0.014788
0.000000
0.000000
-0.000000
0.014788
0.000000
0.000000
-0.000000
0.009182
0.00000
0.00000
0.00000
Maruyama, Y.
Takase, R.
Oiki, S.
Mikami, B.
Murata, K.
Hashimoto, W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
67.621
67.621
108.907
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
1097-0134
84
934
947
10.1002/prot.25042
27028675
Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity
2016
10.2210/pdb4z9x/pdb
pdb_00004z9x
100
1
CCD
2012-04-20
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL38B1
SPring-8
1.0000
SYNCHROTRON
SPRING-8 BEAMLINE BL38B1
28208.229
Gluconate 5-dehydrogenase
1.1.1.127
1
man
polymer
18.015
water
96
nat
water
2-keto-3-deoxy-D-gluconic acid 5-dehydrogenase, Putative 5-keto-D-gluconate 5-reductase
no
no
MENMFSLQGKIALITGASYGIGFEIAKAYAQAGATIVFNDIKQELVDKGLAAYRELGIEAHGYVCDVTDEAGIQQMVSQI
EDEVGAIDILVNNAGIIRRTPMLEMAAEDFRQVIDIDLNAPFIVSKAVLPSMIAKGHGKIINICSMMSELGRETVSAYAA
AKGGLKMLTKNIASEFGEANIQCNGIGPGYIATPQTAPLRERQADGSRHPFDQFIIAKTPAARWGTTEDLAGPAVFLASD
ASNFVNGHILYVDGGILAYIGKQP
MENMFSLQGKIALITGASYGIGFEIAKAYAQAGATIVFNDIKQELVDKGLAAYRELGIEAHGYVCDVTDEAGIQQMVSQI
EDEVGAIDILVNNAGIIRRTPMLEMAAEDFRQVIDIDLNAPFIVSKAVLPSMIAKGHGKIINICSMMSELGRETVSAYAA
AKGGLKMLTKNIASEFGEANIQCNGIGPGYIATPQTAPLRERQADGSRHPFDQFIIAKTPAARWGTTEDLAGPAVFLASD
ASNFVNGHILYVDGGILAYIGKQP
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
sample
1
264
idnO, M5005_Spy0524, SPy_0636
301447
Streptococcus pyogenes serotype M1
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
Biological sequence
1
2.21
44.26
VAPOR DIFFUSION, SITTING DROP
5.6
PEG 4000, sodium citrate, ammonium sulfate, nicotinamide adenine dinucleotide, 5-keto-D-gluconic acid potassium salt
293
citation
diffrn_source
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Data collection
Database references
Refinement description
1
0
2015-04-29
1
1
2016-06-22
1
2
2020-02-19
1
3
2023-11-08
_citation.journal_id_CSD
_diffrn_source.pdbx_synchrotron_site
_pdbx_struct_oper_list.symmetry_operation
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Japan
Grants-in-aid from the Japan Society for the Promotion of Science
Japan
Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of Japan
Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
Japan
Research fellowships from the Japan Society for the Promotion of Science for Young Scientists
