0.011996
0.000000
0.002430
0.000000
0.019143
0.000000
0.000000
0.000000
0.018925
0.00000
0.00000
0.00000
di Salvo, M.L.
Ko, T.P.
Musayev, F.N.
Raboni, S.
Schirch, V.
Safo, M.K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
101.45
90.00
83.358
52.238
53.913
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
C17 H21 N4 O9 P
456.344
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
non-polymer
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C8 H10 N O6 P
247.142
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
non-polymer
O4 P -3
94.971
PHOSPHATE ION
non-polymer
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
N
C
N
90
N
O
N
91
N
N
N
92
N
C
N
93
N
O
N
94
N
C
N
95
N
N
Y
96
N
C
Y
97
N
C
Y
98
N
C
N
99
N
C
Y
100
N
C
N
101
N
C
Y
102
N
C
Y
103
N
C
N
104
N
N
N
105
N
C
N
106
N
C
N
107
S
C
N
108
N
O
N
109
S
C
N
110
N
O
N
111
R
C
N
112
N
O
N
113
N
C
N
114
N
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
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
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
N
C
N
145
N
C
N
146
N
C
N
147
N
O
N
148
N
N
N
149
N
O
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
H
N
159
N
H
N
160
N
N
N
161
S
C
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
C
N
167
N
O
N
168
N
O
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
N
N
180
N
C
N
181
N
C
N
182
N
O
N
183
N
O
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
N
C
Y
194
N
C
Y
195
N
N
Y
196
N
C
Y
197
N
C
Y
198
N
N
N
199
N
O
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
O
N
211
N
H
N
212
N
H
N
213
N
N
N
214
S
C
N
215
N
C
N
216
N
O
N
217
S
C
N
218
N
C
N
219
N
C
N
220
N
C
N
221
N
O
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
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
N
N
236
S
C
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
C
N
243
N
O
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
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
N
N
258
S
C
N
259
N
C
N
260
N
O
N
261
N
C
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
N
N
266
N
O
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
H
N
274
N
H
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
N
N
283
S
C
N
284
N
C
N
285
N
O
N
286
N
C
N
287
N
C
N
288
N
S
N
289
N
C
N
290
N
O
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
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
N
N
303
S
C
N
304
N
C
N
305
N
O
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
SE
N
310
N
C
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
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
N
333
N
O
N
334
N
H
N
335
N
H
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
Y
345
N
N
Y
346
N
C
N
347
N
C
Y
348
N
C
N
349
N
O
Y
350
N
C
N
351
N
C
N
352
N
O
Y
353
N
C
Y
354
N
C
N
355
N
C
N
356
N
O
N
357
N
P
N
358
N
O
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
P
N
372
N
O
N
373
N
O
N
374
N
O
N
375
N
O
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
N
381
N
C
N
382
N
C
N
383
N
O
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
O
N
399
N
O
N
400
N
H
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
