0.010051
0.000000
0.000000
0.000000
0.010051
0.000000
0.000000
0.000000
0.021789
0.00000
0.00000
0.00000
Vivekanandan, S.
Moovarkumudalvan, B.
Lescar, J.
Kolatkar, P.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
99.492
99.492
45.894
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
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
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
Y
90
N
C
N
91
N
N
Y
92
N
N
Y
93
N
C
Y
94
N
N
Y
95
N
C
N
96
N
H
N
97
N
H
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
H
N
109
N
H
N
110
N
O
N
111
N
P
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
C
N
116
R
C
N
117
N
O
N
118
S
C
N
119
N
O
N
120
N
C
N
121
R
C
N
122
N
N
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
C
N
127
N
N
N
128
N
C
N
129
N
C
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
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
Y
156
N
N
Y
157
N
C
Y
158
N
N
Y
159
N
C
N
160
N
C
N
161
N
O
N
162
N
N
N
163
N
C
N
164
N
N
N
165
N
N
Y
166
N
C
N
167
N
H
N
168
N
H
N
169
N
H
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
O
N
182
N
P
N
183
N
O
N
184
N
O
N
185
N
O
N
186
N
C
N
187
R
C
N
188
N
O
N
189
S
C
N
190
N
O
N
191
N
C
N
192
R
C
N
193
N
N
N
194
N
C
N
195
N
O
N
196
N
N
N
197
N
C
N
198
N
O
N
199
N
C
N
200
N
C
N
201
N
C
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
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
C
N
224
N
O
N
225
N
N
N
226
N
O
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
H
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
O
N
246
N
O
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
N
N
257
N
C
N
258
N
C
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
Y
271
N
C
Y
272
N
N
Y
273
N
C
Y
274
N
C
Y
275
N
N
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
O
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
C
N
296
N
C
N
297
N
C
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
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
N
N
321
N
O
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
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
N
C
N
343
N
S
N
344
N
C
N
345
N
O
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
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
N
368
N
O
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
O
N
388
N
H
N
389
N
H
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
N
N
398
S
C
N
399
N
C
N
400
N
O
N
401
N
C
N
402
N
O
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
R
C
N
416
N
O
N
417
N
C
N
418
N
O
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
H
N
427
N
H
N
428
N
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
N
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
N
442
N
O
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
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
Y
465
N
C
N
466
N
O
N
467
N
O
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
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
N
N
480
S
C
N
481
N
C
N
482
N
O
N
483
N
C
N
484
N
C
N
485
N
C
N
486
N
O
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
494
N
H
N
495
N
H
N
496
N
H
N
497
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
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
Y
93
N
sing
Y
94
N
sing
Y
95
N
doub
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
doub
N
102
N
sing
N
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
Y
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
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
doub
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
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
