0.020842
0.000000
0.000000
0.000000
0.013839
0.000000
0.000000
0.000000
0.012095
0.00000
0.00000
0.00000
Blankenfeldt, W.
Kerr, I.D.
Giraud, M.F.
McMiken, H.J.
Leonard, G.A.
Whitfield, C.
Messner, P.
Graninger, M.
Naismith, J.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
47.980
72.261
82.682
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
C21 H30 N7 O17 P3
745.421
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
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
C16 H26 N2 O15 P2
548.330
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
non-polymer
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
MG
N
251
S
P
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
Y
263
N
N
Y
264
N
C
Y
265
N
N
Y
266
N
C
Y
267
N
C
N
268
N
N
Y
269
N
N
Y
270
N
C
Y
271
N
N
Y
272
N
C
N
273
N
O
N
274
S
P
N
275
N
O
N
276
N
O
N
277
N
O
N
278
N
C
N
279
R
C
N
280
N
O
N
281
S
C
N
282
N
O
N
283
R
C
N
284
N
O
N
285
R
C
N
286
N
N
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
O
N
291
N
N
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
P
N
296
N
O
N
297
N
O
N
298
N
O
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
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
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
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
N
N
330
S
C
N
331
N
C
N
332
N
O
N
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
N
N
353
S
C
N
354
N
C
N
355
N
O
N
356
N
C
N
357
N
C
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
N
374
N
O
N
375
N
O
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
R
C
N
388
N
O
N
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
O
N
401
S
P
N
402
N
O
N
403
N
O
N
404
R
C
N
405
R
C
N
406
N
O
N
407
R
C
N
408
N
O
N
409
R
C
N
410
N
O
N
411
S
C
N
412
N
O
N
413
N
C
N
414
N
O
N
415
S
P
N
416
N
O
N
417
N
O
N
418
N
O
N
419
N
C
N
420
R
C
N
421
N
O
N
422
S
C
N
423
N
O
N
424
N
C
N
425
R
C
N
426
N
N
N
427
N
C
N
428
N
O
N
429
N
N
N
430
N
C
N
431
N
O
N
432
N
C
N
433
N
C
N
434
N
C
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
N
N
462
S
C
N
463
N
C
N
464
N
O
N
465
N
C
Y
466
N
C
Y
467
N
C
Y
468
N
C
Y
469
N
N
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
C
Y
474
N
C
N
475
N
O
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
N
N
489
S
C
N
490
N
C
N
491
N
O
N
492
N
C
Y
493
N
C
Y
494
N
C
Y
495
N
C
Y
496
N
C
Y
497
N
C
Y
498
N
C
N
499
N
O
N
500
N
O
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
H
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
H
N
510
N
H
N
511
N
H
N
512
N
N
N
513
S
C
N
514
N
C
N
515
N
O
N
516
N
C
N
517
N
C
N
518
N
C
N
519
N
O
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
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
Y
260
N
sing
Y
261
N
sing
Y
262
N
doub
N
263
N
sing
Y
264
N
sing
Y
265
N
sing
Y
266
N
doub
N
267
N
sing
Y
268
N
doub
N
269
N
sing
N
270
N
sing
Y
271
N
sing
Y
272
N
doub
N
273
N
sing
Y
274
N
sing
N
275
N
sing
N
276
N
doub
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
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
sing
N
298
N
sing
N
299
N
sing
N
300
N
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
doub
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
doub
N
312
N
sing
N
313
N
sing
N
314
N
doub
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
doub
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
doub
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
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
doub
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
N
376
N
sing
N
377
N
sing
N
378
N
doub
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
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
doub
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
doub
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
doub
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
doub
N
444
N
sing
N
445
N
sing
N
446
N
doub
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
doub
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
Y
462
N
doub
Y
463
N
sing
Y
464
N
sing
N
465
N
sing
Y
466
N
doub
Y
467
N
sing
Y
468
N
sing
N
469
N
sing
Y
470
N
sing
Y
471
N
doub
N
472
N
sing
Y
473
N
doub
N
474
N
sing
Y
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
doub
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
Y
490
N
doub
Y
491
N
sing
Y
492
N
sing
N
493
N
sing
Y
494
N
doub
N
495
N
sing
Y
496
N
doub
N
497
N
sing
Y
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
doub
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
UK
Structure
STRUE6
2005
0969-2126
10
773
786
10.1016/S0969-2126(02)00770-0
12057193
Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
2002
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
55
2043
2046
10.1107/S0907444999012251
Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella entrica serovar Typhimurim
1999
UK
Curr.Opin.Struct.Biol.