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
R
C
N
412
N
O
N
413
N
C
N
414
N
O
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
N
N
425
S
C
N
426
N
C
N
427
N
O
N
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
C
Y
432
N
N
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
N
438
N
O
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
N
N
452
S
C
N
453
N
C
N
454
N
O
N
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
N
462
N
O
N
463
N
O
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
N
N
476
S
C
N
477
N
C
N
478
N
O
N
479
N
C
N
480
N
C
N
481
N
C
N
482
N
O
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
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
doub
N
85
N
doub
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
sing
Y
94
N
doub
Y
95
N
sing
Y
96
N
sing
N
97
N
sing
N
98
N
sing
Y
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
Y
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
Y
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
sing
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
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
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
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
doub
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
doub
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
sing
N
180
N
doub
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
doub
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
Y
194
N
sing
Y
195
N
doub
Y
196
N
doub
N
197
N
sing
Y
198
N
sing
N
199
N
sing
Y
200
N
sing
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
doub
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
sing
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
doub
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
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
doub
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
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
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
doub
N
317
N
sing
N
318
N
sing
N
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
doub
N
326
N
sing
Y
327
N
doub
N
328
N
sing
Y
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
N
335
N
sing
Y
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
Y
341
N
doub
N
342
N
sing
N
343
N
sing
Y
344
N
sing
N
345
N
doub
N
346
N
sing
Y
347
N
doub
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
doub
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
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
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
sing
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
doub
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
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
doub
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
doub
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
Y
420
N
doub
Y
421
N
sing
Y
422
N
sing
N
423
N
sing
Y
424
N
doub
Y
425
N
sing
Y
426
N
sing
N
427
N
sing
Y
428
N
sing
Y
429
N
doub
N
430
N
sing
Y
431
N
doub
N
432
N
sing
Y
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
sing
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
