0.00850
0.00000
0.00000
0.00000
0.00850
0.00000
0.00000
0.00000
0.00850
0.00000
0.00000
0.00000
Asojo, O.A.
Friedman, J.M.
Belakhov, V.
Shoham, Y.
Adir, N.
Baasov, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
117.600
117.600
117.600
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 H23 N O13 P2
415.225
{[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID
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
P
N
251
N
O
N
252
N
O
N
253
N
O
N
254
N
O
N
255
N
C
N
256
R
C
N
257
N
O
N
258
R
C
N
259
N
O
N
260
R
C
N
261
N
O
N
262
R
C
N
263
N
O
N
264
N
C
N
265
N
N
N
266
N
C
N
267
N
C
N
268
N
O
N
269
N
O
N
270
N
C
N
271
N
P
N
272
N
O
N
273
N
O
N
274
N
O
N
275
N
H
N
276
N
H
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
H
N
289
N
H
N
290
N
H
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
N
N
299
S
C
N
300
N
C
N
301
N
O
N
302
N
C
Y
303
N
C
Y
304
N
C
Y
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
N
309
N
O
N
310
N
H
N
311
N
H
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
N
326
N
C
N
327
N
C
N
328
N
O
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
H
N
337
N
H
N
338
N
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
N
C
N
343
N
O
N
344
N
O
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
N
N
353
S
C
N
354
N
C
N
355
N
O
N
356
R
C
N
357
N
O
N
358
N
C
N
359
N
O
N
360
N
H
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
N
N
370
S
C
N
371
N
C
N
372
N
O
N
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
N
380
N
O
N
381
N
O
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
N
N
394
S
C
N
395
N
C
N
396
N
O
N
397
N
C
N
398
N
C
N
399
N
C
N
400
N
O
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
H
N
409
N
H
N
410
N
H
N
411
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
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
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
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
doub
N
279
N
sing
N
280
N
sing
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
doub
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
Y
295
N
doub
Y
296
N
sing
Y
297
N
sing
N
298
N
sing
Y
299
N
doub
N
300
N
sing
Y
301
N
doub
N
302
N
sing
Y
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
sing
N
313
N
doub
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
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
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
doub
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
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
doub
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
Y
364
N
doub
Y
365
N
sing
Y
366
N
sing
N
367
N
sing
Y
368
N
doub
N
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
doub
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
40
6326
6334
10.1021/bi010339d
11371194
Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
2001
10.2210/pdb1g7v/pdb
pdb_00001g7v
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
90
1
IMAGE PLATE
1997
RIGAKU RAXIS IV
MAD
M
x-ray
1
0.98104
1.0
0.98066
1.0
0.97719
1.0
X4A
NSLS
0.98104, 0.98066, 0.97719
SYNCHROTRON
NSLS BEAMLINE X4A
30870.676
2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
4.1.2.16
1
man
polymer
415.225
{[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID
1
syn
non-polymer
18.015
water
21
nat
water
KDO 8-P SYNTHASE
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
562
Escherichia coli
562
Escherichia coli
1
2.19
43.94
VAPOR DIFFUSION, HANGING DROP
6.1