COSBEF
0801
0959-440X
10
687
696
10.1016/S0959-440X(00)00145-7
The rhamnose pathway
2000
10.2210/pdb1kc3/pdb
pdb_00001kc3
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
1999-08-27
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
0.934
1.0
ID14-1
ESRF
0.934
SYNCHROTRON
ESRF BEAMLINE ID14-1
32589.943
dTDP-glucose oxidoreductase
1.1.1.133
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
745.421
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
1
syn
non-polymer
548.330
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
1
syn
non-polymer
18.015
water
93
nat
water
dTDP-6-deoxy-L-lyxo-4-hexulose reductase; DTDP-4-DEHYDRORHAMNOSE REDUCTASE; DTDP-4-KETO-L-RHAMNOSE REDUCTASE; DTDP-6-DEOXY-L-MANNOSE DEHYDROGENASE; DTDP-L-RHAMNOSE SYNTHETASE; rfbA protein; TDP-rhamnose synthetase
E.C.1.1.1.133
no
no
MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLL
NATSVEAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFRTSWVYAGKGN
NFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGIT
LALTELNAVPTSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTTI
MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLL
NATSVEAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFRTSWVYAGKGN
NFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGIT
LALTELNAVPTSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTTI
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
Salmonella
Escherichia
sample
rfbA
602
Salmonella typhimurium
562
Escherichia coli
BL21(lambda DE3)pLysS
plasmid
pET30
1
2.20
44.04
VAPOR DIFFUSION, SITTING DROP
6.8
HEPES, PEG-MME 5000, MgCl2, pH 6.8, VAPOR DIFFUSION, SITTING DROP at 298K
298
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-06-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
apo structure
NADH complex
NADPH complex
RCSB
Y
RCSB
2001-11-07
REL
REL
MG
MAGNESIUM ION
NDP
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
TRH
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
HOH
water
MG
501
2
MG
MG
501
A
NDP
901
3
NDP
NDP
901
A
TRH
601
4
TRH
TRH
601
A
HOH
1
5
HOH
HOH
902
A
HOH
2
5
HOH
HOH
903
A
HOH
3
5
HOH
HOH
904
A
HOH
4
5
HOH
HOH
905
A
HOH
5
5
HOH
HOH
906
A
HOH
6
5
HOH
HOH
907
A
HOH
7
5
HOH
HOH
908
A
HOH
8
5
HOH
HOH
909
A
HOH
9
5
HOH
HOH
910
A
HOH
10
5
HOH
HOH
911
A
HOH
11
5
HOH
HOH
912
A
HOH
12
5
HOH
HOH
913
A
HOH
13
5
HOH
HOH
914
A
HOH
14
5
HOH
HOH
915
A
HOH
15
5
HOH
HOH
916
A
HOH
16
5
HOH
HOH
917
A
HOH
17
5
HOH
HOH
918
A
HOH
18
5
HOH
HOH
919
A
HOH
19
5
HOH
HOH
920
A
HOH
20
5
HOH
HOH
921
A
HOH
21
5
