH
HOH
316
A
HOH
17
3
HOH
HOH
317
A
HOH
18
3
HOH
HOH
318
A
HOH
19
3
HOH
HOH
319
A
HOH
20
3
HOH
HOH
320
A
HOH
21
3
HOH
HOH
321
A
HOH
22
3
HOH
HOH
322
A
HOH
23
3
HOH
HOH
323
A
HOH
24
3
HOH
HOH
324
A
HOH
25
3
HOH
HOH
325
A
HOH
26
3
HOH
HOH
326
A
HOH
27
3
HOH
HOH
327
A
HOH
28
3
HOH
HOH
328
A
HOH
29
3
HOH
HOH
329
A
HOH
30
3
HOH
HOH
330
A
HOH
31
3
HOH
HOH
331
A
HOH
32
3
HOH
HOH
332
A
HOH
33
3
HOH
HOH
333
A
HOH
34
3
HOH
HOH
334
A
HOH
35
3
HOH
HOH
335
A
HOH
36
3
HOH
HOH
336
A
HOH
37
3
HOH
HOH
337
A
HOH
38
3
HOH
HOH
338
A
HOH
39
3
HOH
HOH
339
A
HOH
40
3
HOH
HOH
340
A
HOH
41
3
HOH
HOH
341
A
HOH
42
3
HOH
HOH
342
A
HOH
43
3
HOH
HOH
343
A
HOH
44
3
HOH
HOH
344
A
HOH
45
3
HOH
HOH
345
A
HOH
46
3
HOH
HOH
346
A
HOH
47
3
HOH
HOH
347
A
HOH
48
3
HOH
HOH
348
A
HOH
49
3
HOH
HOH
349
A
HOH
50
3
HOH
HOH
350
A
HOH
51
3
HOH
HOH
351
A
HOH
52
3
HOH
HOH
352
A
HOH
53
3
HOH
HOH
353
A
HOH
54
3
HOH
HOH
354
A
HOH
55
3
HOH
HOH
355
A
HOH
56
3
HOH
HOH
356
A
HOH
57
3
HOH
HOH
357
A
HOH
58
3
HOH
HOH
358
A
HOH
59
3
HOH
HOH
359
A
HOH
60
3
HOH
HOH
360
A
HOH
61
3
HOH
HOH
361
A
HOH
62
3
HOH
HOH
362
A
HOH
63
3
HOH
HOH
363
A
HOH
64
3
HOH
HOH
364
A
HOH
65
3
HOH
HOH
365
A
HOH
66
3
HOH
HOH
366
A
HOH
67
3
HOH
HOH
367
A
HOH
68
3
HOH
HOH
368
A
HOH
69
3
HOH
HOH
369
A
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
GLN
3
n
3
GLN
3
A
LYS
4
n
4
LYS
4
A
VAL
5
n
5
VAL
5
A
VAL
6
n
6
VAL
6
A
SER
7
n
7
SER
7
A
ILE
8
n
8
ILE
8
A
GLY
9
n
9
GLY
9
A
ASP
10
n
10
ASP
10
A
ILE
11
n
11
ILE
11
A
ASN
12
n
12
ASN
12
A
VAL
13
n
13
VAL
13
A
ALA
14
n
14
ALA
14
A
ASN
15
n
15
ASN
15
A
ASP
16
n
16
ASP
16
A
LEU
17
n
17
LEU
17
A
PRO
18
n
18
PRO
18
A
PHE
19
n
19
PHE
19
A
VAL
20
n
20
VAL
20
A
LEU
21
n
21
LEU
21
A
PHE
22
n
22
PHE
22
A
GLY
23
n
23
GLY
23
A
GLY
24
n
24
GLY
24
A
MET
25
n
25
MET
25
A
ASN
26
n
26
ASN
26
A
VAL
27
n
27
VAL
27
A
LEU
28
n
28
LEU
28
A
GLU
29
n
29
GLU
29
A
SER
30
n
30
SER
30
A
ARG
31
n
31
ARG
31
A
ASP
32
n
32
ASP
32
A
LEU
33
n
33
LEU
33
A
ALA
34
n
34
ALA
34
A
MET
35
n
35
MET
35
A
ARG
36
n
36
ARG
36
A
ILE
37
n
37
ILE
37
A
CYS
38
n
38
CYS
38
A
GLU
39
n
39
GLU
39
A
HIS
40
n
40
HIS
40
A
TYR
41
n
41
TYR
41
A
VAL
42
n
42
VAL
42
A
THR
43
n
43
THR
43
A
VAL
44
n
44
VAL
44
A
THR
45
n
45
THR
45
A
GLN
46
n
46
GLN
46
A
LYS
47
n
47
LYS
47
A
LEU
48
n
48
LEU
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
PRO
51
n
51
PRO
51
A
TYR
52
n
52
TYR
52
A
VAL
53
n
53
VAL
53
A
PHE
54
n
54
PHE
54
A
LYS
55
n
55
LYS
55
A
ALA
56
n
56
ALA
56
A
SER
57
n
57
SER
57
A
PHE