MES or MOPS 61mM pH 6.1, 25% v/v Glycerol, 20mg/mL protein in tris buffer, 30 microgram/mL inhibitor, 10% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-05-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_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
RCSB
Y
RCSB
2000-11-14
REL
PAI
{[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID
HOH
water
PAI
300
2
PAI
PAI
300
A
H2O
301
3
HOH
HOH
301
A
H2O
302
3
HOH
HOH
302
A
H2O
303
3
HOH
HOH
303
A
H2O
304
3
HOH
HOH
304
A
H2O
305
3
HOH
HOH
305
A
H2O
306
3
HOH
HOH
306
A
H2O
307
3
HOH
HOH
307
A
H2O
308
3
HOH
HOH
308
A
H2O
309
3
HOH
HOH
309
A
H2O
310
3
HOH
HOH
310
A
H2O
311
3
HOH
HOH
311
A
H2O
312
3
HOH
HOH
312
A
H2O
313
3
HOH
HOH
313
A
H2O
314
3
HOH
HOH
314
A
H2O
315
3
HOH
HOH
315
A
H2O
316
3
HOH
HOH
316
A
H2O
317
3
HOH
HOH
317
A
H2O
318
3
HOH
HOH
318
A
H2O
319
3
HOH
HOH
319
A
H2O
320
3
HOH
HOH
320
A
H2O
321
3
HOH
HOH
321
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
CYS
206
n
206
CYS
206
A
ARG
207
n
207
ARG
207
A
ASP
208
n
208
ASP
208
A
PRO
209
n
209
PRO
209
A
PHE
210
n
210
PHE
210
A
GLY
211
n
211
GLY
211
A
ALA
212
n
212
ALA
212
A
ALA
213
n
213
ALA
213
A
SER
214
n
214
SER
214
A
GLY
215
n
215
GLY
215
A
GLY
216
n
216
GLY
216
A
ARG
217
n
217
ARG
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_defined_assembly
1
monomeric
software_defined_assembly
PISA,PQS
4
tetrameric
18000
-85
36760
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_575
-x,-y+2,z
crystal symmetry operation
0.0000000000
235.2000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_556
-x,y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
117.6000000000
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
235.2000000000
117.6000000000
A
N
ILE
8
A
N
ILE
8
A
O
ILE
11
A
O
ILE
11
A
N
ILE
93
A
N
ILE
93
A
O
PHE
54
A
O
PHE
54
A
N
VAL
53
A
N
VAL
53
A
O
LEU
21
A
O
LEU
21
A
O
VAL
20
A
O
VAL
20
A
N
LEU
236
A
N
LEU
236
A
N
GLY
235
A
N
GLY
235
A
O
VAL
196
A
O
VAL
196
A
N
ILE
197
A
N
ILE
197
A
O
LEU
165
A
O
LEU
165
A
N
ILE
164
A
N
ILE
164
A
O
ILE
135
A
O
ILE
135
A
O
ASN
136
A
O
ASN
136
A
N
LEU
114
A
N
LEU
114
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
ARG
207
A
ARG
207
0
Y
1
A
ASP
208
A
ASP
208
0
Y
1
A
PRO
209
A
PRO
209
0
Y
1
A
PHE
210
A
PHE
210
0
Y
1
A
GLY
211
A
GLY
211
0
Y
1
A
ALA
212
A
ALA
212
0
Y
1
A
ALA
213
A
ALA
213
0
Y
1
A
SER
214
A
SER
214
0
Y
1
A
GLY
215
A
GLY
215
0
Y
1
A
GLY
216
A
GLY
216
0
Y
1
A
A
O
N
LEU
GLN
204
205
1.51
1
A
A
O
O
CYS
PRO
206
209
2.10
1
A
LEU
204
-39.73
1
A
A
C
N
LEU
GLN
204
205
1.09
1
13.97
2.30
115.30
129.27
A
A
A
CA
CB
CG
LEU
LEU
LEU
33
33
33
N
1
16.99
2.70
111.00
127.99
A
A
A
N
CA
C
SER
SER
SER
65
65
65
N
1
9.81
1.50
119.30
129.11
A
A
A
C
N
CA
GLU
PRO
PRO
98
99
99
Y
1
30.92
2.20
117.20
148.12
A
A
A
CA
C
N
LEU
LEU
GLN
204
204
205
Y
1
-41.00
1.60
122.70
81.70
A
A
A
O
C
N
LEU
LEU
GLN
204
204
205
Y
1
27.14
2.50
121.70
148.84
A
A
A
C
N
CA
LEU
GLN
GLN
204
205
205
Y
1
-14.83
2.10
128.40
113.57
A
A
A
C
N
CD
ASP
PRO
PRO
208
209
209
Y
1
-19.49
2.70
111.00
91.51
A
A
A
N
CA
C
PHE
PHE
PHE
210
210
210
N
1
14.43
1.50
119.30
133.73
A
A
A
C
N
CA
ASP
PRO
PRO
243
244
244
Y
1
-17.62
2.10
128.40
110.78
A
A
A
C
N
CD
ASP
PRO
PRO
243
244
244
Y
1
9.17
1.10
114.20
123.37
A
A
A
CA
CB
SG
CYS
CYS
CYS
249
249
249
N
1
A
A
C
N
LEU
GLN
204
205
-0.249
0.023
1.336
1.087
Y
1
A
A
CD
N
PRO
PRO
209
209
-0.253
0.014
1.474
1.221
N
1
A
ALA
14
-171.69
143.61
1
A
PRO
18
-23.05
142.50
1
A
PHE
19
-58.13
99.84
1
A
ASN
26
-92.84
-113.54
1
A
LEU
28
-68.32
83.80
1
A
CYS
38
-64.50
-74.79
1
A
THR
43
-49.18
-74.37
1
A
LYS
60
-89.04
-104.32
1
A
ALA
61
75.02
-64.22
1
A
