0.022477
0.000000
0.000000
0.000000
0.019385
0.000000
0.000000
0.000000
0.007575
0.00000
0.00000
0.00000
Kakuda, S.
Takimoto-Kamimura, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
44.489
51.585
132.017
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
C28 H46 O4
446.662
(1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
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
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
C
N
89
N
C
N
90
N
C
N
91
N
C
N
92
S
C
N
93
R
C
N
94
S
C
N
95
N
C
N
96
R
C
N
97
N
C
N
98
N
C
N
99
N
C
N
100
N
C
N
101
R
C
N
102
N
C
N
103
S
C
N
104
N
C
N
105
N
C
N
106
R
C
N
107
N
C
N
108
N
O
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
C
N
117
N
O
N
118
N
O
N
119
N
C
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
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
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
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
N
N
175
N
O
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
H
N
184
N
H
N
185
N
H
N
186
N
N
N
187
S
C
N
188
N
C
N
189
N
O
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
O
N
194
N
O
N
195
N
O
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
N
C
N
207
N
C
N
208
N
O
N
209
N
O
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
Y
220
N
C
Y
221
N
N
Y
222
N
C
Y
223
N
C
Y
224
N
N
N
225
N
O
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
H
N
236
N
O
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
S
C
N
244
N
C
N
245
N
C
N
246
N
C
N
247
N
O
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
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
N
N
262
S
C
N
263
N
C
N
264
N
O
N
265
N
C
N
266
N
C
N
267
N
C
N
268
N
C
N
269
N
O
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
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
C
N
291
N
N
N
292
N
O
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
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
C
N
314
N
S
N
315
N
C
N
316
N
O
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
N
N
329
S
C
N
330
N
C
N
331
N
O
N
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
N
339
N
O
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
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
N
356
N
C
N
357
N
C
N
358
N
O
N
359
N
H
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
N
N
369
S
C
N
370
N
C
N
371
N
O
N
372
N
C
N
373
N
O
N
374
N
O
N
375
N
H
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
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
R
C
N
387
N
O
N
388
N
C
N
389
N
O
N
390
N
H
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
N
N
400
S
C
N
401
N
C
N
402
N
O
N
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
N
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
N
413
N
O
N
414
N
H
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
H
N
425
N
H
N
426
N
N
N
427
S
C
N
428
N
C
N
429
N
O
N
430
N
C
Y
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
N
437
N
O
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
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
N
455
N
C
N
456
N
C
N
457
N
O
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
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
doub
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
E
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
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
doub
N
108
N
sing
N
109
N
sing
N
110
Z
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
sing
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
sing
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
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
sing
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
doub
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
doub
N
178
N
sing
N
179
N
sing
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
doub
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
doub
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
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
doub
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
doub
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
Y
220
N
sing
Y
221
N
doub
Y
222
N
doub
N
223
N
sing
Y
224
N
sing
N
225
N
sing
Y
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
doub
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
doub
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
sing
N
279
N
sing
N
280
N
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
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
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
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
doub
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
Y
328
N
doub
Y
329
N
sing
Y
330
N
sing
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
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
sing
N
344
N
sing
N
345
N
sing
N
346
N
doub
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
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
doub
N
364
N
sing
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
N
376
N
doub
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
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
Y
402
N
sing
Y
403
N
sing
N
404
N
sing
Y
405
N
sing
Y
406
N
doub
N
407
N
sing
Y
408
N
doub
N
409
N
sing
Y
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
sing
N
418
N
sing
N
419
N
sing
N
420
N
doub
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
Y
425
N
doub
Y
426
N
sing
Y
427
N
sing
N
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
sing
N
444
N
doub
N
445
N
sing
N
446
N
sing
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
US
Org.Lett.
1523-7060
13
2852
2855
10.1021/ol200828s
21539305
New C15-substituted active vitamin D3
2011
10.2210/pdb3ax8/pdb
pdb_00003ax8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
CCD
2008-01-25
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
BL-17A
Photon Factory
1.000
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-17A
29805.342
Vitamin D3 receptor
ligand binding domain, residues 118-427
DEL(165-215) mutant
1
man
polymer
446.662
(1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
1
syn
non-polymer
18.015
water
9
nat
water
VDR, 1,25-dihydroxyvitamin D3 receptor, Nuclear receptor subfamily 1 group I member 1
no
no
GSHMDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGF
AKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLN
LHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCL
SFQPECSMKLTPLVLEVFGNEIS
GSHMDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGF
AKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLN
LHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCL
SFQPECSMKLTPLVLEVFGNEIS
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
human
sample
5
51
VDR, NR1I1
9606
Homo sapiens
562
Escherichia coli
human
sample
52
263
VDR, NR1I1
9606
Homo sapiens
562
Escherichia coli
1
2.54
51.60
VAPOR DIFFUSION, HANGING DROP
6.5
0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
entity_src_gen
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Source and taxonomy
Data collection
Database references
Derived calculations
Refinement description
1
0
2011-10-05
1
1
2017-08-16
1
2
2023-11-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PDBJ
Y
PDBJ
2011-03-30
REL
REL
EIM
(1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
HOH
water
THIS ENTRY IS DELETION MUTANT. REISDUES 165-215 WERE DELETED.