sing
N
447
N
sing
Y
448
N
doub
Y
449
N
sing
Y
450
N
sing
N
451
N
sing
Y
452
N
doub
N
453
N
sing
Y
454
N
doub
N
455
N
sing
Y
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
doub
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
315
385
397
10.1006/jmbi.2001.5254
11786019
Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
2002
10.2210/pdb1jnw/pdb
pdb_00001jnw
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
mirrors
IMAGE PLATE
2000-12-04
RIGAKU RAXIS II
OSMIC confocal mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
25819.666
Pyridoxine 5'-phosphate oxidase
1.4.3.5
1
man
polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
456.344
FLAVIN MONONUCLEOTIDE
1
syn
non-polymer
247.142
PYRIDOXAL-5'-PHOSPHATE
1
syn
non-polymer
18.015
water
267
nat
water
no
yes
(MSE)SDNDELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTA(MSE)VVATVDEHGQPYQRIVLLK
HYDEKG(MSE)VFYTNLGSRKAHQIENNPRVSLLFPWHTLERQV(MSE)VIGKAERLSTLEV(MSE)KYFHSRPRDSQIG
AWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP
MSDNDELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMV
FYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKF
LELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP
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
Escherichia
Escherichia
sample
562
Escherichia coli
562
Escherichia coli
plasmid
pET22b
1
2.23
44.77
VAPOR DIFFUSION, HANGING DROP
7.0
potassium phosphate, ammonium phosphate, mercaptoethanol, N-morpholinoethanesulfonate, dioxane, pyridoxal 5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2001-08-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2023-08-16
1
5
2023-11-15
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
1dnl is the original structure solved by MAD
without bound substrate molecule
1g76 is the complex with PNP
1g77 is the complex with PLP
1g78 is the complex with 2 PLP
1g79 is the complex with 2 PLP
RCSB
Y
RCSB
2001-07-25
REL
REL
PO4
PHOSPHATE ION
FMN
FLAVIN MONONUCLEOTIDE
PLP
PYRIDOXAL-5'-PHOSPHATE
HOH
water
1DNL
PDB entry 1dnl with omission of all waters, ligands and ions
PDB
experimental model
PO4
270
2
PO4
PO4
270
A
FMN
250
3
FMN
FMN
250
A
PLP
260
4
PLP
PLP
260
A
TIP
301
5
HOH
HOH
301
A
TIP
302
5
HOH
HOH
302
A
TIP
303
5
HOH
HOH
303
A
TIP
304
5
HOH
HOH
304
A
TIP
305
5
HOH
HOH
305
A
TIP
306
5
HOH
HOH
306
A
TIP
307
5
HOH
HOH
307
A
TIP
308
5
HOH
HOH
308
A
TIP
309
5
HOH
HOH
309
A
TIP
310
5
HOH
HOH
310
A
TIP
311
5
HOH
HOH
311
A
TIP
312
5
HOH
HOH
312
A
TIP
313
5
HOH
HOH
313
A
TIP
314
5
HOH
HOH
314
A
TIP
315
5
HOH
HOH
315
A
TIP
316
5
HOH
HOH
316
A
TIP
317
5
HOH
HOH
317
A
TIP
318
5
HOH
HOH
318
A
TIP
319
5
HOH
HOH
319
A
TIP
320
5
HOH
HOH
320
A
TIP
321
5
HOH
HOH
321
A
TIP
322
5
HOH
HOH
322
A
TIP
323
5
HOH
HOH
323
A
TIP
324
5
HOH
HOH
324
A
TIP
325
5
HOH
HOH
325
A
TIP
326
5
HOH
HOH
326
A
TIP
327
5
HOH
HOH
327
A
TIP
328
5
HOH
HOH
328
A
TIP
329
5
HOH
HOH
329
A
TIP
330
5
HOH
HOH
330
A
TIP
331
5
HOH
HOH
331
A
TIP
332
5
HOH
HOH
332
A
TIP
333
5
HOH
HOH
333
A
TIP
334
5
HOH
HOH
334
A
TIP
335
5
HOH
HOH
335
A
TIP
336
5
HOH
HOH
336
A
TIP
337
5
HOH
HOH
337
A
TIP
338
5
HOH
HOH
338
A
TIP
339
5
HOH
HOH
339
A
TIP
340
5