58
n
58
PHE
58
A
ASP
59
n
59
ASP
59
A
LYS
60
n
60
LYS
60
A
ALA
61
n
61
ALA
61
A
ASN
62
n
62
ASN
62
A
ARG
63
n
63
ARG
63
A
SER
64
n
64
SER
64
A
SER
65
n
65
SER
65
A
ILE
66
n
66
ILE
66
A
HIS
67
n
67
HIS
67
A
SER
68
n
68
SER
68
A
TYR
69
n
69
TYR
69
A
ARG
70
n
70
ARG
70
A
GLY
71
n
71
GLY
71
A
PRO
72
n
72
PRO
72
A
GLY
73
n
73
GLY
73
A
LEU
74
n
74
LEU
74
A
GLU
75
n
75
GLU
75
A
GLU
76
n
76
GLU
76
A
GLY
77
n
77
GLY
77
A
MET
78
n
78
MET
78
A
LYS
79
n
79
LYS
79
A
ILE
80
n
80
ILE
80
A
PHE
81
n
81
PHE
81
A
GLN
82
n
82
GLN
82
A
GLU
83
n
83
GLU
83
A
LEU
84
n
84
LEU
84
A
LYS
85
n
85
LYS
85
A
GLN
86
n
86
GLN
86
A
THR
87
n
87
THR
87
A
PHE
88
n
88
PHE
88
A
GLY
89
n
89
GLY
89
A
VAL
90
n
90
VAL
90
A
LYS
91
n
91
LYS
91
A
ILE
92
n
92
ILE
92
A
ILE
93
n
93
ILE
93
A
THR
94
n
94
THR
94
A
ASP
95
n
95
ASP
95
A
VAL
96
n
96
VAL
96
A
HIS
97
n
97
HIS
97
A
GLU
98
n
98
GLU
98
A
PRO
99
n
99
PRO
99
A
SER
100
n
100
SER
100
A
GLN
101
n
101
GLN
101
A
ALA
102
n
102
ALA
102
A
GLN
103
n
103
GLN
103
A
PRO
104
n
104
PRO
104
A
VAL
105
n
105
VAL
105
A
ALA
106
n
106
ALA
106
A
ASP
107
n
107
ASP
107
A
VAL
108
n
108
VAL
108
A
VAL
109
n
109
VAL
109
A
ASP
110
n
110
ASP
110
A
VAL
111
n
111
VAL
111
A
ILE
112
n
112
ILE
112
A
GLN
113
n
113
GLN
113
A
LEU
114
n
114
LEU
114
A
PRO
115
n
115
PRO
115
A
ALA
116
n
116
ALA
116
A
PHE
117
n
117
PHE
117
A
LEU
118
n
118
LEU
118
A
ALA
119
n
119
ALA
119
A
ARG
120
n
120
ARG
120
A
GLN
121
n
121
GLN
121
A
THR
122
n
122
THR
122
A
ASP
123
n
123
ASP
123
A
LEU
124
n
124
LEU
124
A
VAL
125
n
125
VAL
125
A
GLU
126
n
126
GLU
126
A
ALA
127
n
127
ALA
127
A
MET
128
n
128
MET
128
A
ALA
129
n
129
ALA
129
A
LYS
130
n
130
LYS
130
A
THR
131
n
131
THR
131
A
GLY
132
n
132
GLY
132
A
ALA
133
n
133
ALA
133
A
VAL
134
n
134
VAL
134
A
ILE
135
n
135
ILE
135
A
ASN
136
n
136
ASN
136
A
VAL
137
n
137
VAL
137
A
LYS
138
n
138
LYS
138
A
LYS
139
n
139
LYS
139
A
PRO
140
n
140
PRO
140
A
GLN
141
n
141
GLN
141
A
PHE
142
n
142
PHE
142
A
VAL
143
n
143
VAL
143
A
SER
144
n
144
SER
144
A
PRO
145
n
145
PRO
145
A
GLY
146
n
146
GLY
146
A
GLN
147
n
147
GLN
147
A
MET
148
n
148
MET
148
A
GLY
149
n
149
GLY
149
A
ASN
150
n
150
ASN
150
A
ILE
151
n
151
ILE
151
A
VAL
152
n
152
VAL
152
A
ASP
153
n
153
ASP
153
A
LYS
154
n
154
LYS
154
A
PHE
155
n
155
PHE
155
A
LYS
156
n
156
LYS
156
A
GLU
157
n
157
GLU
157
A
GLY
158
n
158
GLY
158
A
GLY
159
n
159
GLY
159
A
ASN
160
n
160
ASN
160
A
GLU
161
n
161
GLU
161
A
LYS
162
n
162
LYS
162
A
VAL
163
n
163
VAL
163
A
ILE
164
n
164
ILE