1DB1
PDB
experimental model
MOL
1
2
EIM
EIM
1
A
HOH
2
3
HOH
HOH
2
A
HOH
3
3
HOH
HOH
3
A
HOH
4
3
HOH
HOH
4
A
HOH
5
3
HOH
HOH
5
A
HOH
6
3
HOH
HOH
6
A
HOH
7
3
HOH
HOH
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
1
3
HOH
HOH
428
A
n
1
114
A
n
2
115
A
n
3
116
A
n
4
117
A
ASP
118
n
5
ASP
118
A
SER
119
n
6
SER
119
A
LEU
120
n
7
LEU
120
A
ARG
121
n
8
ARG
121
A
PRO
122
n
9
PRO
122
A
LYS
123
n
10
LYS
123
A
LEU
124
n
11
LEU
124
A
SER
125
n
12
SER
125
A
GLU
126
n
13
GLU
126
A
GLU
127
n
14
GLU
127
A
GLN
128
n
15
GLN
128
A
GLN
129
n
16
GLN
129
A
ARG
130
n
17
ARG
130
A
ILE
131
n
18
ILE
131
A
ILE
132
n
19
ILE
132
A
ALA
133
n
20
ALA
133
A
ILE
134
n
21
ILE
134
A
LEU
135
n
22
LEU
135
A
LEU
136
n
23
LEU
136
A
ASP
137
n
24
ASP
137
A
ALA
138
n
25
ALA
138
A
HIS
139
n
26
HIS
139
A
HIS
140
n
27
HIS
140
A
LYS
141
n
28
LYS
141
A
THR
142
n
29
THR
142
A
TYR
143
n
30
TYR
143
A
ASP
144
n
31
ASP
144
A
PRO
145
n
32
PRO
145
A
THR
146
n
33
THR
146
A
TYR
147
n
34
TYR
147
A
SER
148
n
35
SER
148
A
ASP
149
n
36
ASP
149
A
PHE
150
n
37
PHE
150
A
CYS
151
n
38
CYS
151
A
GLN
152
n
39
GLN
152
A
PHE
153
n
40
PHE
153
A
ARG
154
n
41
ARG
154
A
PRO
155
n
42
PRO
155
A
PRO
156
n
43
PRO
156
A
VAL
157
n
44
VAL
157
A
ARG
158
n
45
ARG
158
A
VAL
159
n
46
VAL
159
A
ASN
160
n
47
ASN
160
A
ASP
161
n
48
ASP
161
A
GLY
162
n
49
GLY
162
A
n
50
163
A
n
51
164
A
SER
216
n
52
SER
216
A
VAL
217
n
53
VAL
217
A
THR
218
n
54
THR
218
A
LEU
219
n
55
LEU
219
A
GLU
220
n
56
GLU
220
A
LEU
221
n
57
LEU
221
A
SER
222
n
58
SER
222
A
GLN
223
n
59
GLN
223
A
LEU
224
n
60
LEU
224
A
SER
225
n
61
SER
225
A
MET
226
n
62
MET
226
A
LEU
227
n
63
LEU
227
A
PRO
228
n
64
PRO
228
A
HIS
229
n
65
HIS
229
A
LEU
230
n
66
LEU
230
A
ALA
231
n
67
ALA
231
A
ASP
232
n
68
ASP
232
A
LEU
233
n
69
LEU
233
A
VAL
234
n
70
VAL
234
A
SER
235
n
71
SER
235
A
TYR
236
n
72
TYR
236
A
SER
237
n
73
SER
237
A
ILE
238
n
74
ILE
238
A
GLN
239
n
75
GLN
239
A
LYS
240
n
76
LYS
240
A
VAL
241
n
77
VAL
241
A
ILE
242
n
78
ILE
242
A
GLY
243
n
79
GLY
243
A
PHE
244
n
80
PHE
244
A
ALA
245
n
81
ALA
245
A
LYS
246
n
82
LYS
246
A
MET
247
n
83
MET
247
A
ILE
248
n
84
ILE
248
A
PRO
249
n
85
PRO
249
A
GLY
250
n
86
GLY
250
A
PHE
251
n
87
PHE
251
A
ARG
252
n
88
ARG
252
A
ASP
253
n
89
ASP
253
A
LEU
254
n
90
LEU
254
A
THR
255
n
91
THR
255
A
SER
256
n
92
SER
256
A
GLU
257
n
93
GLU
257
A
ASP
258
n
94
ASP
258
A
GLN
259
n
95
GLN
259
A
ILE
260
n
96
ILE
260
A
VAL
261
n
97
VAL
261
A
LEU
262
n
98
LEU
262
A
LEU
263
n
99
LEU
263
A
LYS
264
n
100
LYS
264
A
SER
265
n
101
SER