HOH
HOH
340
A
TIP
341
5
HOH
HOH
341
A
TIP
342
5
HOH
HOH
342
A
TIP
343
5
HOH
HOH
343
A
TIP
344
5
HOH
HOH
344
A
TIP
345
5
HOH
HOH
345
A
TIP
346
5
HOH
HOH
346
A
TIP
347
5
HOH
HOH
347
A
TIP
348
5
HOH
HOH
348
A
TIP
349
5
HOH
HOH
349
A
TIP
350
5
HOH
HOH
350
A
TIP
351
5
HOH
HOH
351
A
TIP
352
5
HOH
HOH
352
A
TIP
353
5
HOH
HOH
353
A
TIP
354
5
HOH
HOH
354
A
TIP
355
5
HOH
HOH
355
A
TIP
356
5
HOH
HOH
356
A
TIP
357
5
HOH
HOH
357
A
TIP
358
5
HOH
HOH
358
A
TIP
359
5
HOH
HOH
359
A
TIP
360
5
HOH
HOH
360
A
TIP
361
5
HOH
HOH
361
A
TIP
362
5
HOH
HOH
362
A
TIP
363
5
HOH
HOH
363
A
TIP
364
5
HOH
HOH
364
A
TIP
365
5
HOH
HOH
365
A
TIP
366
5
HOH
HOH
366
A
TIP
367
5
HOH
HOH
367
A
TIP
368
5
HOH
HOH
368
A
TIP
369
5
HOH
HOH
369
A
TIP
370
5
HOH
HOH
370
A
TIP
371
5
HOH
HOH
371
A
TIP
372
5
HOH
HOH
372
A
TIP
373
5
HOH
HOH
373
A
TIP
374
5
HOH
HOH
374
A
TIP
375
5
HOH
HOH
375
A
TIP
376
5
HOH
HOH
376
A
TIP
377
5
HOH
HOH
377
A
TIP
378
5
HOH
HOH
378
A
TIP
379
5
HOH
HOH
379
A
TIP
380
5
HOH
HOH
380
A
TIP
381
5
HOH
HOH
381
A
TIP
382
5
HOH
HOH
382
A
TIP
383
5
HOH
HOH
383
A
TIP
384
5
HOH
HOH
384
A
TIP
385
5
HOH
HOH
385
A
TIP
386
5
HOH
HOH
386
A
TIP
387
5
HOH
HOH
387
A
TIP
388
5
HOH
HOH
388
A
TIP
389
5
HOH
HOH
389
A
TIP
390
5
HOH
HOH
390
A
TIP
391
5
HOH
HOH
391
A
TIP
392
5
HOH
HOH
392
A
TIP
393
5
HOH
HOH
393
A
TIP
394
5
HOH
HOH
394
A
TIP
395
5
HOH
HOH
395
A
TIP
396
5
HOH
HOH
396
A
TIP
397
5
HOH
HOH
397
A
TIP
398
5
HOH
HOH
398
A
TIP
399
5
HOH
HOH
399
A
TIP
400
5
HOH
HOH
400
A
TIP
401
5
HOH
HOH
401
A
TIP
402
5
HOH
HOH
402
A
TIP
403
5
HOH
HOH
403
A
TIP
404
5
HOH
HOH
404
A
TIP
405
5
HOH
HOH
405
A
TIP
406
5
HOH
HOH
406
A
TIP
407
5
HOH
HOH
407
A
TIP
408
5
HOH
HOH
408
A
TIP
409
5
HOH
HOH
409
A
TIP
410
5
HOH
HOH
410
A
TIP
411
5
HOH
HOH
411
A
TIP
412
5
HOH
HOH
412
A
TIP
413
5
HOH
HOH
413
A
TIP
414
5
HOH
HOH
414
A
TIP
415
5
HOH
HOH
415
A
TIP
416
5
HOH
HOH
416
A
TIP
417
5
HOH
HOH
417
A
TIP
418
5
HOH
HOH
418
A
TIP
419
5
HOH
HOH
419
A
TIP
420
5
HOH
HOH
420
A
TIP
421
5
HOH
HOH
421
A
TIP
422
5
HOH
HOH
422
A
TIP
423
5
HOH
HOH
423
A
TIP
424
5
HOH
HOH
424
A
TIP
425
5
HOH
HOH
425
A
TIP
426
5
HOH
HOH
426
A
TIP
427
5
HOH
HOH
427
A
TIP
428
5
HOH
HOH
428
A
TIP
429
5
HOH
HOH
429
A
TIP
430
5
HOH
HOH
430
A
TIP
431
5
HOH
HOH
431
A
TIP
432
5
HOH
HOH
432
A
TIP
433
5
HOH
HOH
433
A
TIP
434
5
HOH
HOH
434
A
TIP
435
5
HOH
HOH
435
A
TIP
436
5
HOH
HOH
436
A
TIP
437
5
HOH
HOH
437
A
TIP
438
5
HOH
HOH
438
A
TIP
439
5
HOH
HOH
439
A
TIP
440
5
HOH
HOH
440
A
TIP
441
5
HOH
HOH
441
A
TIP
442
5
HOH
HOH
442
A
TIP
443
5
HOH
HOH
443
A
TIP
444
5
HOH
HOH
444
A
TIP
445
5
HOH
HOH
445
A
TIP
446
5
HOH
HOH
446
A
TIP
447
5
HOH
HOH
447
A
TIP
448
5
HOH
HOH
448
A
TIP
449
5
HOH
HOH
449
A
TIP
450
5
HOH
HOH
450
A
TIP
451
5
HOH
HOH
451
A
TIP
452
5
HOH
HOH
452
A
TIP
453
5
HOH
HOH
453
A
TIP
454
5
HOH
HOH
454
A
TIP
455
5
HOH
HOH
455
A
TIP
456
5
HOH
HOH
456
A
TIP
457
5
HOH
HOH
457
A
TIP
458
5
HOH
HOH
458
A
TIP
459
5
HOH
HOH
459
A
TIP
460
5
HOH
HOH
460
A
TIP
461
5
HOH
HOH
461
A
TIP
462
5
HOH
HOH
462
A
TIP
463
5
HOH
HOH
463
A
TIP
464
5
HOH
HOH
464
A
TIP
465
5
HOH
HOH
465
A
TIP
466
5
HOH
HOH
466
A
TIP
467
5
HOH
HOH
467
A
TIP
468
5
HOH
HOH
468
A
TIP
469
5
HOH
HOH
469
A
TIP
470