164
A
LEU
165
n
165
LEU
165
A
CYS
166
n
166
CYS
166
A
ASP
167
n
167
ASP
167
A
ARG
168
n
168
ARG
168
A
GLY
169
n
169
GLY
169
A
ALA
170
n
170
ALA
170
A
ASN
171
n
171
ASN
171
A
PHE
172
n
172
PHE
172
A
GLY
173
n
173
GLY
173
A
TYR
174
n
174
TYR
174
A
ASP
175
n
175
ASP
175
A
ASN
176
n
176
ASN
176
A
LEU
177
n
177
LEU
177
A
VAL
178
n
178
VAL
178
A
VAL
179
n
179
VAL
179
A
ASP
180
n
180
ASP
180
A
MET
181
n
181
MET
181
A
LEU
182
n
182
LEU
182
A
GLY
183
n
183
GLY
183
A
PHE
184
n
184
PHE
184
A
SER
185
n
185
SER
185
A
ILE
186
n
186
ILE
186
A
MET
187
n
187
MET
187
A
LYS
188
n
188
LYS
188
A
LYS
189
n
189
LYS
189
A
VAL
190
n
190
VAL
190
A
SER
191
n
191
SER
191
A
GLY
192
n
192
GLY
192
A
ASN
193
n
193
ASN
193
A
SER
194
n
194
SER
194
A
PRO
195
n
195
PRO
195
A
VAL
196
n
196
VAL
196
A
ILE
197
n
197
ILE
197
A
PHE
198
n
198
PHE
198
A
ASP
199
n
199
ASP
199
A
VAL
200
n
200
VAL
200
A
THR
201
n
201
THR
201
A
HIS
202
n
202
HIS
202
A
ALA
203
n
203
ALA
203
A
LEU
204
n
204
LEU
204
A
GLN
205
n
205
GLN
205
A
n
206
206
A
n
207
207
A
n
208
208
A
n
209
209
A
n
210
210
A
n
211
211
A
n
212
212
A
n
213
213
A
n
214
214
A
n
215
215
A
n
216
216
A
n
217
217
A
ARG
218
n
218
ARG
218
A
ALA
219
n
219
ALA
219
A
GLN
220
n
220
GLN
220
A
VAL
221
n
221
VAL
221
A
ALA
222
n
222
ALA
222
A
GLU
223
n
223
GLU
223
A
LEU
224
n
224
LEU
224
A
ALA
225
n
225
ALA
225
A
ARG
226
n
226
ARG
226
A
ALA
227
n
227
ALA
227
A
GLY
228
n
228
GLY
228
A
MET
229
n
229
MET
229
A
ALA
230
n
230
ALA
230
A
VAL
231
n
231
VAL
231
A
GLY
232
n
232
GLY
232
A
LEU
233
n
233
LEU
233
A
ALA
234
n
234
ALA
234
A
GLY
235
n
235
GLY
235
A
LEU
236
n
236
LEU
236
A
PHE
237
n
237
PHE
237
A
ILE
238
n
238
ILE
238
A
GLU
239
n
239
GLU
239
A
ALA
240
n
240
ALA
240
A
HIS
241
n
241
HIS
241
A
PRO
242
n
242
PRO
242
A
ASP
243
n
243
ASP
243
A
PRO
244
n
244
PRO
244
A
GLU
245
n
245
GLU
245
A
HIS
246
n
246
HIS
246
A
ALA
247
n
247
ALA
247
A
LYS
248
n
248
LYS
248
A
CYS
249
n
249
CYS
249
A
ASP
250
n
250
ASP
250
A
GLY
251
n
251
GLY
251
A
PRO
252
n
252
PRO
252
A
SER
253
n
253
SER
253
A
ALA
254
n
254
ALA
254
A
LEU
255
n
255
LEU
255
A
PRO
256
n
256
PRO
256
A
LEU
257
n
257
LEU
257
A
ALA
258
n
258
ALA
258
A
LYS
259
n
259
LYS
259
A
LEU
260
n
260
LEU
260
A
GLU
261
n
261
GLU
261
A
PRO
262
n
262
PRO
262
A
PHE
263
n
263
PHE
263
A
LEU
264
n
264
LEU
264
A
LYS
265
n
265
LYS
265
A
GLN
266
n
266
GLN
266
A
MET
267
n
267
MET
267
A
LYS
268
n
268
LYS
268
A
ALA
269
n
269
ALA
269
A
ILE
270
n
270
ILE
270
A
ASP
271
n
271
ASP
271
A