265
A
SER
266
n
102
SER
266
A
ALA
267
n
103
ALA
267
A
ILE
268
n
104
ILE
268
A
GLU
269
n
105
GLU
269
A
VAL
270
n
106
VAL
270
A
ILE
271
n
107
ILE
271
A
MET
272
n
108
MET
272
A
LEU
273
n
109
LEU
273
A
ARG
274
n
110
ARG
274
A
SER
275
n
111
SER
275
A
ASN
276
n
112
ASN
276
A
GLU
277
n
113
GLU
277
A
SER
278
n
114
SER
278
A
PHE
279
n
115
PHE
279
A
THR
280
n
116
THR
280
A
MET
281
n
117
MET
281
A
ASP
282
n
118
ASP
282
A
ASP
283
n
119
ASP
283
A
MET
284
n
120
MET
284
A
SER
285
n
121
SER
285
A
TRP
286
n
122
TRP
286
A
THR
287
n
123
THR
287
A
CYS
288
n
124
CYS
288
A
GLY
289
n
125
GLY
289
A
ASN
290
n
126
ASN
290
A
GLN
291
n
127
GLN
291
A
ASP
292
n
128
ASP
292
A
TYR
293
n
129
TYR
293
A
LYS
294
n
130
LYS
294
A
TYR
295
n
131
TYR
295
A
ARG
296
n
132
ARG
296
A
VAL
297
n
133
VAL
297
A
SER
298
n
134
SER
298
A
ASP
299
n
135
ASP
299
A
VAL
300
n
136
VAL
300
A
THR
301
n
137
THR
301
A
LYS
302
n
138
LYS
302
A
ALA
303
n
139
ALA
303
A
GLY
304
n
140
GLY
304
A
HIS
305
n
141
HIS
305
A
SER
306
n
142
SER
306
A
LEU
307
n
143
LEU
307
A
GLU
308
n
144
GLU
308
A
LEU
309
n
145
LEU
309
A
ILE
310
n
146
ILE
310
A
GLU
311
n
147
GLU
311
A
PRO
312
n
148
PRO
312
A
LEU
313
n
149
LEU
313
A
ILE
314
n
150
ILE
314
A
LYS
315
n
151
LYS
315
A
PHE
316
n
152
PHE
316
A
GLN
317
n
153
GLN
317
A
VAL
318
n
154
VAL
318
A
GLY
319
n
155
GLY
319
A
LEU
320
n
156
LEU
320
A
LYS
321
n
157
LYS
321
A
LYS
322
n
158
LYS
322
A
LEU
323
n
159
LEU
323
A
ASN
324
n
160
ASN
324
A
LEU
325
n
161
LEU
325
A
HIS
326
n
162
HIS
326
A
GLU
327
n
163
GLU
327
A
GLU
328
n
164
GLU
328
A
GLU
329
n
165
GLU
329
A
HIS
330
n
166
HIS
330
A
VAL
331
n
167
VAL
331
A
LEU
332
n
168
LEU
332
A
LEU
333
n
169
LEU
333
A
MET
334
n
170
MET
334
A
ALA
335
n
171
ALA
335
A
ILE
336
n
172
ILE
336
A
CYS
337
n
173
CYS
337
A
ILE
338
n
174
ILE
338
A
VAL
339
n
175
VAL
339
A
SER
340
n
176
SER
340
A
PRO
341
n
177
PRO
341
A
ASP
342
n
178
ASP
342
A
ARG
343
n
179
ARG
343
A
PRO
344
n
180
PRO
344
A
GLY
345
n
181
GLY
345
A
VAL
346
n
182
VAL
346
A
GLN
347
n
183
GLN
347
A
ASP
348
n
184
ASP
348
A
ALA
349
n
185
ALA
349
A
ALA
350
n
186
ALA
350
A
LEU
351
n
187
LEU
351
A
ILE
352
n
188
ILE
352
A
GLU
353
n
189
GLU
353
A
ALA
354
n
190
ALA
354
A
ILE
355
n
191
ILE
355
A
GLN
356
n
192
GLN
356
A
ASP
357
n
193
ASP
357
A
ARG
358
n
194
ARG
358
A
LEU
359
n
195
LEU
359
A
SER
360
n
196
SER
360
A
ASN
361
n
197
ASN
361
A
THR
362
n
198
THR
362
A
LEU
363
n
199
LEU
363
A
GLN
364
n
200
GLN
364
A
THR
365
n
201
THR
365
A
TYR
366
n
202
TYR
366
A
ILE
367
n
203
ILE
367
A
ARG
368
n
204
ARG