5
HOH
HOH
470
A
TIP
471
5
HOH
HOH
471
A
TIP
472
5
HOH
HOH
472
A
TIP
473
5
HOH
HOH
473
A
TIP
474
5
HOH
HOH
474
A
TIP
475
5
HOH
HOH
475
A
TIP
476
5
HOH
HOH
476
A
TIP
477
5
HOH
HOH
477
A
TIP
478
5
HOH
HOH
478
A
TIP
479
5
HOH
HOH
479
A
TIP
480
5
HOH
HOH
480
A
TIP
481
5
HOH
HOH
481
A
TIP
482
5
HOH
HOH
482
A
TIP
483
5
HOH
HOH
483
A
TIP
484
5
HOH
HOH
484
A
TIP
485
5
HOH
HOH
485
A
TIP
486
5
HOH
HOH
486
A
TIP
487
5
HOH
HOH
487
A
TIP
488
5
HOH
HOH
488
A
TIP
489
5
HOH
HOH
489
A
TIP
490
5
HOH
HOH
490
A
TIP
491
5
HOH
HOH
491
A
TIP
492
5
HOH
HOH
492
A
TIP
493
5
HOH
HOH
493
A
TIP
494
5
HOH
HOH
494
A
TIP
495
5
HOH
HOH
495
A
TIP
496
5
HOH
HOH
496
A
TIP
497
5
HOH
HOH
497
A
TIP
498
5
HOH
HOH
498
A
TIP
499
5
HOH
HOH
499
A
TIP
500
5
HOH
HOH
500
A
TIP
501
5
HOH
HOH
501
A
TIP
502
5
HOH
HOH
502
A
TIP
503
5
HOH
HOH
503
A
TIP
504
5
HOH
HOH
504
A
TIP
505
5
HOH
HOH
505
A
TIP
506
5
HOH
HOH
506
A
TIP
507
5
HOH
HOH
507
A
TIP
508
5
HOH
HOH
508
A
TIP
509
5
HOH
HOH
509
A
TIP
510
5
HOH
HOH
510
A
TIP
511
5
HOH
HOH
511
A
TIP
512
5
HOH
HOH
512
A
TIP
513
5
HOH
HOH
513
A
TIP
514
5
HOH
HOH
514
A
TIP
515
5
HOH
HOH
515
A
TIP
516
5
HOH
HOH
516
A
TIP
517
5
HOH
HOH
517
A
TIP
518
5
HOH
HOH
518
A
TIP
519
5
HOH
HOH
519
A
TIP
520
5
HOH
HOH
520
A
TIP
521
5
HOH
HOH
521
A
TIP
522
5
HOH
HOH
522
A
TIP
523
5
HOH
HOH
523
A
TIP
524
5
HOH
HOH
524
A
TIP
525
5
HOH
HOH
525
A
TIP
526
5
HOH
HOH
526
A
TIP
527
5
HOH
HOH
527
A
TIP
528
5
HOH
HOH
528
A
TIP
529
5
HOH
HOH
529
A
TIP
530
5
HOH
HOH
530
A
TIP
531
5
HOH
HOH
531
A
TIP
532
5
HOH
HOH
532
A
TIP
533
5
HOH
HOH
533
A
TIP
534
5
HOH
HOH
534
A
TIP
535
5
HOH
HOH
535
A
TIP
536
5
HOH
HOH
536
A
TIP
537
5
HOH
HOH
537
A
TIP
538
5
HOH
HOH
538
A
TIP
539
5
HOH
HOH
539
A
TIP
540
5
HOH
HOH
540
A
TIP
541
5
HOH
HOH
541
A
TIP
542
5
HOH
HOH
542
A
TIP
543
5
HOH
HOH
543
A
TIP
544
5
HOH
HOH
544
A
TIP
545
5
HOH
HOH
545
A
TIP
546
5
HOH
HOH
546
A
TIP
547
5
HOH
HOH
547
A
TIP
548
5
HOH
HOH
548
A
TIP
549
5
HOH
HOH
549
A
TIP
550
5
HOH
HOH
550
A
TIP
551
5
HOH
HOH
551
A
TIP
552
5
HOH
HOH
552
A
TIP
553
5
HOH
HOH
553
A
TIP
554
5
HOH
HOH
554
A
TIP
555
5
HOH
HOH
555
A
TIP
556
5
HOH
HOH
556
A
TIP
557
5
HOH
HOH
557
A
TIP
558
5
HOH
HOH
558
A
TIP
559
5
HOH
HOH
559
A
TIP
560
5
HOH
HOH
560
A
TIP
561
5
HOH
HOH
561
A
TIP
562
5
HOH
HOH
562
A
TIP
563
5
HOH
HOH
563
A
TIP
564
5
HOH
HOH
564
A
TIP
565
5
HOH
HOH
565
A
TIP
566
5
HOH
HOH
566
A
TIP
567
5
HOH
HOH
567
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
ASP
5
n
5
ASP
5
A
GLU
6
n
6
GLU
6
A
LEU
7
n
7
LEU
7
A
GLN
8
n
8
GLN
8
A
GLN
9
n
9
GLN
9
A
ILE
10
n
10
ILE
10
A
ALA
11
n
11
ALA
11
A
HIS
12
n
12
HIS
12
A
LEU
13
n
13
LEU
13
A
ARG
14
n
14
ARG
14
A
ARG
15
n
15
ARG
15
A
GLU
16
n
16
GLU
16
A
TYR
17
n
17
TYR
17
A
THR
18
n
18
THR
18
A
LYS
19
n
19
LYS
19
A
GLY
20
n
20
GLY
20
A
GLY
21
n
21
GLY
21
A
LEU
22
n
22
LEU
22
A
ARG
23
n
23
ARG
23
A
ARG
24
n
24
ARG
24
A
ARG
25
n
25
ARG
25
A
ASP
26
n
26
ASP
26
A
LEU
27
n
27
LEU
27
A
PRO
28
n
28
PRO
28
A
ALA
29
n
29
ALA
29
A
ASP
30
n
30
ASP
30
A
PRO
31
n
31
PRO
31
A
LEU
32
n
32
LEU
32
A
THR
33
n
33
THR
33
A
LEU
34
n
34
LEU
34
A
PHE
35
n
35
PHE
35
A
GLU
36
n
36
GLU
36
A
ARG
37
n
37
ARG
37
A
TRP
38
n
38
TRP
38
A
LEU
39
n
39
LEU
39
A
SER
