0.007821
0.000000
0.004273
0.000000
0.022200
0.000000
0.000000
0.000000
0.015489
0.00000
0.00000
0.00000
Feldman, M.E.
Simon, M.D.
Shokat, K.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
118.65
90.00
127.856
45.046
73.568
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C6 H7 N O2
125.125
3-PROP-2-YN-1-YL-1,3-OXAZOLIDIN-2-ONE
1-(PROP-2-YNYL)-OXAZOLIDINE-2-ONE
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
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
C
N
267
N
O
N
268
N
C
N
269
N
O
N
270
N
C
N
271
N
O
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
O
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
S
C
N
288
N
C
N
289
N
C
N
290
N
C
N
291
N
O
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
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
C
N
313
N
O
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
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
C
N
335
N
N
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
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
S
N
359
N
C
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
C
N
373
N
C
N
374
N
C
N
375
N
C
N
376
N
C
N
377
N
C
N
378
N
O
N
379
N
N
N
380
N
O
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
N
N
389
S
C
N
390
N
C
N
391
N
O
N
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
C
Y
397
N
C
Y
398
N
C
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
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
N
C
N
416
N
C
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
N
433
N
O
N
434
N
O
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
N
N
443
S
C
N
444
N
C
N
445
N
O
N
446
R
C
N
447
N
O
N
448
N
C
N
449
N
O
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
N
N
460
S
C
N
461
N
C
N
462
N
O
N
463
N
C
Y
464
N
C
Y
465
N
C
Y
466
N
C
Y
467
N
N
Y
468
N
C
Y
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
N
473
N
O
N
474
N
H
N
475
N
H
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
N
N
487
S
C
N
488
N
C
N
489
N
O
N
490
N
C
Y
491
N
C
Y
492
N
C
Y
493
N
C
Y
494
N
C
Y
495
N
C
Y
496
N
C
N
497
N
O
N
498
N
O
N
499
N
H
N
500
N
H
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
N
N
511
S
C
N
512
N
C
N
513
N
O
N
514
N
C
N
515
N
C
N
516
N
C
N
517
N
O
N
518
N
H
N
519
N
H
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
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
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
doub
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
sing
N
305
N
sing
N
306
N
sing
N
307
N
doub
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
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
doub
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
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
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
doub
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
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
doub
N
374
N
sing
N
375
N
sing
N
376
N
trip
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
doub
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
Y
392
N
doub
Y
393
N
sing
Y
394
N
sing
N
395
N
sing
Y
396
N
doub
N
397
N
sing
Y
398
N
doub
N
399
N
sing
Y
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
doub
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
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
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
sing
N
440
N
doub
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
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
N
456
N
doub
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
Y
461
N
doub
Y
462
N
sing
Y
463
N
sing
N
464
N
sing
Y
465
N
doub
Y
466
N
sing
Y
467
N
sing
N
468
N
sing
Y
469
N
sing
Y
470
N
doub
N
471
N
sing
Y
472
N
doub
N
473
N
sing
Y
474
N
sing
N
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
doub
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
Y
489
N
doub
Y
490
N
sing
Y
491
N
sing
N
492
N
sing
Y
493
N
doub
N
494
N
sing
Y
495
N
doub
N
496
N
sing
Y
497
N
sing
N
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
doub
N
509
N
sing
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
US
Acs Chem.Biol.
1554-8929
1
755
760
10.1021/cb6003756
17240973
Structure and properties of a re-engineered homeodomain protein-DNA interface.
2006
10.2210/pdb2hot/pdb
pdb_00002hot
100
1
KOHZU:Double Crystal Si(111)
CCD
2005-07-25
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