HOH
HOH
922
A
HOH
22
5
HOH
HOH
923
A
HOH
23
5
HOH
HOH
924
A
HOH
24
5
HOH
HOH
925
A
HOH
25
5
HOH
HOH
926
A
HOH
26
5
HOH
HOH
927
A
HOH
27
5
HOH
HOH
928
A
HOH
28
5
HOH
HOH
929
A
HOH
29
5
HOH
HOH
930
A
HOH
30
5
HOH
HOH
931
A
HOH
31
5
HOH
HOH
932
A
HOH
32
5
HOH
HOH
933
A
HOH
33
5
HOH
HOH
934
A
HOH
34
5
HOH
HOH
935
A
HOH
35
5
HOH
HOH
936
A
HOH
36
5
HOH
HOH
937
A
HOH
37
5
HOH
HOH
938
A
HOH
38
5
HOH
HOH
939
A
HOH
39
5
HOH
HOH
940
A
HOH
40
5
HOH
HOH
941
A
HOH
41
5
HOH
HOH
942
A
HOH
42
5
HOH
HOH
943
A
HOH
43
5
HOH
HOH
944
A
HOH
44
5
HOH
HOH
945
A
HOH
45
5
HOH
HOH
946
A
HOH
46
5
HOH
HOH
947
A
HOH
47
5
HOH
HOH
948
A
HOH
48
5
HOH
HOH
949
A
HOH
49
5
HOH
HOH
950
A
HOH
50
5
HOH
HOH
951
A
HOH
51
5
HOH
HOH
952
A
HOH
52
5
HOH
HOH
953
A
HOH
53
5
HOH
HOH
954
A
HOH
54
5
HOH
HOH
955
A
HOH
55
5
HOH
HOH
956
A
HOH
56
5
HOH
HOH
957
A
HOH
57
5
HOH
HOH
958
A
HOH
58
5
HOH
HOH
959
A
HOH
59
5
HOH
HOH
960
A
HOH
60
5
HOH
HOH
961
A
HOH
61
5
HOH
HOH
962
A
HOH
62
5
HOH
HOH
963
A
HOH
63
5
HOH
HOH
964
A
HOH
64
5
HOH
HOH
965
A
HOH
65
5
HOH
HOH
966
A
HOH
66
5
HOH
HOH
967
A
HOH
67
5
HOH
HOH
968
A
HOH
68
5
HOH
HOH
969
A
HOH
69
5
HOH
HOH
970
A
HOH
70
5
HOH
HOH
971
A
HOH
71
5
HOH
HOH
972
A
HOH
72
5
HOH
HOH
973
A
HOH
73
5
HOH
HOH
974
A
HOH
74
5
HOH
HOH
975
A
HOH
75
5
HOH
HOH
976
A
HOH
76
5
HOH
HOH
977
A
HOH
77
5
HOH
HOH
978
A
HOH
78
5
HOH
HOH
979
A
HOH
79
5
HOH
HOH
980
A
HOH
80
5
HOH
HOH
981
A
HOH
81
5
HOH
HOH
982
A
HOH
82
5
HOH
HOH
983
A
HOH
83
5
HOH
HOH
984
A
HOH
84
5
HOH
HOH
985
A
HOH
85
5
HOH
HOH
986
A
HOH
86
5
HOH
HOH
987
A
HOH
87
5
HOH
HOH
988
A
HOH
88
5
HOH
HOH
989
A
HOH
89
5
HOH
HOH
990
A
HOH
90
5
HOH
HOH
991
A
HOH
91
5
HOH
HOH
992
A
HOH
92
5
HOH
HOH
993
A
HOH
93
5
HOH
HOH
994
A
MET
1
n
1
MET
1
A
ASN
2
n
2
ASN
2
A
ILE
3
n
3
ILE
3
A
LEU
4
n
4
LEU
4
A
LEU
5
n
5
LEU
5
A
PHE
6
n
6
PHE
6
A
GLY
7
n
7
GLY
7
A
LYS
8
n
8
LYS
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
GLN
11
n
11
GLN
11
A
VAL
12
n
12
VAL
12
A
GLY
13
n
13
GLY
13
A
TRP
14
n
14
TRP
14
A
GLU
15
n
15
GLU
15
A
LEU
16
n
16
LEU
16
A
GLN
17
n
17
GLN
17
A
ARG
18
n
18
ARG
18
A
SER
19
n
19
SER
19
A
LEU
20
n
20
LEU
20
A
ALA
21
n
21
ALA
21
A
PRO
22
n
22
PRO
22
A
VAL
23
n
23
VAL
23
A
GLY
24
n
24
GLY
24
A
ASN
25
n
25
ASN
25
A
LEU
26
n
26
LEU
26
A
ILE
27
n
27
ILE
27
A
ALA
28
n
28
ALA
28
A
LEU
29
n
29
LEU
29
A
ASP
30
n
30
ASP
30
A
VAL
31
n
31
VAL
31
A
HIS
32
n
32
HIS
32
A
SER
33
n
33
SER
33
A
LYS
34
n
34
LYS
34
A
GLU
35
n
35
GLU
35
A
PHE
36
n
36
PHE
36
A
CYS
37
n
37
CYS
37
A
GLY
38
n
38
GLY
38
A
ASP
39
n
39
ASP
39
A
PHE
40
n
40
PHE
40
A