40
n
40
SER
40
A
GLN
41
n
41
GLN
41
A
ALA
42
n
42
ALA
42
A
CYS
43
n
43
CYS
43
A
GLU
44
n
44
GLU
44
A
ALA
45
n
45
ALA
45
A
LYS
46
n
46
LYS
46
A
LEU
47
n
47
LEU
47
A
ALA
48
n
48
ALA
48
A
ASP
49
n
49
ASP
49
A
PRO
50
n
50
PRO
50
A
THR
51
n
51
THR
51
A
ALA
52
n
52
ALA
52
A
MSE
53
n
53
MSE
53
A
VAL
54
n
54
VAL
54
A
VAL
55
n
55
VAL
55
A
ALA
56
n
56
ALA
56
A
THR
57
n
57
THR
57
A
VAL
58
n
58
VAL
58
A
ASP
59
n
59
ASP
59
A
GLU
60
n
60
GLU
60
A
HIS
61
n
61
HIS
61
A
GLY
62
n
62
GLY
62
A
GLN
63
n
63
GLN
63
A
PRO
64
n
64
PRO
64
A
TYR
65
n
65
TYR
65
A
GLN
66
n
66
GLN
66
A
ARG
67
n
67
ARG
67
A
ILE
68
n
68
ILE
68
A
VAL
69
n
69
VAL
69
A
LEU
70
n
70
LEU
70
A
LEU
71
n
71
LEU
71
A
LYS
72
n
72
LYS
72
A
HIS
73
n
73
HIS
73
A
TYR
74
n
74
TYR
74
A
ASP
75
n
75
ASP
75
A
GLU
76
n
76
GLU
76
A
LYS
77
n
77
LYS
77
A
GLY
78
n
78
GLY
78
A
MSE
79
n
79
MSE
79
A
VAL
80
n
80
VAL
80
A
PHE
81
n
81
PHE
81
A
TYR
82
n
82
TYR
82
A
THR
83
n
83
THR
83
A
ASN
84
n
84
ASN
84
A
LEU
85
n
85
LEU
85
A
GLY
86
n
86
GLY
86
A
SER
87
n
87
SER
87
A
ARG
88
n
88
ARG
88
A
LYS
89
n
89
LYS
89
A
ALA
90
n
90
ALA
90
A
HIS
91
n
91
HIS
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLU
94
n
94
GLU
94
A
ASN
95
n
95
ASN
95
A
ASN
96
n
96
ASN
96
A
PRO
97
n
97
PRO
97
A
ARG
98
n
98
ARG
98
A
VAL
99
n
99
VAL
99
A
SER
100
n
100
SER
100
A
LEU
101
n
101
LEU
101
A
LEU
102
n
102
LEU
102
A
PHE
103
n
103
PHE
103
A
PRO
104
n
104
PRO
104
A
TRP
105
n
105
TRP
105
A
HIS
106
n
106
HIS
106
A
THR
107
n
107
THR
107
A
LEU
108
n
108
LEU
108
A
GLU
109
n
109
GLU
109
A
ARG
110
n
110
ARG
110
A
GLN
111
n
111
GLN
111
A
VAL
112
n
112
VAL
112
A
MSE
113
n
113
MSE
113
A
VAL
114
n
114
VAL
114
A
ILE
115
n
115
ILE
115
A
GLY
116
n
116
GLY
116
A
LYS
117
n
117
LYS
117
A
ALA
118
n
118
ALA
118
A
GLU
119
n
119
GLU
119
A
ARG
120
n
120
ARG
120
A
LEU
121
n
121
LEU
121
A
SER
122
n
122
SER
122
A
THR
123
n
123
THR
123
A
LEU
124
n
124
LEU
124
A
GLU
125
n
125
GLU
125
A
VAL
126
n
126
VAL
126
A
MSE
127
n
127
MSE
127
A
LYS
128
n
128
LYS
128
A
TYR
129
n
129
TYR
129
A
PHE
130
n
130
PHE
130
A
HIS
131
n
131
HIS
131
A
SER
132
n
132
SER
132
A
ARG
133
n
133
ARG
133
A
PRO
134
n
134
PRO
134
A
ARG
135
n
135
ARG
135
A
ASP
136
n
136
ASP
136
A
SER
137
n
137
SER
137
A
GLN
138
n
138
GLN
138
A
ILE
139
n
139
ILE
139
A
GLY
140
n
140
GLY
140
A
ALA
141
n
141
ALA
141
A
TRP
142
n
142
TRP
142
A
VAL
143
n
143
VAL
143
A
SER
144
n
144
SER
144
A
LYS
145
n
145
LYS
145
A
GLN
146
n
146
GLN
146
A
SER
147
n
147
SER
147
A
SER
148
n
148
SER
148
A
ARG
149
n
149
ARG
149
A
ILE
150
n
150
ILE
150
A
SER
151
n
151
SER
151
A
ALA
152
n
152
ALA
152
A
ARG
153
n
153
ARG
153
A
GLY
154
n
154
GLY
154
A
ILE
155
n
155
ILE
155
A
LEU
156
n
156
LEU
156
A
GLU
157
n
157
GLU
157
A
SER
158
n
158
SER
158
A
LYS
159
n
159
LYS
159
A
PHE
160
n
160
PHE
160
A
LEU
161
n
161
LEU
161
A
GLU
162
n
162
GLU
162
A
LEU
163
n
163
LEU
163
A
LYS
164
n
164
LYS
164
A
GLN
165
n
165
GLN
165
A
LYS
166
n
166
LYS
166
A
PHE
167
n
167
PHE
167
A
GLN
168
n
168
GLN
168
A
GLN
169
n
169
GLN
169
A
GLY
170
n
170
GLY
170
A
GLU
171
n
171
GLU
171
A
VAL
172
n
172
VAL
172
A
PRO
173
n
173
PRO
173
A
LEU
174
n
174
LEU
174
A
PRO
175
n
175
PRO
175
A
SER
176
n
176
SER
176
A
PHE
177
n