N
RCSB
Y
PDBJ
2015-04-13
REL
REL
HOH
water
3CXR
PDB
experimental model
HOH
41
2
HOH
HOH
301
A
HOH
90
2
HOH
HOH
302
A
HOH
63
2
HOH
HOH
303
A
HOH
28
2
HOH
HOH
304
A
HOH
47
2
HOH
HOH
305
A
HOH
60
2
HOH
HOH
306
A
HOH
22
2
HOH
HOH
307
A
HOH
54
2
HOH
HOH
308
A
HOH
49
2
HOH
HOH
309
A
HOH
77
2
HOH
HOH
310
A
HOH
12
2
HOH
HOH
311
A
HOH
73
2
HOH
HOH
312
A
HOH
84
2
HOH
HOH
313
A
HOH
88
2
HOH
HOH
314
A
HOH
40
2
HOH
HOH
315
A
HOH
15
2
HOH
HOH
316
A
HOH
56
2
HOH
HOH
317
A
HOH
61
2
HOH
HOH
318
A
HOH
68
2
HOH
HOH
319
A
HOH
19
2
HOH
HOH
320
A
HOH
35
2
HOH
HOH
321
A
HOH
85
2
HOH
HOH
322
A
HOH
43
2
HOH
HOH
323
A
HOH
57
2
HOH
HOH
324
A
HOH
89
2
HOH
HOH
325
A
HOH
8
2
HOH
HOH
326
A
HOH
62
2
HOH
HOH
327
A
HOH
7
2
HOH
HOH
328
A
HOH
51
2
HOH
HOH
329
A
HOH
18
2
HOH
HOH
330
A
HOH
42
2
HOH
HOH
331
A
HOH
29
2
HOH
HOH
332
A
HOH
1
2
HOH
HOH
333
A
HOH
93
2
HOH
HOH
334
A
HOH
81
2
HOH
HOH
335
A
HOH
4
2
HOH
HOH
336
A
HOH
6
2
HOH
HOH
337
A
HOH
52
2
HOH
HOH
338
A
HOH
69
2
HOH
HOH
339
A
HOH
45
2
HOH
HOH
340
A
HOH
66
2
HOH
HOH
341
A
HOH
33
2
HOH
HOH
342
A
HOH
31
2
HOH
HOH
343
A
HOH
58
2
HOH
HOH
344
A
HOH
86
2
HOH
HOH
345
A
HOH
25
2
HOH
HOH
346
A
HOH
95
2
HOH
HOH
347
A
HOH
2
2
HOH
HOH
348
A
HOH
74
2
HOH
HOH
349
A
HOH
48
2
HOH
HOH
350
A
HOH
9
2
HOH
HOH
351
A
HOH
14
2
HOH
HOH
352
A
HOH
72
2
HOH
HOH
353
A
HOH
11
2
HOH
HOH
354
A
HOH
82
2
HOH
HOH
355
A
HOH
5
2
HOH
HOH
356
A
HOH
53
2
HOH
HOH
357
A
HOH
83
2
HOH
HOH
358
A
HOH
27
2
HOH
HOH
359
A
HOH
79
2
HOH
HOH
360
A
HOH
36
2
HOH
HOH
361
A
HOH
64
2
HOH
HOH
362
A
HOH
38
2
HOH
HOH
363
A
HOH
46
2
HOH
HOH
364
A
HOH
21
2
HOH
HOH
365
A
HOH
13
2
HOH
HOH
366
A
HOH
70
2
HOH
HOH
367
A
HOH
26
2
HOH
HOH
368
A
HOH
32
2
HOH
HOH
369
A
HOH
3
2
HOH
HOH
370
A
HOH
37
2
HOH
HOH
371
A
HOH
39
2
HOH
HOH
372
A
HOH
91
2
HOH
HOH
373
A
HOH
10
2
HOH
HOH
374
A
HOH
30
2
HOH
HOH
375
A
HOH
59
2
HOH
HOH
376
A
HOH
16
2
HOH
HOH
377
A
HOH
20
2
HOH
HOH
378
A
HOH
17
2
HOH
HOH
379
A
HOH
94
2
HOH
HOH
380
A
HOH
50
2
HOH
HOH
381
A
HOH
92
2
HOH
HOH
382
A
HOH
87
2
HOH
HOH
383
A
HOH
76
2
HOH
HOH
384
A
HOH
24
2
HOH
HOH
385
A
HOH
34
2
HOH
HOH
386
A
HOH
23
2
HOH
HOH
387
A
HOH
75
2
HOH
HOH
388
A
HOH
65
2
HOH
HOH
389
A
HOH
80
2
HOH
HOH
390
A
HOH
96
2
HOH
HOH
391
A
HOH
44
2
HOH
HOH
392
A
HOH
67
2
HOH
HOH
393
A
HOH
97
2
HOH
HOH
394
A
HOH
55
2
HOH
HOH
395
A
HOH
78
2
HOH
HOH
396
A
n
1
1
A