Y
166
N
sing
Y
167
N
sing
Y
168
N
doub
N
169
N
sing
Y
170
N
sing
N
171
N
sing
Y
172
N
doub
N
173
N
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
doub
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
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
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
doub
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
doub
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
doub
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
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
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
doub
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
Y
276
N
sing
Y
277
N
doub
Y
278
N
doub
N
279
N
sing
Y
280
N
sing
N
281
N
sing
Y
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
doub
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
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
doub
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
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
doub
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
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
doub
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
Y
363
N
doub
Y
364
N
sing
Y
365
N
sing
N
366
N
sing
Y
367
N
doub
N
368
N
sing
Y
369
N
doub
N
370
N
sing
Y
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
doub
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
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
doub
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
doub
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
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
doub
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
Y
432
N
doub
Y
433
N
sing
Y
434
N
sing
N
435
N
sing
Y
436
N
doub
Y
437
N
sing
Y
438
N
sing
N
439
N
sing
Y
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
443
N
doub
N
444
N
sing
Y
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
doub
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
Y
460
N
doub
Y
461
N
sing
Y
462
N
sing
N
463
N
sing
Y
464
N
doub
N
465
N
sing
Y
466
N
doub
N
467
N
sing
Y
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
N
479
N
doub
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
To be Published
0353
Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element
10.2210/pdb4s2q/pdb
pdb_00004s2q
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
2012-08-10
ADSC QUANTUM 315
ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.075
1.0
X29A
NSLS
1.075
SYNCHROTRON
NSLS BEAMLINE X29A
4871.149
DNA (5'-D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3')
1
syn
polymer
4965.257
DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')
1
syn
polymer
9264.711
Transcription factor SOX-9
UNP residues 103-178
1
man
polymer
18.015
water
2
nat
water
no
no
(DA)(DG)(DG)(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DC)(DC)(DT)(DG)
AGGCTTTGTTCTCCTG
A
polydeoxyribonucleotide
no
no
(DA)(DG)(DG)(DA)(DG)(DA)(DA)(DC)(DA)(DA)(DA)(DG)(DC)(DC)(DT)(DG)
AGGAGAACAAAGCCTG
B
polydeoxyribonucleotide
no
no
PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR
PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR
D
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
mouse
sample
Sox9, Sox-9
10090
Mus musculus
562
Escherichia coli
Bl21(DE3)
pETG20A
pETG20A-Sox9HMG
1
2.97
58.63
VAPOR DIFFUSION, HANGING DROP
8.5
20% PEG 3350, 200mM Sodium/potassium phosphate, 100mM Bis Tris propane, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
-7.729
1
19
A
4
B
13
-8.089
A_DG4:DC13_B
1
3.707
0.752