ASP
272
n
272
ASP
272
A
LEU
273
n
273
LEU
273
A
VAL
274
n
274
VAL
274
A
LYS
275
n
275
LYS
275
A
GLY
276
n
276
GLY
276
A
PHE
277
n
277
PHE
277
A
GLU
278
n
278
GLU
278
A
GLU
279
n
279
GLU
279
A
LEU
280
n
280
LEU
280
A
ASP
281
n
281
ASP
281
A
THR
282
n
282
THR
282
A
SER
283
n
283
SER
283
A
LYS
284
n
284
LYS
284
A
author_and_software_defined_assembly
PISA,PQS
4
tetrameric
14840
-102
38850
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
2_675
-x+1,-y+2,z
crystal symmetry operation
118.4410000000
236.8820000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_656
-x+1,y,-z+1
crystal symmetry operation
118.4410000000
0.0000000000
118.4410000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_576
x,-y+2,-z+1
crystal symmetry operation
0.0000000000
236.8820000000
118.4410000000
A
N
PHE
54
A
N
PHE
54
A
O
LYS
91
A
O
LYS
91
A
N
THR
94
A
N
THR
94
A
O
GLN
113
A
O
GLN
113
A
N
ILE
112
A
N
ILE
112
A
O
ASN
136
A
O
ASN
136
A
N
VAL
137
A
N
VAL
137
A
O
ILE
164
A
O
ILE
164
A
N
ASP
167
A
N
ASP
167
A
O
ASP
199
A
O
ASP
199
A
N
PHE
198
A
N
PHE
198
A
O
PHE
237
A
O
PHE
237
A
N
ALA
170
A
N
ALA
170
A
O
VAL
178
A
O
VAL
178
A
N
HIS
241
A
N
HIS
241
A
O
LEU
255
A
O
LEU
255
1
A
CYS
206
A
CYS
206
1
Y
1
A
ARG
207
A
ARG
207
1
Y
1
A
ASP
208
A
ASP
208
1
Y
1
A
PRO
209
A
PRO
209
1
Y
1
A
PHE
210
A
PHE
210
1
Y
1
A
GLY
211
A
GLY
211
1
Y
1
A
ALA
212
A
ALA
212
1
Y
1
A
ALA
213
A
ALA
213
1
Y
1
A
SER
214
A
SER
214
1
Y
1
A
GLY
215
A
GLY
215
1
Y
1
A
GLY
216
A
GLY
216
1
Y
1
A
ARG
217
A
ARG
217
1
Y
1
A
A
NE2
CG
HIS
PRO
202
252
1.44
1
A
A
CD2
CG
HIS
PRO
202
252
1.77
1
A
A
OG1
O
THR
HOH
201
349
2.00
1
A
A
CD2
CB
HIS
PRO
202
252
2.05
1
A
A
OD2
O
ASP
HOH
180
366
2.06
1
A
A
OD1
O
ASP
HOH
123
359
2.07
1
A
A
CE1
O2
HIS
PEP
202
300
2.09
1
A
A
NZ
O
LYS
HOH
55
369
2.12
1
A
A
ND1
O2
HIS
PEP
202
300
2.15
1
A
A
O
O
GLY
HOH
24
351
2.18
1
A
A
OD2
O
ASP
HOH
271
362
2.18
1
A
A
O
O
ASN
HOH
26
369
2.18
1
A
ILE
8
-103.03
52.05
1
A
PHE
22
-92.01
51.04
1
A
ASN
26
-80.42
-96.01
1
A
GLU
29
-67.26
-95.99
1
A
ALA
34
-52.65
-71.22
1
A
THR
45
-55.49
-76.41
1
A
ALA
61
-57.92
2.29
1
A
ARG
63
-157.94
-127.49
1
A
SER
65
175.58
159.43
1
A
HIS
67
-73.52
45.23
1
A
GLN
82
-35.57
-71.45
1
A
GLU
83
-36.44
-75.20
1
A
PHE
88
-140.63
-21.58
1
A
SER
100
-40.43
-74.85
1
A
GLN
101
-26.12
-42.53
1
A
ALA
102
-37.57
-79.04
1
A
VAL
134
-17.16
128.55
1
A
LYS
154
-46.16
-19.21
1
A
LYS
189
-31.58
-76.89
1
A
ALA
219
-77.54
21.26
1
A
VAL
221
-39.90
-33.62
1
A
ALA
222
-77.61
-71.91
1
A