SER
41
n
41
SER
41
A
ASN
42
n
42
ASN
42
A
PRO
43
n
43
PRO
43
A
LYS
44
n
44
LYS
44
A
GLY
45
n
45
GLY
45
A
VAL
46
n
46
VAL
46
A
ALA
47
n
47
ALA
47
A
GLU
48
n
48
GLU
48
A
THR
49
n
49
THR
49
A
VAL
50
n
50
VAL
50
A
ARG
51
n
51
ARG
51
A
LYS
52
n
52
LYS
52
A
LEU
53
n
53
LEU
53
A
ARG
54
n
54
ARG
54
A
PRO
55
n
55
PRO
55
A
ASP
56
n
56
ASP
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
VAL
59
n
59
VAL
59
A
ASN
60
n
60
ASN
60
A
ALA
61
n
61
ALA
61
A
ALA
62
n
62
ALA
62
A
ALA
63
n
63
ALA
63
A
HIS
64
n
64
HIS
64
A
THR
65
n
65
THR
65
A
ALA
66
n
66
ALA
66
A
VAL
67
n
67
VAL
67
A
ASP
68
n
68
ASP
68
A
LYS
69
n
69
LYS
69
A
ALA
70
n
70
ALA
70
A
GLU
71
n
71
GLU
71
A
SER
72
n
72
SER
72
A
GLU
73
n
73
GLU
73
A
PRO
74
n
74
PRO
74
A
GLU
75
n
75
GLU
75
A
LEU
76
n
76
LEU
76
A
ALA
77
n
77
ALA
77
A
GLN
78
n
78
GLN
78
A
LEU
79
n
79
LEU
79
A
LEU
80
n
80
LEU
80
A
ASN
81
n
81
ASN
81
A
ALA
82
n
82
ALA
82
A
THR
83
n
83
THR
83
A
SER
84
n
84
SER
84
A
VAL
85
n
85
VAL
85
A
GLU
86
n
86
GLU
86
A
ALA
87
n
87
ALA
87
A
ILE
88
n
88
ILE
88
A
ALA
89
n
89
ALA
89
A
LYS
90
n
90
LYS
90
A
ALA
91
n
91
ALA
91
A
ALA
92
n
92
ALA
92
A
ASN
93
n
93
ASN
93
A
GLU
94
n
94
GLU
94
A
THR
95
n
95
THR
95
A
GLY
96
n
96
GLY
96
A
ALA
97
n
97
ALA
97
A
TRP
98
n
98
TRP
98
A
VAL
99
n
99
VAL
99
A
VAL
100
n
100
VAL
100
A
HIS
101
n
101
HIS
101
A
TYR
102
n
102
TYR
102
A
SER
103
n
103
SER
103
A
THR
104
n
104
THR
104
A
ASP
105
n
105
ASP
105
A
TYR
106
n
106
TYR
106
A
VAL
107
n
107
VAL
107
A
PHE
108
n
108
PHE
108
A
PRO
109
n
109
PRO
109
A
GLY
110
n
110
GLY
110
A
THR
111
n
111
THR
111
A
GLY
112
n
112
GLY
112
A
ASP
113
n
113
ASP
113
A
ILE
114
n
114
ILE
114
A
PRO
115
n
115
PRO
115
A
TRP
116
n
116
TRP
116
A
GLN
117
n
117
GLN
117
A
GLU
118
n
118
GLU
118
A
THR
119
n
119
THR
119
A
ASP
120
n
120
ASP
120
A
ALA
121
n
121
ALA
121
A
THR
122
n
122
THR
122
A
SER
123
n
123
SER
123
A
PRO
124
n
124
PRO
124
A
LEU
125
n
125
LEU
125
A
ASN
126
n
126
ASN
126
A
VAL
127
n
127
VAL
127
A
TYR
128
n
128
TYR
128
A
GLY
129
n
129
GLY
129
A
LYS
130
n
130
LYS
130
A
THR
131
n
131
THR
131
A
LYS
132
n
132
LYS
132
A
LEU
133
n
133
LEU
133
A
ALA
134
n
134
ALA
134
A
GLY
135
n
135
GLY
135
A
GLU
136
n
136
GLU
136
A
LYS
137
n
137
LYS
137
A
ALA
138
n
138
ALA
138
A
LEU
139
n
139
LEU
139
A
GLN
140
n
140
GLN
140
A
ASP
141
n
141
ASP
141
A
ASN
142
n
142
ASN
142
A
CYS
143
n
143
CYS
143
A
PRO
144
n
144
PRO
144
A
LYS
145
n
145
LYS
145
A
HIS
146
n
146
HIS
146
A
LEU
147
n
147
LEU
147
A
ILE
148
n
148
ILE
148
A
PHE
149
n
149
PHE
149
A
ARG
150
n
150
ARG
150
A
THR
151
n
151
THR
151
A
SER