-0.393
-0.057
-7.349
1
19
A
5
B
12
-2.252
A_DG5:DC12_B
2
-3.879
0.294
-0.175
0.044
-1.785
1
19
A
6
B
11
-0.131
A_DC6:DG11_B
3
5.971
0.112
-0.031
-0.005
5.366
1
20
A
7
B
10
1.451
A_DT7:DA10_B
4
6.302
-0.578
-0.022
0.072
26.440
1
20
A
8
B
9
2.697
A_DT8:DA9_B
5
9.770
0.155
0.163
0.046
-20.353
1
20
A
9
B
8
1.590
A_DT9:DA8_B
6
-18.446
-0.702
0.097
-0.083
-13.943
1
19
A
10
B
7
5.603
A_DG10:DC7_B
7
-5.504
-0.068
-0.354
0.270
-0.054
1
20
A
11
B
6
-2.001
A_DT11:DA6_B
8
-13.318
-0.001
0.009
-0.140
-1.027
1
20
A
12
B
5
-4.452
A_DT12:DA5_B
9
-5.630
-0.431
0.103
-0.209
-9.490
1
19
A
13
B
4
-2.889
A_DC13:DG4_B
10
-18.921
-0.751
0.255
-0.262
-7.314
1
20
A
14
B
3
-15.144
A_DT14:DA3_B
11
-13.126
0.153
0.107
-0.177
-11.521
1
19
A
15
B
2
-13.193
A_DC15:DG2_B
12
-13.739
-0.339
0.395
-0.307
4.550
1
19
A
16
B
1
-8.535
A_DC16:DG1_B
13
1.573
0.208
-0.238
-0.607
3.278
31.528
A
A
4
5
17.285
B
B
13
12
3.346
9.193
-0.488
0.156
AA_DG4DG5:DC12DC13_BB
1
-6.561
12.336
29.484
-1.508
-0.382
3.223
30.192
A
A
5
6
-1.536
B
B
12
11
3.205
-0.800
0.573
-0.132
AA_DG5DC6:DG11DC12_BB
2
0.979
-1.880
30.166
-0.094
-0.904
2.202
29.457
A
A
6
7
67.637
B
B
11
10
3.599
27.137
0.395
0.845
AA_DC6DT7:DA10DG11_BB
3
2.531
-6.308
11.281
-5.892
-0.073
3.019
31.467
A
A
7
8
34.139
B
B
10
9
3.261
17.497
0.330
0.569
AA_DT7DT8:DA9DA10_BB
4
-1.687
3.291
26.203
-2.396
-0.941
2.800
56.519
A
A
8
9
65.881
B
B
9
8
5.423
51.148
-0.255
0.419
AA_DT8DT9:DA8DA9_BB
5
3.626
-4.670
24.623
-4.890
0.648
3.164
38.182
A
A
9
10
6.999
B
B
8
7
3.076
4.568
0.368
0.976
AA_DT9DG10:DC7DA8_BB
6
-0.390
0.597
37.916
0.940
-0.610
3.258
31.438
A
A
10
11
7.664
B
B
7
6
3.204
4.129
-0.736
0.098
AA_DG10DT11:DA6DC7_BB
7
-4.166
7.732
30.900
-0.590
0.581
3.059
32.918
A
A
11
12
8.072
B
B
6
5
3.104
4.558
0.627
-0.353
AA_DT11DT12:DA5DA6_BB
8
1.905
-3.373
32.556
-1.360
-0.798
3.541
34.341
A
A
12
13
-2.233
B
B
5
4
3.527
-1.317
-0.107
-0.461
AA_DT12DC13:DG4DA5_BB
9
-2.360
4.001
34.237
-0.558
-0.218
3.095
39.964
A
A
13
14
16.794
B
B
4
3
3.375
11.328
-0.688
-0.423
AA_DC13DT14:DA3DG4_BB
10
1.976
-2.930
38.339
-1.935
1.237
3.222
35.855
A
A
14
15
-11.257
B
B
3
2
3.314
-6.889
1.053
0.095
AA_DT14DC15:DG2DA3_BB
11
-0.544
0.889
35.204
1.151
-1.789
3.214
31.023
A
A
15
16
1.377
B
B
2
1
3.095
0.725
0.881
-0.102
AA_DC15DC16:DG1DG2_BB
12
9.553
-18.143
29.542
-0.329
0.171
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Refinement description
1
0
2016-02-17
1
1
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2015-01-21
REL
REL
HOH
water
32630
synthetic construct
sample
32630
synthetic construct
sample
3F27
PDB entry 3F27
PDB
experimental model
HOH
3
4
HOH
HOH
201
D
HOH
4
4
HOH
HOH
202
D
DA
3
n
1
DA
3
A
DG
4
n
2
DG
4
A
DG
5
n
3
DG
5
A
DC
6
n
4
DC
6
A
DT
7
n
5
DT
7
A
DT
8
n
6
DT
8
A
DT
9
n
7
DT
9
A
DG
10
n
8
DG
10
A
DT
11
n
9
DT
11
A
DT
12
n
10
DT
12
A
DC
13
n
11
DC
13
A
DT
14
n
12
DT
14
A
DC
15
n
13
DC
15
A
DC
16
n
14
DC
16
A
DT
17
n
15
DT
17
A
DG
18
n
16
DG
18
A
DA
0
n
1
DA
0
B
DG
1
n
2
DG
1
B
DG
2
n
3
DG
2
B
DA
3
n
4
DA
3
B
DG
4
n
5
DG
4
B
DA
5
n
6
DA
5
B
DA
6
n
7
DA
6
B
DC
7
n
8
DC
7
B
DA
8
n
9
DA
8
B
DA
9
n
10
DA
9
B
DA
10
n
11
DA
10
B
DG
11
n
12
DG
11
B
DC
12
n
13
DC
12
B
DC
13
n
14
DC
13
B
DT
14
n
15
DT
14
B
DG
15
n
16
DG
15
B
PRO
66
n
1
PRO
66
D
HIS
67
n
2
HIS
67
D
VAL
68
n
3
VAL
68
D
LYS
69
n
4
LYS
69
D
ARG
70
n
5
ARG
70
D
PRO
71
n
6
PRO
71
D
MET
72
n
7
MET
72
D
ASN
73
n
8
ASN
73
D
ALA
74
n
9
ALA
74
D
PHE
75
n
10
PHE
75
D
MET
76
n
11
MET
76
D
VAL
77
n
12
VAL
77
D
TRP
78
n
13
TRP
78
D
ALA
79
n
14
ALA
79
D
GLN
80
n
15
GLN
80
D
ALA
81
n
16
ALA
81
D
ALA
82
n
17
ALA
82
D
ARG
83
n
18
ARG
83
D
ARG
84
n
19
ARG
84
D
LYS