368
A
CYS
369
n
205
CYS
369
A
ARG
370
n
206
ARG
370
A
HIS
371
n
207
HIS
371
A
PRO
372
n
208
PRO
372
A
PRO
373
n
209
PRO
373
A
PRO
374
n
210
PRO
374
A
GLY
375
n
211
GLY
375
A
SER
376
n
212
SER
376
A
HIS
377
n
213
HIS
377
A
LEU
378
n
214
LEU
378
A
LEU
379
n
215
LEU
379
A
TYR
380
n
216
TYR
380
A
ALA
381
n
217
ALA
381
A
LYS
382
n
218
LYS
382
A
MET
383
n
219
MET
383
A
ILE
384
n
220
ILE
384
A
GLN
385
n
221
GLN
385
A
LYS
386
n
222
LYS
386
A
LEU
387
n
223
LEU
387
A
ALA
388
n
224
ALA
388
A
ASP
389
n
225
ASP
389
A
LEU
390
n
226
LEU
390
A
ARG
391
n
227
ARG
391
A
SER
392
n
228
SER
392
A
LEU
393
n
229
LEU
393
A
ASN
394
n
230
ASN
394
A
GLU
395
n
231
GLU
395
A
GLU
396
n
232
GLU
396
A
HIS
397
n
233
HIS
397
A
SER
398
n
234
SER
398
A
LYS
399
n
235
LYS
399
A
GLN
400
n
236
GLN
400
A
TYR
401
n
237
TYR
401
A
ARG
402
n
238
ARG
402
A
CYS
403
n
239
CYS
403
A
LEU
404
n
240
LEU
404
A
SER
405
n
241
SER
405
A
PHE
406
n
242
PHE
406
A
GLN
407
n
243
GLN
407
A
PRO
408
n
244
PRO
408
A
GLU
409
n
245
GLU
409
A
CYS
410
n
246
CYS
410
A
SER
411
n
247
SER
411
A
MET
412
n
248
MET
412
A
LYS
413
n
249
LYS
413
A
LEU
414
n
250
LEU
414
A
THR
415
n
251
THR
415
A
PRO
416
n
252
PRO
416
A
LEU
417
n
253
LEU
417
A
VAL
418
n
254
VAL
418
A
LEU
419
n
255
LEU
419
A
GLU
420
n
256
GLU
420
A
VAL
421
n
257
VAL
421
A
PHE
422
n
258
PHE
422
A
GLY
423
n
259
GLY
423
A
n
260
424
A
n
261
425
A
n
262
426
A
n
263
427
A
author_and_software_defined_assembly
PISA
1
monomeric
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
A
N
THR
280
A
N
THR
116
A
O
SER
285
A
O
SER
121
A
N
TRP
286
A
N
TRP
122
A
O
TYR
295
A
O
TYR
131
1
A
GLY
114
A
GLY
1
1
Y
1
A
SER
115
A
SER
2
1
Y
1
A
HIS
116
A
HIS
3
1
Y
1
A
MET
117
A
MET
4
1
Y
1
A
GLY
163
A
GLY
50
1
Y
1
A
GLY
164
A
GLY
51
1
Y
1
A
ASN
424
A
ASN
260
1
Y
1
A
GLU
425
A
GLU
261
1
Y
1
A
ILE
426
A
ILE
262
1
Y
1
A
SER
427
A
SER
263
1
Y
1
A
A
SER
HIS
376
377
148.53
1
A
ASN
160
-38.45
126.35
1
A
ASN
290
69.35
85.89
1
A
GLN
291
-20.91
-42.77
1
A
ASP
342
-101.35
68.65
1
A
GLN
347
-85.80
-79.00
1
A
PRO
373
-22.70
-68.87
1
A
LEU
414
-103.80
-158.89
15.758
-0.05
0.00
0.00
-0.03
0.00
0.07
0.908
0.844
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.29369
0.21490
0.21844
2.60
48.06
472
9319
4.8
99.32
9.986
0.224
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.366
0.80
0.80
1.40
1DB1
MAXIMUM LIKELIHOOD
MASK
2.60
48.06
9
2059
32
0
2018
0.015
0.022
2092
1.814
2.004
2835
6.277
5.000
251
39.782
24.286
91
18.314
15.000
383
20.832
15.000
13
0.212
0.200
328
0.005
0.020
1535