ARG
63
88.40
-131.51
1
A
ILE
66
71.40
-29.00
1
A
HIS
67
177.14
-30.75
1
A
SER
68
-11.62
74.79
1
A
PRO
72
-32.83
-27.31
1
A
LEU
74
-50.74
-73.50
1
A
GLU
75
-32.62
-74.68
1
A
GLN
82
-48.03
-13.96
1
A
LYS
85
-38.29
-89.88
1
A
PHE
88
-152.29
28.88
1
A
HIS
97
-130.64
-54.70
1
A
PRO
99
-3.82
-72.04
1
A
SER
100
-26.24
-63.97
1
A
GLN
101
-67.36
15.77
1
A
PRO
104
-55.31
-70.77
1
A
ALA
106
-62.85
74.79
1
A
ASP
107
-167.81
-66.20
1
A
VAL
111
-114.82
66.27
1
A
ILE
112
-41.58
153.09
1
A
ALA
119
-48.74
-84.71
1
A
THR
122
60.78
-84.92
1
A
ASP
123
-48.54
-6.95
1
A
ALA
127
-49.65
-17.23
1
A
THR
131
-164.07
-67.33
1
A
GLN
141
-67.13
0.05
1
A
ILE
151
-138.57
-39.59
1
A
LYS
162
-60.49
71.12
1
A
ASP
175
25.75
82.36
1
A
ASN
176
177.55
154.05
1
A
MET
181
-57.68
-8.94
1
A
THR
201
-69.37
-70.60
1
A
ALA
203
-23.07
-89.97
1
A
LEU
204
-64.15
47.10
1
A
ALA
212
93.26
-83.69
1
A
SER
214
149.24
154.26
1
A
ARG
217
56.70
-125.87
1
A
ARG
218
91.11
152.08
1
A
GLN
220
-153.36
65.22
1
A
HIS
241
166.79
155.44
1
A
PRO
242
-56.40
-92.69
1
A
PRO
244
35.21
-54.98
1
A
GLU
245
148.77
159.37
1
A
ASP
250
-157.69
-29.78
1
A
PRO
252
-112.02
-90.44
1
A
ASP
272
-25.30
-66.49
1
A
PHE
277
-9.12
117.51
1
A
GLU
279
-20.97
124.19
0.2420000
0.2210000
0.2250000
2.4
8.0
360
7501
7041
Random
1
3
3
MOLECULAR REPLACEMENT
Engh & Huber
2.4
8.0
21
2210
25
0
2164
0.017
25.5
2.2
2.4
46.7
2.27
30
1G7V
30388
26690
1
1
0.0910000
1
14
3.6
71
0.1430000
2.3
2.4
1
2.1
47.4
phasing
AMoRE
refinement
X-PLOR
3.1
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR
1
N
N
2
N
N
3
N
N
A
ASP
32
A
ASP
32
HELX_P
A
LEU
48
A
LEU
48
1
1
17
A
GLY
73
A
GLY
73
HELX_P
A
ILE
80
A
ILE
80
1
2
8
A
ILE
80
A
ILE
80
HELX_P
A
PHE
88
A
PHE
88
1
3
9
A
GLU
98
A
GLU
98
HELX_P
A
GLN
103
A
GLN
103
5
4
6
A
PRO
115
A
PRO
115
HELX_P
A
ALA
119
A
ALA
119
5
5
5
A
LEU
118
A
LEU
118
HELX_P
A
GLN
121
A
GLN
121
5
6
4
A
THR
122
A
THR
122
HELX_P
A
MET
128
A
MET
128
1
7
7
A
SER
144
A
SER
144
HELX_P
A
GLN
147
A
GLN
147
5
8
4
A
MET
148
A
MET
148
HELX_P
A
GLU
157
A
GLU
157
1
9
10
A
LEU
182
A
LEU
182
HELX_P
A
SER
191
A
SER
191
1
10
10
A
VAL
200
A
VAL
200
HELX_P
A
ASP
208
A
ASP
208
1
11
9
A
GLN
220
A
GLN
220
HELX_P
A
ALA
230
A
ALA
230
1
12
11
A
LEU
260
A
LEU
260
HELX_P
A
LYS
275
A
LYS
275
1
13
16
LYASE
beta-alpha-barrels, lyase, lipopolysaccharide
KDSA_ECOLI
UNP
1
1
P0A715
MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKI
FQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGN
EKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEA
HPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK
1
284
1G7V
1
284
P0A715
A
1
1
284
2
8
2
2
anti-parallel
parallel
parallel
parallel
parallel
parallel
parallel
parallel
anti-parallel
parallel
A
SER
7
A
SER
7
A
ILE
8
A
ILE
8
A
ILE
11
A
ILE
11
A
ASN
12
A
ASN
12
A
ILE
92
A
ILE
92
A
ILE
93
A
ILE
93
A
TYR
52
A
TYR
52
A
SER
57
A
SER
57
A
VAL
20
A
VAL
20
A
VAL
27
A
VAL
27
A
GLY
235
A
GLY
235
A
PHE
237
A
PHE
237
A
VAL
196
A
VAL
196
A
ASP
199
A
ASP
199
A
VAL
163
A
VAL
163
A
ASP
167
A
ASP
167
A
ILE
135
A
ILE
135
A
LYS
139
A
LYS
139
A
GLN
113
A
GLN
113
A
LEU
114
A
LEU
114
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 PAI A 300
A
PAI
300
Software
13
A
VAL
27
A
VAL
27
13
1_555
A
ASN
62
A
ASN
62
13
1_555
A
ARG
63
A
ARG
63
13
1_555
A
PHE
117
A
PHE
117
13
1_555
A
GLN
141
A
GLN
141
13
1_555
A
ARG
168
A
ARG
168
13
1_555
A
HIS
202
A
HIS
202
13
1_555
A
GLN
205
A
GLN
205
13
1_555
A
CYS
206
A
CYS
206
13
1_555
A
ALA
247
A
ALA
247
13
1_555
A
ASP
250
A
ASP
250
13
1_555
A
GLY
251
A
GLY
251
13
1_555
A
PRO
252
A
PRO
252
13
1_555
197
I 2 3