85
n
20
LYS
85
D
LEU
86
n
21
LEU
86
D
ALA
87
n
22
ALA
87
D
ASP
88
n
23
ASP
88
D
GLN
89
n
24
GLN
89
D
TYR
90
n
25
TYR
90
D
PRO
91
n
26
PRO
91
D
HIS
92
n
27
HIS
92
D
LEU
93
n
28
LEU
93
D
HIS
94
n
29
HIS
94
D
ASN
95
n
30
ASN
95
D
ALA
96
n
31
ALA
96
D
GLU
97
n
32
GLU
97
D
LEU
98
n
33
LEU
98
D
SER
99
n
34
SER
99
D
LYS
100
n
35
LYS
100
D
THR
101
n
36
THR
101
D
LEU
102
n
37
LEU
102
D
GLY
103
n
38
GLY
103
D
LYS
104
n
39
LYS
104
D
LEU
105
n
40
LEU
105
D
TRP
106
n
41
TRP
106
D
ARG
107
n
42
ARG
107
D
LEU
108
n
43
LEU
108
D
LEU
109
n
44
LEU
109
D
ASN
110
n
45
ASN
110
D
GLU
111
n
46
GLU
111
D
SER
112
n
47
SER
112
D
GLU
113
n
48
GLU
113
D
LYS
114
n
49
LYS
114
D
ARG
115
n
50
ARG
115
D
PRO
116
n
51
PRO
116
D
PHE
117
n
52
PHE
117
D
VAL
118
n
53
VAL
118
D
GLU
119
n
54
GLU
119
D
GLU
120
n
55
GLU
120
D
ALA
121
n
56
ALA
121
D
GLU
122
n
57
GLU
122
D
ARG
123
n
58
ARG
123
D
LEU
124
n
59
LEU
124
D
ARG
125
n
60
ARG
125
D
VAL
126
n
61
VAL
126
D
GLN
127
n
62
GLN
127
D
HIS
128
n
63
HIS
128
D
LYS
129
n
64
LYS
129
D
LYS
130
n
65
LYS
130
D
ASP
131
n
66
ASP
131
D
HIS
132
n
67
HIS
132
D
PRO
133
n
68
PRO
133
D
ASP
134
n
69
ASP
134
D
TYR
135
n
70
TYR
135
D
LYS
136
n
71
LYS
136
D
TYR
137
n
72
TYR
137
D
GLN
138
n
73
GLN
138
D
PRO
139
n
74
PRO
139
D
ARG
140
n
75
ARG
140
D
ARG
141
n
76
ARG
141
D
2.3093
-0.6000
1.2166
2.4284
1.0806
4.6442
0.3797
0.2757
-0.4596
-0.2644
-0.2457
0.2621
0.5429
-0.2253
-0.1342
0.3766
-0.0053
-0.1381
0.3453
-0.0201
0.4220
refined
-16.7256
-0.6508
-0.2605
X-RAY DIFFRACTION
4.1755
2.9486
1.1188
2.7858
2.0884
2.2606
0.2035
-0.4833
-0.3472
-0.1738
0.1518
1.2160
-0.4893
-1.4533
-0.0104
0.5603
0.1756
-0.0429
0.7483
0.0557
0.5124
refined
-29.5227
0.3193
1.8315
X-RAY DIFFRACTION
3.5264
0.8023
-0.2317
1.1500
2.2414
4.6476
0.1082
0.4528
-0.5019
-0.2113
0.0520
1.6161
-0.0820
-1.0791
-0.5795
0.6293
0.0167
-0.2352
0.6074
0.1189
0.9497
refined
-32.0382
2.5412
-2.4048
X-RAY DIFFRACTION
D
66
D
141
X-RAY DIFFRACTION
1
( CHAIN D AND RESID 66:141 )
B
0
B
15
X-RAY DIFFRACTION
2
( CHAIN B AND RESID 0:15 )
A
3
A
18
X-RAY DIFFRACTION
3
( CHAIN A AND RESID 3:18 )
author_and_software_defined_assembly
PISA
3
trimeric
4020
-13
10610
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
-6.91
0.80
102.40
95.49
A
A
A
C3'
C2'
C1'
DA
DA
DA
3
3
3
N
1
-3.56
0.40
104.50
100.94
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
-5.08
0.80
102.40
97.32
A
A
A
C3'
C2'
C1'
DG
DG
DG
4
4
4
N
1
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-6.14
1.00
110.10
103.96
A
A
A
C1'
O4'
C4'
DT
DT
DT
12
12
12
N
1
3.03
0.50
106.80
109.83
A
A
A
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
-6.35
0.80
102.40
96.05
A
A
A
C3'
C2'
C1'
DT
DT
DT
17
17
17
N
1
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
4.90
0.60
119.00
123.90
A
A
A
C4
C5
C7
DT
DT
DT
17
17
17
N
1
-5.95
0.60
122.90
116.95
A
A
A
C6
C5
C7
DT
DT
DT
17
17
17
N
1
3.24
0.30
108.30
111.54
B
B
B
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.89
0.30
108.30
112.19
B
B
B
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
2.44
0.30
108.30
110.74
B
B
B
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
3.31
0.50
106.80
110.11
B
B
B
O4'
C1'
C2'
DA
DA
DA
9
9
9
N
1
-5.62
0.80
102.40
96.78
B
B
B
C3'
C2'
C1'
DC
DC
DC
13
13
13
N
1
-9.49
0.80
102.40
92.91
B
B
B
C3'
C2'
C1'
DT
DT
DT
14
14
14
N
1
5.40
0.30
108.30
113.70
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
6.48
0.60
119.00
125.48
B
B
B
C4
C5
C7
DT
DT
DT
14
14
14
N
1
-8.20
0.60
122.90
114.70
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
A
A
O3'
C3'
DA
DA
3
3
-0.051
0.006
1.419
1.368
N
1
D
VAL
68
-65.14
-176.38
0.2688