0.234
0.200
978
0.311
0.200
1431
0.131
0.200
73
0.196
0.200
37
0.163
0.200
5
0.888
1.500
1316
1.469
2.000
2065
2.080
3.000
870
3.375
4.500
770
0.363
0.255
2.669
29
624
20
93.42
2.60
50.0
3AX8
9906
3
3
1
3.5
99.3
2.60
2.70
3.27
1
2.1
94.7
data collection
HKL-2000
phasing
MOLREP
refinement
REFMAC
5.2.0019
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3
1
N
N
2
N
N
3
N
N
A
SER
125
A
SER
12
HELX_P
A
TYR
143
A
TYR
30
1
1
19
A
ASP
149
A
ASP
36
HELX_P
A
PHE
153
A
PHE
40
5
2
5
A
SER
216
A
SER
52
HELX_P
A
LEU
224
A
LEU
60
1
3
9
A
MET
226
A
MET
62
HELX_P
A
MET
247
A
MET
83
1
4
22
A
GLY
250
A
GLY
86
HELX_P
A
LEU
254
A
LEU
90
5
5
5
A
THR
255
A
THR
91
HELX_P
A
SER
275
A
SER
111
1
6
21
A
ASN
290
A
ASN
126
HELX_P
A
ASP
292
A
ASP
128
5
7
3
A
ARG
296
A
ARG
132
HELX_P
A
LYS
302
A
LYS
138
1
8
7
A
SER
306
A
SER
142
HELX_P
A
LEU
323
A
LEU
159
1
9
18
A
HIS
326
A
HIS
162
HELX_P
A
VAL
339
A
VAL
175
1
10
14
A
ASP
348
A
ASP
184
HELX_P
A
HIS
371
A
HIS
207
1
11
24
A
HIS
377
A
HIS
213
HELX_P
A
SER
405
A
SER
241
1
12
29
A
CYS
410
A
CYS
246
HELX_P
A
LEU
414
A
LEU
250
5
13
5
A
THR
415
A
THR
251
HELX_P
A
GLY
423
A
GLY
259
1
14
9
TRANSCRIPTION
Hormone Receptor, Transcription
A
GLY
289
A
GLY
125
1
A
ASN
290
A
ASN
126
19.73
A
PRO
372
A
PRO
208
1
A
PRO
373
A
PRO
209
-15.65
A
PRO
373
A
PRO
209
1
A
PRO
374
A
PRO
210
2.28
VDR_HUMAN
UNP
1
118
P11473
DSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGG
VDR_HUMAN
UNP
1
216
P11473
SVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKY
RVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPG
SHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS
118
164
3AX8
118
164
P11473
A
1
5
51
216
427
3AX8
216
427
P11473
A
2
52
263
1
expression tag
GLY
114
3AX8
A
P11473
UNP
1
1
expression tag
SER
115
3AX8
A
P11473
UNP
2
1
expression tag
HIS
116
3AX8
A
P11473
UNP
3
1
expression tag
MET
117
3AX8
A
P11473
UNP
4
3
anti-parallel
anti-parallel
A
PHE
279
A
PHE
115
A
THR
280
A
THR
116
A
SER
285
A
SER
121
A
THR
287
A
THR
123
A
LYS
294
A
LYS
130
A
TYR
295
A
TYR
131
BINDING SITE FOR RESIDUE EIM A 1
A
EIM
1
Software
14
A
TYR
143
A
TYR
30
14
1_555
A
LEU
227
A
LEU
63
14
1_555
A
VAL
234
A
VAL
70
14
1_555
A
SER
237
A
SER
73
14
1_555
A
MET
272
A
MET
108
14
1_555
A
ARG
274
A
ARG
110
14
1_555
A
SER
275
A
SER
111
14
1_555
A
SER
278
A
SER
114
14
1_555
A
TRP
286
A
TRP
122
14
1_555
A
CYS
288
A
CYS
124
14
1_555
A
HIS
305
A
HIS
141
14
1_555
A
LEU
313
A
LEU
149
14
1_555
A
HIS
397
A
HIS
233
14
1_555
A
VAL
418
A
VAL
254
14
1_555
19
P 21 21 21