152
n
152
SER
152
A
TRP
153
n
153
TRP
153
A
VAL
154
n
154
VAL
154
A
TYR
155
n
155
TYR
155
A
ALA
156
n
156
ALA
156
A
GLY
157
n
157
GLY
157
A
LYS
158
n
158
LYS
158
A
GLY
159
n
159
GLY
159
A
ASN
160
n
160
ASN
160
A
ASN
161
n
161
ASN
161
A
PHE
162
n
162
PHE
162
A
ALA
163
n
163
ALA
163
A
LYS
164
n
164
LYS
164
A
THR
165
n
165
THR
165
A
MET
166
n
166
MET
166
A
LEU
167
n
167
LEU
167
A
ARG
168
n
168
ARG
168
A
LEU
169
n
169
LEU
169
A
ALA
170
n
170
ALA
170
A
LYS
171
n
171
LYS
171
A
GLU
172
n
172
GLU
172
A
ARG
173
n
173
ARG
173
A
GLN
174
n
174
GLN
174
A
THR
175
n
175
THR
175
A
LEU
176
n
176
LEU
176
A
SER
177
n
177
SER
177
A
VAL
178
n
178
VAL
178
A
ILE
179
n
179
ILE
179
A
ASN
180
n
180
ASN
180
A
ASP
181
n
181
ASP
181
A
GLN
182
n
182
GLN
182
A
TYR
183
n
183
TYR
183
A
GLY
184
n
184
GLY
184
A
ALA
185
n
185
ALA
185
A
PRO
186
n
186
PRO
186
A
THR
187
n
187
THR
187
A
GLY
188
n
188
GLY
188
A
ALA
189
n
189
ALA
189
A
GLU
190
n
190
GLU
190
A
LEU
191
n
191
LEU
191
A
LEU
192
n
192
LEU
192
A
ALA
193
n
193
ALA
193
A
ASP
194
n
194
ASP
194
A
CYS
195
n
195
CYS
195
A
THR
196
n
196
THR
196
A
ALA
197
n
197
ALA
197
A
HIS
198
n
198
HIS
198
A
ALA
199
n
199
ALA
199
A
ILE
200
n
200
ILE
200
A
ARG
201
n
201
ARG
201
A
VAL
202
n
202
VAL
202
A
ALA
203
n
203
ALA
203
A
LEU
204
n
204
LEU
204
A
ASN
205
n
205
ASN
205
A
LYS
206
n
206
LYS
206
A
PRO
207
n
207
PRO
207
A
GLU
208
n
208
GLU
208
A
VAL
209
n
209
VAL
209
A
ALA
210
n
210
ALA
210
A
GLY
211
n
211
GLY
211
A
LEU
212
n
212
LEU
212
A
TYR
213
n
213
TYR
213
A
HIS
214
n
214
HIS
214
A
LEU
215
n
215
LEU
215
A
VAL
216
n
216
VAL
216
A
ALA
217
n
217
ALA
217
A
GLY
218
n
218
GLY
218
A
GLY
219
n
219
GLY
219
A
THR
220
n
220
THR
220
A
THR
221
n
221
THR
221
A
THR
222
n
222
THR
222
A
TRP
223
n
223
TRP
223
A
HIS
224
n
224
HIS
224
A
ASP
225
n
225
ASP
225
A
TYR
226
n
226
TYR
226
A
ALA
227
n
227
ALA
227
A
ALA
228
n
228
ALA
228
A
LEU
229
n
229
LEU
229
A
VAL
230
n
230
VAL
230
A
PHE
231
n
231
PHE
231
A
ASP
232
n
232
ASP
232
A
GLU
233
n
233
GLU
233
A
ALA
234
n
234
ALA
234
A
ARG
235
n
235
ARG
235
A
LYS
236
n
236
LYS
236
A
ALA
237
n
237
ALA
237
A
GLY
238
n
238
GLY
238
A
ILE
239
n
239
ILE
239
A
THR
240
n
240
THR
240
A
LEU
241
n
241
LEU
241
A
ALA
242
n
242
ALA
242
A
LEU
243
n
243
LEU
243
A
THR
244
n
244
THR
244
A
GLU
245
n
245
GLU
245
A
LEU
246
n
246
LEU
246
A
ASN
247
n
247
ASN
247
A
ALA
248
n
248
ALA
248
A
VAL
249
n
249
VAL
249
A
PRO
250
n
250
PRO
250
A
THR
251
n
251
THR
251
A
SER
252
n
252
SER
252
A
ALA
253
n
253
ALA
253
A
TYR
254
n
254
TYR
254
A
PRO
255
n
255
PRO
255
A