ALA
230
-65.27
0.32
1
A
ALA
247
-65.21
22.03
1
A
LYS
248
-68.93
71.02
1
A
CYS
249
-89.73
-155.72
1
A
LEU
257
-7.42
-70.00
1
A
ALA
258
-32.85
-35.66
1
A
ILE
270
-89.84
-75.15
1
A
LEU
273
-49.83
-18.58
1
A
GLU
279
-29.75
126.73
0.268
0.2349
0.265
0.2423
2.7
24
651
7735
7242
94.6
RANDOM
1
4
2
MOLECULAR REPLACEMENT
PDB entry 1D9E
Engh & Huber
2.7
24
69
2161
10
0
2082
0.006807
1.20943
23.52687
0.91537
0.34
0.27
2.8
28
253
2.62
100
1Q3N
8169
0.06
0.074
1
6
96.3
0.396
2.62
2.68
526
0.074
1
2.5
94.6
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Crystal structure of KDO8P synthase in its binary complex with substrate PEP
1
N
N
2
N
N
3
N
N
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x,-y,z; -x,y,-z; x,y,-z;
A
SER
30
A
SER
30
HELX_P
A
GLY
49
A
GLY
49
1
1
20
A
GLY
73
A
GLY
73
HELX_P
A
GLY
89
A
GLY
89
1
2
17
A
GLN
101
A
GLN
101
HELX_P
A
ASP
107
A
ASP
107
1
3
7
A
PRO
115
A
PRO
115
HELX_P
A
ALA
119
A
ALA
119
5
4
5
A
GLN
121
A
GLN
121
HELX_P
A
LYS
130
A
LYS
130
1
5
10
A
SER
144
A
SER
144
HELX_P
A
GLY
146
A
GLY
146
5
6
3
A
GLN
147
A
GLN
147
HELX_P
A
GLY
159
A
GLY
159
1
7
13
A
LEU
182
A
LEU
182
HELX_P
A
VAL
190
A
VAL
190
1
8
9
A
THR
201
A
THR
201
HELX_P
A
LEU
204
A
LEU
204
5
9
4
A
GLN
220
A
GLN
220
HELX_P
A
ALA
230
A
ALA
230
1
10
11
A
LYS
259
A
LYS
259
HELX_P
A
GLY
276
A
GLY
276
1
11
18
TRANSFERASE
BETA-ALPHA-BARRELS, LYASE, LIPOPOLYSACCHARIDE, Phosphoenolpyruvate, TRANSFERASE
KDSA_ECOLI
UNP
1
1
P0A715
MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKI
FQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGN
EKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEA
HPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK
1
284
1Q3N
1
284
P0A715
A
1
1
284
7
2
2
parallel
parallel
parallel
parallel
parallel
parallel
anti-parallel
parallel
A
VAL
53
A
VAL
53
A
LYS
55
A
LYS
55
A
LYS
91
A
LYS
91
A
ASP
95
A
ASP
95
A
VAL
111
A
VAL
111
A
LEU
114
A
LEU
114
A
ILE
135
A
ILE
135
A
LYS
139
A
LYS
139
A
VAL
163
A
VAL
163
A
ASP
167
A
ASP
167
A
VAL
196
A
VAL
196
A
ASP
199
A
ASP
199
A
GLY
235
A
GLY
235
A
PHE
237
A
PHE
237
A
ALA
170
A
ALA
170
A
ASN
171
A
ASN
171
A
LEU
177
A
LEU
177
A
VAL
178
A
VAL
178
A
ALA
240
A
ALA
240
A
HIS
241
A
HIS
241
A
LEU
255
A
LEU
255
A
PRO
256
A
PRO
256
BINDING SITE FOR RESIDUE PEP A 300
A
PEP
300
Software
6
A
LYS
138
A
LYS
138
6
1_555
A
ARG
168
A
ARG
168
6
1_555
A
HIS
202
A
HIS
202
6
1_555
A
GLY
251
A
GLY
251
6
1_555
A
PRO
252
A
PRO
252
6
1_555
A
HOH
357
C
HOH
6
1_555
197
I 2 3