n
2
2
A
ASN
3
n
3
ASN
3
A
MET
4
n
4
MET
4
A
PHE
5
n
5
PHE
5
A
SER
6
n
6
SER
6
A
LEU
7
n
7
LEU
7
A
GLN
8
n
8
GLN
8
A
GLY
9
n
9
GLY
9
A
LYS
10
n
10
LYS
10
A
ILE
11
n
11
ILE
11
A
ALA
12
n
12
ALA
12
A
LEU
13
n
13
LEU
13
A
ILE
14
n
14
ILE
14
A
THR
15
n
15
THR
15
A
GLY
16
n
16
GLY
16
A
ALA
17
n
17
ALA
17
A
SER
18
n
18
SER
18
A
TYR
19
n
19
TYR
19
A
GLY
20
n
20
GLY
20
A
ILE
21
n
21
ILE
21
A
GLY
22
n
22
GLY
22
A
PHE
23
n
23
PHE
23
A
GLU
24
n
24
GLU
24
A
ILE
25
n
25
ILE
25
A
ALA
26
n
26
ALA
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
TYR
29
n
29
TYR
29
A
ALA
30
n
30
ALA
30
A
GLN
31
n
31
GLN
31
A
ALA
32
n
32
ALA
32
A
GLY
33
n
33
GLY
33
A
ALA
34
n
34
ALA
34
A
THR
35
n
35
THR
35
A
ILE
36
n
36
ILE
36
A
VAL
37
n
37
VAL
37
A
PHE
38
n
38
PHE
38
A
ASN
39
n
39
ASN
39
A
ASP
40
n
40
ASP
40
A
ILE
41
n
41
ILE
41
A
LYS
42
n
42
LYS
42
A
GLN
43
n
43
GLN
43
A
GLU
44
n
44
GLU
44
A
LEU
45
n
45
LEU
45
A
VAL
46
n
46
VAL
46
A
ASP
47
n
47
ASP
47
A
LYS
48
n
48
LYS
48
A
GLY
49
n
49
GLY
49
A
LEU
50
n
50
LEU
50
A
ALA
51
n
51
ALA
51
A
ALA
52
n
52
ALA
52
A
TYR
53
n
53
TYR
53
A
ARG
54
n
54
ARG
54
A
GLU
55
n
55
GLU
55
A
LEU
56
n
56
LEU
56
A
GLY
57
n
57
GLY
57
A
ILE
58
n
58
ILE
58
A
GLU
59
n
59
GLU
59
A
ALA
60
n
60
ALA
60
A
HIS
61
n
61
HIS
61
A
GLY
62
n
62
GLY
62
A
TYR
63
n
63
TYR
63
A
VAL
64
n
64
VAL
64
A
CYS
65
n
65
CYS
65
A
ASP
66
n
66
ASP
66
A
VAL
67
n
67
VAL
67
A
THR
68
n
68
THR
68
A
ASP
69
n
69
ASP
69
A
GLU
70
n
70
GLU
70
A
ALA
71
n
71
ALA
71
A
GLY
72
n
72
GLY
72
A
ILE
73
n
73
ILE
73
A
GLN
74
n
74
GLN
74
A
GLN
75
n
75
GLN
75
A
MET
76
n
76
MET
76
A
VAL
77
n
77
VAL
77
A
SER
78
n
78
SER
78
A
GLN
79
n
79
GLN
79
A
ILE
80
n
80
ILE
80
A
GLU
81
n
81
GLU
81
A
ASP
82
n
82
ASP
82
A
GLU
83
n
83
GLU
83
A
VAL
84
n
84
VAL
84
A
GLY
85
n
85
GLY
85
A
ALA
86
n
86
ALA
86
A
ILE
87
n
87
ILE
87
A
ASP
88
n
88
ASP
88
A
ILE
89
n
89
ILE
89
A
LEU
90
n
90
LEU
90
A
VAL
91
n
91
VAL
91
A
ASN
92
n
92
ASN
92
A
ASN
93
n
93
ASN
93
A
ALA
94
n
94
ALA
94
A
GLY
95
n
95
GLY
95
A
ILE
96
n
96
ILE
96
A
ILE
97
n
97
ILE
97
A
ARG
98
n
98
ARG
98
A
ARG
99
n
99
ARG
99
A
THR
100
n
100
THR
100
A
PRO
101
n
101
PRO
101
A
MET
102
n
102
MET
102
A
LEU
103
n
103
LEU
103
A
GLU
104
n
104
GLU
104
A
MET
105
n
105
MET
105
A
ALA
106
n
106
ALA
106
A
ALA
107
n
107
ALA
107
A
GLU
108
n
108
GLU
108
A
ASP
109
n
109
ASP
109
A
PHE
110
n
110
PHE
110
A
ARG