THR
256
n
256
THR
256
A
PRO
257
n
257
PRO
257
A
ALA
258
n
258
ALA
258
A
SER
259
n
259
SER
259
A
ARG
260
n
260
ARG
260
A
PRO
261
n
261
PRO
261
A
GLY
262
n
262
GLY
262
A
ASN
263
n
263
ASN
263
A
SER
264
n
264
SER
264
A
ARG
265
n
265
ARG
265
A
LEU
266
n
266
LEU
266
A
ASN
267
n
267
ASN
267
A
THR
268
n
268
THR
268
A
GLU
269
n
269
GLU
269
A
LYS
270
n
270
LYS
270
A
PHE
271
n
271
PHE
271
A
GLN
272
n
272
GLN
272
A
ARG
273
n
273
ARG
273
A
ASN
274
n
274
ASN
274
A
PHE
275
n
275
PHE
275
A
ASP
276
n
276
ASP
276
A
LEU
277
n
277
LEU
277
A
ILE
278
n
278
ILE
278
A
LEU
279
n
279
LEU
279
A
PRO
280
n
280
PRO
280
A
GLN
281
n
281
GLN
281
A
TRP
282
n
282
TRP
282
A
GLU
283
n
283
GLU
283
A
LEU
284
n
284
LEU
284
A
GLY
285
n
285
GLY
285
A
VAL
286
n
286
VAL
286
A
LYS
287
n
287
LYS
287
A
ARG
288
n
288
ARG
288
A
MET
289
n
289
MET
289
A
LEU
290
n
290
LEU
290
A
THR
291
n
291
THR
291
A
GLU
292
n
292
GLU
292
A
MET
293
n
293
MET
293
A
PHE
294
n
294
PHE
294
A
THR
295
n
295
THR
295
A
THR
296
n
296
THR
296
A
THR
297
n
297
THR
297
A
THR
298
n
298
THR
298
A
n
299
299
A
author_and_software_defined_assembly
PISA,PQS
2
dimeric
7110
-40
23850
A
HOH
908
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
908
E
O
HOH
2_555
174.5
A
HOH
908
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
1_555
97.2
A
HOH
908
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
1_555
78.4
A
HOH
908
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
2_555
81.8
A
HOH
908
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
2_555
94.1
A
HOH
909
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
2_555
77.7
A
HOH
908
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
1_555
95.6
A
HOH
908
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
1_555
88.3
A
HOH
909
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
1_555
98.5
A
HOH
909
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
1_555
175.0
A
HOH
908
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
92.3
A
HOH
908
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
92.0
A
HOH
909
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
169.7
A
HOH
909
E
O
HOH
2_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
99.7
A
HOH
910
E
O
HOH
1_555
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
84.6
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
A
O
ASN
25
A
O
ASN
25
A
N
ILE
3
A
N
ILE
3
A
N
LEU
4
A
N
LEU
4
A
O
VAL
59
A
O
VAL
59
A
N
ILE
58
A
N
ILE
58
A
O
VAL
100
A
O
VAL
100
A
N
VAL
99
A
N
VAL
99
A
O
LEU
147
A
O
LEU
147
A
N
ILE
148
A
N