177
PHE
177
A
TRP
178
n
178
TRP
178
A
GLY
179
n
179
GLY
179
A
GLY
180
n
180
GLY
180
A
PHE
181
n
181
PHE
181
A
ARG
182
n
182
ARG
182
A
VAL
183
n
183
VAL
183
A
SER
184
n
184
SER
184
A
LEU
185
n
185
LEU
185
A
GLU
186
n
186
GLU
186
A
GLN
187
n
187
GLN
187
A
ILE
188
n
188
ILE
188
A
GLU
189
n
189
GLU
189
A
PHE
190
n
190
PHE
190
A
TRP
191
n
191
TRP
191
A
GLN
192
n
192
GLN
192
A
GLY
193
n
193
GLY
193
A
GLY
194
n
194
GLY
194
A
GLU
195
n
195
GLU
195
A
HIS
196
n
196
HIS
196
A
ARG
197
n
197
ARG
197
A
LEU
198
n
198
LEU
198
A
HIS
199
n
199
HIS
199
A
ASP
200
n
200
ASP
200
A
ARG
201
n
201
ARG
201
A
PHE
202
n
202
PHE
202
A
LEU
203
n
203
LEU
203
A
TYR
204
n
204
TYR
204
A
GLN
205
n
205
GLN
205
A
ARG
206
n
206
ARG
206
A
GLU
207
n
207
GLU
207
A
ASN
208
n
208
ASN
208
A
ASP
209
n
209
ASP
209
A
ALA
210
n
210
ALA
210
A
TRP
211
n
211
TRP
211
A
LYS
212
n
212
LYS
212
A
ILE
213
n
213
ILE
213
A
ASP
214
n
214
ASP
214
A
ARG
215
n
215
ARG
215
A
LEU
216
n
216
LEU
216
A
ALA
217
n
217
ALA
217
A
PRO
218
n
218
PRO
218
A
author_and_software_defined_assembly
PISA,PQS
2
dimeric
11140
-37
17850
A
MSE
53
SELENOMETHIONINE
A
MSE
53
MET
A
MSE
79
SELENOMETHIONINE
A
MSE
79
MET
A
MSE
113
SELENOMETHIONINE
A
MSE
113
MET
A
MSE
127
SELENOMETHIONINE
A
MSE
127
MET
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_656
-x+1,y,-z+1
crystal symmetry operation
72.6555841048
0.0000000000
52.8400403388
A
O
VAL
69
A
O
VAL
69
A
N
MSE
53
A
N
MSE
53
A
N
ALA
56
A
N
ALA
56
A
O
SER
100
A
O
SER
100
A
O
TRP
105
A
O
TRP
105
A
N
ARG
110
A
N
ARG
110
A
O
GLU
119
A
O
GLU
119
A
N
ARG
182
A
N
ARG
182
A
N
VAL
183
A
N
VAL
183
A
O
MSE
79
A
O
MSE
79
A
N
VAL
80
A
N
VAL
80
A
O
HIS
73
A
O
HIS
73
A
O
VAL
69
A
O
VAL
69
A
N
MSE
53
A
N
MSE
53
A
N
ALA
56
A
N
ALA
56
A
O
SER
100
A
O
SER
100
A
O
TRP
105
A
O
TRP
105
A
N
ARG
110
A
N
ARG
110
A
N
ILE
115
A
N
ILE
115
A
O
GLN
187
A
O
GLN
187
A
O
GLN
192
A
O
GLN
192
A
N
ASP
200
A
N
ASP
200
A
N
GLU
207
A
N
GLU
207
A
O
ALA
210
A
O
ALA
210
1
A
HOH
301
E
HOH
1
A
HOH
302
E
HOH
1
A
HOH
303
E
HOH
1
A
MSE
1
A
MSE
1
1
Y
1
A
SER
2
A
SER
2
1
Y
1
A
ASP
3
A
ASP
3
1
Y
1
A
ASN
4
A
ASN
4
1
Y
1
A
GLN
146
-29.45
128.43
1
A
SER
147
81.20
-23.58
1
A
GLN
168
-3.01
102.14
1
A
GLN
169
56.87
-23.28
1
A
LEU
198
-103.88
74.87
1
A
ASN
208
67.36
-113.74
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
FMN.PARAM
FMN.TOP
PLP.PARAM
PLP.TOP
28.4
-2.20
0.00
-0.27
8.07
0.00
-5.87
0.2310000
0.009
0.1780000
0.1820000
0.1780000
2.07
44.01
684
13510
13510
5.1
96.4
RANDOM
5761739.72
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB entry 1dnl with omission of all waters, ligands and ions
Engh & Huber
FLAT MODEL
61.7459
0.365904
0.29
0.21
6.00
0.34
0.29
2.07
44.01
267
2094
52
0
1775
0.010
1.5
23.0
0.94
1.01
1.50
1.65
2.00
1.67
2.00
2.45
2.50
0.3500000
0.045
0.2930000
2.14
60
1244
1403
10
4.6
92.9
25.2
2.07
44
1JNW
13991
13510
1.0
1.0
0.0770000
1
8.3
2.4
96.6
0.2640000
2.07
2.14
2.1
1
92.9
phasing
AMoRE
refinement
CNS
1.0
data reduction
bioteX
data scaling
bioteX
Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
The enzyme is a dimer, which can be generated
by applying the crystallographic dyad symmetry
to the monomer asymmetric unit.