111
n
111
ARG
111
A
GLN
112
n
112
GLN
112
A
VAL
113
n
113
VAL
113
A
ILE
114
n
114
ILE
114
A
ASP
115
n
115
ASP
115
A
ILE
116
n
116
ILE
116
A
ASP
117
n
117
ASP
117
A
LEU
118
n
118
LEU
118
A
ASN
119
n
119
ASN
119
A
ALA
120
n
120
ALA
120
A
PRO
121
n
121
PRO
121
A
PHE
122
n
122
PHE
122
A
ILE
123
n
123
ILE
123
A
VAL
124
n
124
VAL
124
A
SER
125
n
125
SER
125
A
LYS
126
n
126
LYS
126
A
ALA
127
n
127
ALA
127
A
VAL
128
n
128
VAL
128
A
LEU
129
n
129
LEU
129
A
PRO
130
n
130
PRO
130
A
SER
131
n
131
SER
131
A
MET
132
n
132
MET
132
A
ILE
133
n
133
ILE
133
A
ALA
134
n
134
ALA
134
A
LYS
135
n
135
LYS
135
A
GLY
136
n
136
GLY
136
A
HIS
137
n
137
HIS
137
A
GLY
138
n
138
GLY
138
A
LYS
139
n
139
LYS
139
A
ILE
140
n
140
ILE
140
A
ILE
141
n
141
ILE
141
A
ASN
142
n
142
ASN
142
A
ILE
143
n
143
ILE
143
A
CYS
144
n
144
CYS
144
A
SER
145
n
145
SER
145
A
MET
146
n
146
MET
146
A
MET
147
n
147
MET
147
A
SER
148
n
148
SER
148
A
GLU
149
n
149
GLU
149
A
LEU
150
n
150
LEU
150
A
GLY
151
n
151
GLY
151
A
ARG
152
n
152
ARG
152
A
GLU
153
n
153
GLU
153
A
THR
154
n
154
THR
154
A
VAL
155
n
155
VAL
155
A
SER
156
n
156
SER
156
A
ALA
157
n
157
ALA
157
A
TYR
158
n
158
TYR
158
A
ALA
159
n
159
ALA
159
A
ALA
160
n
160
ALA
160
A
ALA
161
n
161
ALA
161
A
LYS
162
n
162
LYS
162
A
GLY
163
n
163
GLY
163
A
GLY
164
n
164
GLY
164
A
LEU
165
n
165
LEU
165
A
LYS
166
n
166
LYS
166
A
MET
167
n
167
MET
167
A
LEU
168
n
168
LEU
168
A
THR
169
n
169
THR
169
A
LYS
170
n
170
LYS
170
A
ASN
171
n
171
ASN
171
A
ILE
172
n
172
ILE
172
A
ALA
173
n
173
ALA
173
A
SER
174
n
174
SER
174
A
GLU
175
n
175
GLU
175
A
PHE
176
n
176
PHE
176
A
GLY
177
n
177
GLY
177
A
GLU
178
n
178
GLU
178
A
ALA
179
n
179
ALA
179
A
ASN
180
n
180
ASN
180
A
ILE
181
n
181
ILE
181
A
GLN
182
n
182
GLN
182
A
CYS
183
n
183
CYS
183
A
ASN
184
n
184
ASN
184
A
GLY
185
n
185
GLY
185
A
ILE
186
n
186
ILE
186
A
GLY
187
n
187
GLY
187
A
PRO
188
n
188
PRO
188
A
GLY
189
n
189
GLY
189
A
TYR
190
n
190
TYR
190
A
ILE
191
n
191
ILE
191
A
ALA
192
n
192
ALA
192
A
THR
193
n
193
THR
193
A
PRO
194
n
194
PRO
194
A
GLN
195
n
195
GLN
195
A
THR
196
n
196
THR
196
A
ALA
197
n
197
ALA
197
A
PRO
198
n
198
PRO
198
A
LEU
199
n
199
LEU
199
A
ARG
200
n
200
ARG
200
A
GLU
201
n
201
GLU
201
A
ARG
202
n
202
ARG
202
A
n
203
203
A
n
204
204
A
n
205
205
A
n
206
206
A
n
207
207
A
ARG
208
n
208
ARG
208
A
HIS
209
n
209