ILE
148
A
O
TYR
213
A
O
TYR
213
A
N
TYR
155
A
N
TYR
155
A
O
THR
187
A
O
THR
187
A
N
LEU
176
A
N
LEU
176
A
O
ASN
247
A
O
ASN
247
A
O
THR
221
A
O
THR
221
A
N
GLY
184
A
N
GLY
184
A
N
TYR
183
A
N
TYR
183
A
O
SER
264
A
O
SER
264
1
A
MG
501
B
MG
1
A
ILE
299
A
ILE
299
1
Y
1
A
A
CD
OE1
GLU
GLU
15
15
-0.066
0.011
1.252
1.186
N
1
A
HIS
32
-78.59
23.17
1
A
PHE
36
178.91
128.39
1
A
ALA
82
-128.81
-60.86
1
A
THR
111
39.03
79.02
1
A
ASP
113
69.99
-91.27
1
A
CYS
143
-151.66
89.28
1
A
ALA
217
-48.26
154.98
1
A
THR
251
7.72
-75.82
1
A
PHE
294
-69.26
1.64
1
A
THR
296
-104.34
70.39
39.02
5.95
0.00
0.00
-5.28
0.00
-0.67
TLS-option with cofactor-binding, substrate-binding domains and waters as three separate TLS-bodies was used throughout
0.2889700
0.1910000
0.1986970
0.1960000
2.70
28.87
413
7806
7806
5.0
98.67
18.382
0.364
0.449
RANDOM
1
isotropic
THROUGHOUT
0
MAD
0.449
Engh & Huber
0.449
2.70
28.87
93
2464
84
0
2287
0.024
0.021
2.282
1.987
0.938
1.50
1.700
2.00
2.266
3.00
3.195
4.50
0.2900000
0.2140000
2.77
30
581
20
66
2.70
28.75
1KC3
7905
7905
1.8
0.1050000
1
3.8
3.5
99.1
0.3770000
2.70
2.77
1.8
1
3.4
99.3
phasing
SOLVE
refinement
REFMAC
5.0
data reduction
DENZO
data scaling
SCALEPACK
Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
The biological assembly is a dimer generated by the twofold axis along c: -x, -y, z.
A
GLY
10
A
GLY
10
HELX_P
A
ALA
21
A
ALA
21
1
1
12
A
ASN
42
A
ASN
42
HELX_P
A
ARG
54
A
ARG
54
1
2
13
A
ALA
66
A
ALA
66
HELX_P
A
GLU
73
A
GLU
73
1
3
8
A
GLU
73
A
GLU
73
HELX_P
A
ALA
82
A
ALA
82
1
4
10
A
ALA
82
A
ALA
82
HELX_P
A
GLY
96
A
GLY
96
1
5
15
A
TYR
106
A
TYR
106
HELX_P
A
PHE
108
A
PHE
108
5
6
3
A
ASN
126
A
ASN
126
HELX_P
A
CYS
143
A
CYS
143
1
7
18
A
ASN
161
A
ASN
161
HELX_P
A
ARG
173
A
ARG
173
1
8
13
A
ALA
189
A
ALA
189
HELX_P
A
LYS
206
A
LYS
206
1
9
18
A
PRO
207
A
PRO
207
HELX_P
A
ALA
210
A
ALA
210
5
10
4
A
TRP
223
A
TRP
223
HELX_P
A
ALA
237
A
ALA
237
1
11
15
A
PRO
250
A
PRO
250
HELX_P
A
TYR
254
A
TYR
254
5
12
5
A
THR
268
A
THR
268
HELX_P
A
ASP
276
A
ASP
276
1
13
9
A
GLN
281
A
GLN
281
HELX_P
A
PHE
294
A
PHE
294
1
14
14
metalc
2.233
A
MG
501
B
MG
MG
1_555
A
HOH
908
E
O
HOH
1_555
metalc
2.366
A
MG
501
B
MG
MG
1_555
A
HOH
908
E
O
HOH
2_555
metalc
2.229
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
1_555
metalc
2.205
A
MG
501
B
MG
MG
1_555
A
HOH
909
E
O
HOH
2_555
metalc
2.081
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
1_555
metalc
2.070
A
MG
501
B
MG
MG
1_555
A
HOH
910
E
O
HOH
2_555
OXIDOREDUCTASE