0.2134
0.2162
2.70
24.873
316
6721
6675
4.73
99.69
0.23
RANDOM
1
1.34
MOLECULAR REPLACEMENT
32.56
0.90
1.11
PDB entry 3F27
ML
FLAT BULK SOLVENT MODEL
2.70
24.873
2
1314
0
659
653
0.008
1410
1.490
2038
26.547
582
0.069
216
0.005
149
0.4013
0.2581
3.4011
155
3094
100.00
0.2415
0.2028
24.8740
161
3265
100.00
2.7
50.0
4S2Q
6721
6675
0
2
0.133
1
19.0
30.3
99.9
2.7
3.4011
19
6721
0.133
1
30.3
99.9
data collection
ADSC
Quantum
phasing
PHASES
refinement
PHENIX
(phenix.refine: 1.8_1069)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element
1
N
N
2
N
N
3
N
N
4
N
N
D
ASN
73
C
ASN
8
HELX_P
D
TYR
90
C
TYR
25
1
1
18
D
HIS
94
C
HIS
29
HELX_P
D
LEU
108
C
LEU
43
1
2
15
D
ASN
110
C
ASN
45
HELX_P
D
HIS
132
C
HIS
67
1
3
23
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
2
1_555
B
DC
13
B
N3
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
2
1_555
B
DC
13
B
O2
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
2
1_555
B
DC
13
B
N4
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
3
1_555
B
DC
12
B
N3
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
3
1_555
B
DC
12
B
O2
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
3
1_555
B
DC
12
B
N4
DC
13
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
4
1_555
B
DG
11
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
4
1_555
B
DG
11
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
4
1_555
B
DG
11
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
5
1_555
B
DA
10
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
5
1_555
B
DA
10
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
6
1_555
B
DA
9
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
6
1_555
B
DA
9
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
7
1_555
B
DA
8
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
7
1_555
B
DA
8
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
8
1_555
B
DC
7
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
8
1_555
B
DC
7
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
8
1_555
B
DC
7
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DT
11
A
N3
DT
9
1_555
B
DA
6
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
11
A
O4
DT
9
1_555
B
DA
6
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
12
A
N3
DT
10
1_555
B
DA
5
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
12
A
O4
DT
10
1_555
B
DA
5
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N3
DC
11
1_555
B
DG
4
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N4
DC
11
1_555
B
DG
4
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
13
A
O2
DC
11
1_555
B
DG
4
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DT
14
A
N3
DT
12
1_555
B
DA
3
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
14
A
O4
DT
12
1_555
B
DA
3
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DC
15
A
N3
DC
13
1_555
B
DG
2
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
15
A
N4
DC
13
1_555
B
DG
2
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
15
A
O2
DC
13
1_555
B
DG
2
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
16
A
N3
DC
14
1_555
B
DG
1
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
16
A
N4
DC
14
1_555
B
DG
1
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
16
A
O2
DC
14
1_555
B
DG
1
B
N2
DG
2
1_555
DNA BINDING PROTEIN/DNA
DNA Bending, Minor groove binding, Transcription Regulation, DNA BINDING PROTEIN-DNA complex
SOX9_MOUSE
UNP
3
103
Q04887
PHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRR
4S2Q
PDB
1
4S2Q
4S2Q
PDB
2
4S2Q
103
178
4S2Q
66
141
Q04887
D
1
1
76
3
18
4S2Q
3
18
4S2Q
A
2
1
16
0
15
4S2Q
0
15
4S2Q
B
3
1
16
92
P 41 21 2