HIS
209
A
PRO
210
n
210
PRO
210
A
PHE
211
n
211
PHE
211
A
ASP
212
n
212
ASP
212
A
GLN
213
n
213
GLN
213
A
PHE
214
n
214
PHE
214
A
ILE
215
n
215
ILE
215
A
ILE
216
n
216
ILE
216
A
ALA
217
n
217
ALA
217
A
LYS
218
n
218
LYS
218
A
THR
219
n
219
THR
219
A
PRO
220
n
220
PRO
220
A
ALA
221
n
221
ALA
221
A
ALA
222
n
222
ALA
222
A
ARG
223
n
223
ARG
223
A
TRP
224
n
224
TRP
224
A
GLY
225
n
225
GLY
225
A
THR
226
n
226
THR
226
A
THR
227
n
227
THR
227
A
GLU
228
n
228
GLU
228
A
ASP
229
n
229
ASP
229
A
LEU
230
n
230
LEU
230
A
ALA
231
n
231
ALA
231
A
GLY
232
n
232
GLY
232
A
PRO
233
n
233
PRO
233
A
ALA
234
n
234
ALA
234
A
VAL
235
n
235
VAL
235
A
PHE
236
n
236
PHE
236
A
LEU
237
n
237
LEU
237
A
ALA
238
n
238
ALA
238
A
SER
239
n
239
SER
239
A
ASP
240
n
240
ASP
240
A
ALA
241
n
241
ALA
241
A
SER
242
n
242
SER
242
A
ASN
243
n
243
ASN
243
A
PHE
244
n
244
PHE
244
A
VAL
245
n
245
VAL
245
A
ASN
246
n
246
ASN
246
A
GLY
247
n
247
GLY
247
A
HIS
248
n
248
HIS
248
A
ILE
249
n
249
ILE
249
A
LEU
250
n
250
LEU
250
A
TYR
251
n
251
TYR
251
A
VAL
252
n
252
VAL
252
A
ASP
253
n
253
ASP
253
A
GLY
254
n
254
GLY
254
A
GLY
255
n
255
GLY
255
A
ILE
256
n
256
ILE
256
A
LEU
257
n
257
LEU
257
A
ALA
258
n
258
ALA
258
A
TYR
259
n
259
TYR
259
A
ILE
260
n
260
ILE
260
A
GLY
261
n
261
GLY
261
A
LYS
262
n
262
LYS
262
A
GLN
263
n
263
GLN
263
A
PRO
264
n
264
PRO
264
A
author_and_software_defined_assembly
PISA
4
tetrameric
16070
-107
34270
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_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_555
-y,-x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
HIS
61
A
O
HIS
61
A
N
PHE
38
A
N
PHE
38
A
O
THR
35
A
O
THR
35
A
N
ALA
12
A
N
ALA
12
A
N
LEU
13
A
N
LEU
13
A
O
VAL
91
A
O
VAL
91
A
N
LEU
90
A
N
LEU
90
A
O
ILE
141
A
O
ILE
141
A
N
ASN
142
A
N
ASN
142
A
O
ASN
184
A
O
ASN
184
A
N
GLY
185
A
N
GLY
185
A
O
LEU
250
A
O
LEU
250
1
A
HOH
366
B
HOH
1
A
MET
1
A
MET
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
GLN
203
A
GLN
203
1
Y
1
A
ALA
204
A
ALA
204
1
Y
1
A
ASP
205
A
ASP
205
1
Y
1
A
GLY
206
A
GLY
206
1
Y
1
A
SER
207
A
SER
207
1
Y
1
A
ALA
17
-85.38
39.05
1
A
VAL
84
-126.91
-54.32
1
A
LEU
118
-123.66
-53.09
1
A
CYS
144
-94.38
-148.12
1
A
THR
154
81.38
-10.92
23.612
0.59
0.00
-0.00
0.59
0.00
-1.17
0.963
0.958
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.20066