Rossman-fold, sugar-nucleotide-binding domain, OXIDOREDUCTASE
RFBD_SALTY
UNP
1
1
P26392
MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLL
NATSVEAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFRTSWVYAGKGN
NFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGIT
LALTELNAVPTSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTTI
1
299
1KC3
1
299
P26392
A
1
1
299
6
2
2
3
parallel
parallel
parallel
parallel
parallel
parallel
parallel
anti-parallel
parallel
A
ASN
25
A
ASN
25
A
LEU
29
A
LEU
29
A
ASN
2
A
ASN
2
A
PHE
6
A
PHE
6
A
VAL
57
A
VAL
57
A
ASN
60
A
ASN
60
A
TRP
98
A
TRP
98
A
THR
104
A
THR
104
A
HIS
146
A
HIS
146
A
THR
151
A
THR
151
A
GLY
211
A
GLY
211
A
HIS
214
A
HIS
214
A
VAL
154
A
VAL
154
A
TYR
155
A
TYR
155
A
THR
187
A
THR
187
A
GLY
188
A
GLY
188
A
THR
175
A
THR
175
A
ILE
179
A
ILE
179
A
GLU
245
A
GLU
245
A
VAL
249
A
VAL
249
A
THR
221
A
THR
221
A
THR
222
A
THR
222
A
TYR
183
A
TYR
183
A
GLY
184
A
GLY
184
A
ASN
263
A
ASN
263
A
SER
264
A
SER
264
BINDING SITE FOR RESIDUE MG A 501
A
MG
501
Software
6
BINDING SITE FOR RESIDUE NDP A 901
A
NDP
901
Software
26
BINDING SITE FOR RESIDUE TRH A 601
A
TRH
601
Software
18
A
HOH
908
E
HOH
6
1_555
A
HOH
908
E
HOH
6
2_555
A
HOH
909
E
HOH
6
2_555
A
HOH
909
E
HOH
6
1_555
A
HOH
910
E
HOH
6
2_555
A
HOH
910
E
HOH
6
1_555
A
GLY
10
A
GLY
10
26
1_555
A
GLN
11
A
GLN
11
26
1_555
A
VAL
12
A
VAL
12
26
1_555
A
VAL
31
A
VAL
31
26
1_555
A
GLY
38
A
GLY
38
26
1_555
A
ASP
39
A
ASP
39
26
1_555
A
PHE
40
A
PHE
40
26
1_555
A
SER
41
A
SER
41
26
1_555
A
ALA
61
A
ALA
61
26
1_555
A
ALA
62
A
ALA
62
26
1_555
A
ALA
63
A
ALA
63
26
1_555
A
THR
65
A
THR
65
26
1_555
A
LEU
80
A
LEU
80
26
1_555
A
TYR
102
A
TYR
102
26
1_555
A
SER
103
A
SER
103
26
1_555
A
THR
104
A
THR
104
26
1_555
A
TYR
128
A
TYR
128
26
1_555
A
LYS
132
A
LYS
132
26
1_555
A
THR
151
A
THR
151
26
1_555
A
VAL
154
A
VAL
154
26
1_555
A
GLN
174
A
GLN
174
26
4_545
A
TRH
601
D
TRH
26
1_555
A
HOH
904
E
HOH
26
1_555
A
HOH
907
E
HOH
26
1_555
A
HOH
978
E
HOH
26
1_555
A
HOH
994
E
HOH
26
1_555
A
VAL
67
A
VAL
67
18
1_555
A
THR
104
A
THR
104
18
1_555
A
ASP
105
A
ASP
105
18
1_555
A
TYR
106
A
TYR
106
18
1_555
A
TYR
128
A
TYR
128
18
1_555
A
SER
152
A
SER
152
18
1_555
A
TRP
153
A
TRP
153
18
1_555
A
PHE
162
A
PHE
162
18
1_555
A
SER
177
A
SER
177
18
1_555
A
VAL
178
A
VAL
178
18
1_555
A
ILE
179
A
ILE
179
18
1_555
A
GLN
182
A
GLN
182
18
1_555
A
TRP
223
A
TRP
223
18
1_555
A
ARG
260
A
ARG
260
18
1_555
A
NDP
901
C
NDP
18
1_555
A
HOH
951
E
HOH
18
1_555
A
HOH
952
E
HOH
18
1_555
A
HOH
988
E
HOH
18
1_555
18
orthorhombic
P 21 21 2