A
GLN
8
A
GLN
8
HELX_P
A
LEU
13
A
LEU
13
5
1
6
A
ARG
23
A
ARG
23
HELX_P
A
LEU
27
A
LEU
27
5
2
5
A
ASP
30
A
ASP
30
HELX_P
A
LYS
46
A
LYS
46
1
3
17
A
SER
87
A
SER
87
HELX_P
A
ASN
96
A
ASN
96
1
4
10
A
HIS
106
A
HIS
106
HELX_P
A
LEU
108
A
LEU
108
5
5
3
A
SER
122
A
SER
122
HELX_P
A
HIS
131
A
HIS
131
1
6
10
A
PRO
134
A
PRO
134
HELX_P
A
SER
144
A
SER
144
1
7
11
A
ARG
153
A
ARG
153
HELX_P
A
GLN
168
A
GLN
168
1
8
16
A
GLY
194
A
GLY
194
HELX_P
A
LEU
198
A
LEU
198
5
9
5
covale
1.326
both
A
ALA
52
A
C
ALA
52
1_555
A
MSE
53
A
N
MSE
53
1_555
covale
1.327
both
A
MSE
53
A
C
MSE
53
1_555
A
VAL
54
A
N
VAL
54
1_555
covale
1.336
both
A
GLY
78
A
C
GLY
78
1_555
A
MSE
79
A
N
MSE
79
1_555
covale
1.329
both
A
MSE
79
A
C
MSE
79
1_555
A
VAL
80
A
N
VAL
80
1_555
covale
1.332
both
A
VAL
112
A
C
VAL
112
1_555
A
MSE
113
A
N
MSE
113
1_555
covale
1.324
both
A
MSE
113
A
C
MSE
113
1_555
A
VAL
114
A
N
VAL
114
1_555
covale
1.325
both
A
VAL
126
A
C
VAL
126
1_555
A
MSE
127
A
N
MSE
127
1_555
covale
1.333
both
A
MSE
127
A
C
MSE
127
1_555
A
LYS
128
A
N
LYS
128
1_555
OXIDOREDUCTASE
n-terminal segment, PLP, FMN, OXIDOREDUCTASE
PDXH_ECOLI
UNP
1
0
P28225
MSDNDELQQIAHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMV
FYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKF
LELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP
0
217
1JNW
1
218
P28225
A
1
1
218
1
MET
modified residue
MSE
1
1JNW
A
P28225
UNP
0
1
1
MET
modified residue
MSE
53
1JNW
A
P28225
UNP
52
53
1
MET
modified residue
MSE
79
1JNW
A
P28225
UNP
78
79
1
MET
modified residue
MSE
113
1JNW
A
P28225
UNP
112
113
1
MET
modified residue
MSE
127
1JNW
A
P28225
UNP
126
127
7
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
PRO
64
A
PRO
64
A
LEU
70
A
LEU
70
A
ALA
52
A
ALA
52
A
VAL
58
A
VAL
58
A
ARG
98
A
ARG
98
A
TRP
105
A
TRP
105
A
ARG
110
A
ARG
110
A
ARG
120
A
ARG
120
A
TRP
178
A
TRP
178
A
VAL
183
A
VAL
183
A
GLY
78
A
GLY
78
A
ASN
84
A
ASN
84
A
HIS
73
A
HIS
73
A
ASP
75
A
ASP
75
A
PRO
64
A
PRO
64
A
LEU
70
A
LEU
70
A
ALA
52
A
ALA
52
A
VAL
58
A
VAL
58
A
ARG
98
A
ARG
98
A
TRP
105
A
TRP
105
A
ARG
110
A
ARG
110
A
ARG
120
A
ARG
120
A
GLN
187
A
GLN
187
A
GLN
192
A
GLN
192
A
ASP
200
A
ASP
200
A
GLU
207
A
GLU
207
A
ALA
210
A
ALA
210
A
ARG
215
A
ARG
215
BINDING SITE FOR RESIDUE PO4 A 270
A
PO4
270
Software
9
BINDING SITE FOR RESIDUE FMN A 250
A
FMN
250
Software
19
BINDING SITE FOR RESIDUE PLP A 260
A
PLP
260
Software
10
A
ARG
23
A
ARG
23
9
1_555
A
ARG
24
A
ARG
24
9
1_555
A
ALA
152
A
ALA
152
9
2_656
A
ARG
153
A
ARG
153
9
2_656
A
PHE
202
A
PHE
202
9
1_555
A
ARG
215
A
ARG
215
9
1_555
A
HOH
399
E
HOH
9
1_555
A
HOH
400
E
HOH
9
1_555
A
HOH
507
E
HOH
9
1_555
A
TYR
17
A
TYR
17
19
1_555
A
ARG
67
A
ARG
67
19
2_656
A
ILE
68
A
ILE
68
19
2_656
A
VAL
69
A
VAL
69
19
2_656
A
LEU
70
A
LEU
70
19
2_656
A
TYR
82
A
TYR
82
19
2_656
A
THR
83
A
THR
83
19
2_656
A
SER
87
A
SER
87
19
2_656
A
ARG
88
A
ARG
88
19
2_656
A
LYS
89
A
LYS
89
19
2_656
A
GLN
111
A
GLN
111
19
1_555
A
GLN
146
A
GLN
146
19
2_656
A
SER
147
A
SER
147
19
2_656
A
TRP
191
A
TRP
191
19
1_555
A
ARG
201
A
ARG
201
19
1_555
A
PLP
260
D
PLP
19
1_555
A
HOH
348
E
HOH
19
2_656
A
HOH
375
E
HOH
19
1_555
A
HOH
407
E
HOH
19
1_555
A
ARG
14
A
ARG
14
10
1_555
A
TYR
17
A
TYR
17
10
1_555
A
LYS
72
A
LYS
72
10
2_656
A
TYR
129
A
TYR
129
10
2_656
A
ARG
133
A
ARG
133
10
2_656
A
ARG
197
A
ARG
197
10
1_555
A
HIS
199
A
HIS
199
10
1_555
A
PRO
218
A
PRO
218
10
1_555
A
FMN
250
C
FMN
10
1_555
A
HOH
408
E
HOH
10
2_656
5
C 1 2 1