0.18234
0.18326
1.70
32.01
1420
26769
5.0
98.73
1.829
0.062
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.104
0.096
0.80
0.80
1.20
3CXR
MAXIMUM LIKELIHOOD
MASK
1.70
32.01
96
2024
0
0
1928
0.006
0.019
1967
0.001
0.020
1916
1.102
1.962
2662
0.726
3.000
4403
5.547
5.000
257
33.880
25.060
83
13.251
15.000
331
13.230
15.000
9
0.066
0.200
303
0.004
0.021
2263
0.001
0.020
430
0.911
2.217
1028
0.909
2.215
1027
1.521
3.313
1282
1.520
3.315
1283
1.277
2.493
939
1.277
2.495
940
2.117
3.666
1380
3.368
18.137
2252
3.322
18.055
2226
0.233
0.205
1.744
97
1938
20
98.36
1.70
50.00
4Z9X
28162
0.067
1
58.0
12.0
99.8
0.460
1.70
1.76
5.1
1
9.2
98.8
refinement
REFMAC
5.7.0032
data scaling
HKL-2000
data reduction
SCALEPACK
phasing
MOLREP
Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes
1
N
N
2
N
N
A
TYR
19
A
TYR
19
HELX_P
A
ALA
32
A
ALA
32
1
AA1
14
A
LYS
42
A
LYS
42
HELX_P
A
LEU
56
A
LEU
56
1
AA2
15
A
ASP
69
A
ASP
69
HELX_P
A
VAL
84
A
VAL
84
1
AA3
16
A
PRO
101
A
PRO
101
HELX_P
A
MET
105
A
MET
105
5
AA4
5
A
ALA
106
A
ALA
106
HELX_P
A
LEU
118
A
LEU
118
1
AA5
13
A
LEU
118
A
LEU
118
HELX_P
A
GLY
136
A
GLY
136
1
AA6
19
A
SER
145
A
SER
145
HELX_P
A
GLU
149
A
GLU
149
5
AA7
5
A
VAL
155
A
VAL
155
HELX_P
A
GLY
177
A
GLY
177
1
AA8
23
A
THR
193
A
THR
193
HELX_P
A
GLU
201
A
GLU
201
5
AA9
9
A
HIS
209
A
HIS
209
HELX_P
A
THR
219
A
THR
219
1
AB1
11
A
THR
227
A
THR
227
HELX_P
A
SER
239
A
SER
239
1
AB2
13
A
ASP
240
A
ASP
240
HELX_P
A
ASN
243
A
ASN
243
5
AB3
4
A
GLY
255
A
GLY
255
HELX_P
A
TYR
259
A
TYR
259
5
AB4
5
OXIDOREDUCTASE
Glycosaminoglycan metabolism, Short-chain dehydrogenase/reductase, Rossmann fold, NADH specificity, OXIDOREDUCTASE
Q9A0T1_STRP1
UNP
1
1
Q9A0T1
MENMFSLQGKIALITGASYGIGFEIAKAYAQAGATIVFNDIKQELVDKGLAAYRELGIEAHGYVCDVTDEAGIQQMVSQI
EDEVGAIDILVNNAGIIRRTPMLEMAAEDFRQVIDIDLNAPFIVSKAVLPSMIAKGHGKIINICSMMSELGRETVSAYAA
AKGGLKMLTKNIASEFGEANIQCNGIGPGYIATPQTAPLRERQADGSRHPFDQFIIAKTPAARWGTTEDLAGPAVFLASD
ASNFVNGHILYVDGGILAYIGKQP
1
264
4Z9X
1
264
Q9A0T1
A
1
1
264
7
parallel
parallel
parallel
parallel
parallel
parallel
A
HIS
61
A
HIS
61
A
VAL
64
A
VAL
64
A
THR
35
A
THR
35
A
ASP
40
A
ASP
40
A
ILE
11
A
ILE
11
A
THR
15
A
THR
15
A
ILE
89
A
ILE
89
A
ASN
92
A
ASN
92
A
GLY
138
A
GLY
138
A
ILE
143
A
ILE
143
A
ILE
181
A
ILE
181
A
PRO
188
A
PRO
188
A
ILE
249
A
ILE
249
A
VAL
252
A
VAL
252
94
P 42 21 2