1.11588
1.0
8.3.1
ALS
1.11588
SYNCHROTRON
ALS BEAMLINE 8.3.1
6389.133
5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*CP*CP*GP*GP*A)-3'
1
syn
polymer
6496.224
5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'
1
syn
polymer
7516.522
Segmentation polarity homeobox protein engrailed
Engrailed homeodomain
I45V,I47G,Q50K,K52M
2
man
polymer
125.125
3-PROP-2-YN-1-YL-1,3-OXAZOLIDIN-2-ONE
1
syn
non-polymer
92.094
GLYCEROL
2
syn
non-polymer
18.015
water
80
nat
water
Homeobox
no
no
(DT)(DT)(DT)(DT)(DG)(DC)(DC)(DA)(DT)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG)
(DA)
TTTTGCCATGTAATCCCCGGA
C
polydeoxyribonucleotide
no
no
(DA)(DT)(DC)(DC)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DA)
(DA)
ATCCGGGGATTACATGGCAAA
D
polydeoxyribonucleotide
no
no
GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST
GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST
A,B
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
fruit fly
Drosophila
Escherichia
Escherichia coli
sample
En
7227
Drosophila melanogaster
511693
Escherichia coli BL21
BL21
pMal-c2
pMal-EnHDf
1
3.27
62.40
VAPOR DIFFUSION, HANGING DROP
7
PEG-400/NH4OAc, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
PEG400
1
NH4OAc
1
H2O
1
NH4OAc
2
bis-Tris-Propane
2
PEG400
2
-5.405
1
20
C
2
D
42
5.577
C_DT2:DA42_D
1
-9.605
-0.257
0.001
-0.176
-0.560
1
20
C
3
D
41
1.656
C_DT3:DA41_D
2
-5.966
0.053
0.168
-0.319
2.102
1
20
C
4
D
40
5.104
C_DT4:DA40_D
3
-19.506
0.038
-0.201
-0.355
-12.720
1
19
C
5
D
39
-1.728
C_DG5:DC39_D
4
-9.667
-0.738
-0.266
-0.463
-6.061
1
19
C
6
D
38
-5.502
C_DC6:DG38_D
5
-4.771
-0.009
0.179
-0.006
3.148
1
19
C
7
D
37
-0.031
C_DC7:DG37_D
6
-5.295
0.518
-0.025
-0.424
-2.353
1
20
C
8
D
36
-3.041
C_DA8:DT36_D
7
-12.477
1.041
0.195
-0.287
-0.374
1
20
C
9
D
35
-4.223
C_DT9:DA35_D
8
-10.265
0.266
0.040
-0.280
-2.473
1
19
C
10
D
34
0.720
C_DG10:DC34_D
9
-7.129
-0.225
0.042
-0.204
7.642
1
20
C
11
D
33
8.184
C_DT11:DA33_D
10
-9.036
0.001
-0.112
-0.074
0.204
1
20
C
12
D
32
2.949
C_DA12:DT32_D
11
-16.220
0.325
-0.386
-0.354
2.608
1
20
C
13
D
31
2.817
C_DA13:DT31_D
12
-15.675
-0.109
0.040
-0.379
-3.859
1
20
C
14
D
30
0.832
C_DT14:DA30_D
13
-16.867
-0.237
-0.030
-0.290
-0.925
1
19
C
15
D
29
1.936
C_DC15:DG29_D
14
-8.191
0.300
-0.082
-0.145
5.899
1
19
C
16
D
28
-1.463
C_DC16:DG28_D
15
-8.368
0.375
-0.105
-0.426
0.911
1
19
C
17
D
27
-2.480
C_DC17:DG27_D
16
-20.609
0.462
0.323
-0.439
-9.006
1
19
C
18
D
26
-1.504
C_DC18:DG26_D
17
-10.676
-0.226
0.055
-0.262
3.418
1
19
C
19
D
25
0.297
C_DG19:DC25_D
18
-10.463
0.005
-0.090
-0.231
-0.568
1
19
C
20
D
24
-0.410
C_DG20:DC24_D
19
-11.427
-0.387
-0.302
-0.311
4.770
1
20
C
21
D
23
4.276
C_DA21:DT23_D
20
-18.739
0.126
-0.080
-0.174
3.440
37.227
C
C
2
3
12.822
D
D
42
41
3.268
8.121
1.034
0.977
CC_DT2DT3:DA41DA42_DD
1
1.611
-2.544
36.327
0.410
-1.397
3.269
31.177
C
C
3
4
1.257
D
D
41
40
3.279
0.675
-0.140
0.130
CC_DT3DT4:DA40DA41_DD
2
1.627
-3.028
31.128
0.113
0.572
3.255
38.047
C
C
4
5
19.274
D
D
40
39
3.587
12.346
0.224
-0.501
CC_DT4DG5:DC39DA40_DD
3
2.281
-3.561
35.988
-2.459
-0.031
3.168
34.971
C
C
5
6
-1.710
D
D
39
38
3.171
-1.027
-0.090
0.022
CC_DG5DC6:DG38DC39_DD
4
-2.243
3.736
34.887
0.187
-0.179
3.138
33.137
C
C
6
7
-2.495
D
D
38
37
3.169
-1.421
-0.073
0.327
CC_DC6DC7:DG37DG38_DD
5
2.591
-4.548
33.009
0.804
0.548
3.508
48.065
C
C
7
8
-2.741
D
D
37
36
3.519
-2.229
-0.424
0.700
CC_DC7DA8:DT36DG37_DD
6
-4.236
5.209
47.840
1.049
0.162
3.256
28.118
C
C
8
9
-9.225
D
D
36
35
3.245
-4.463
0.041
-0.321
CC_DA8DT9:DA35DT36_DD
7
0.717
-1.482
27.760
0.387
0.083
3.353
38.077
C
C
9
10
7.447
D
D
35
34
3.306
4.845
0.536
0.451
CC_DT9DG10:DC34DA35_DD
8
1.372
-2.109
37.755
0.063
-0.643
3.006
25.476
C
C
10
11
10.637
D
D
34
33
3.076
4.664
-0.018
-0.097
CC_DG10DT11:DA33DC34_DD
9
1.008
-2.300
25.033
-1.472
0.311
3.545
44.429
C
C
11
12
7.564
D
D
33
32
3.428
5.705
-0.838
1.107
CC_DT11DA12:DT32DA33_DD
10
-0.437
0.579
44.077
0.900
1.065
3.132
32.825
C
C
12
13
3.507
D
D
32
31
3.214
1.976
0.388
-0.145
CC_DA12DA13:DT31DT32_DD
11
-3.955
7.020
32.534
-0.586
-1.348
3.369
31.949
C
C
13
14
2.346
D
D
31
30
3.399
1.291
-0.737
-1.091
CC_DA13DT14:DA30DT31_DD
12
-0.743
1.350
31.916
-2.224
1.200
3.323
34.910
C
C
14
15
-2.500
D
D
30
29
3.307
-1.499
-0.108
-0.421
CC_DT14DC15:DG29DA30_DD
13
-1.635
2.728
34.842
-0.472
-0.071
3.010
32.421
C
C
15
16
14.986
D
D
29
28
3.178
8.279
0.297
-0.274
CC_DC15DC16:DG28DG29_DD
14
0.038
-0.068
31.373
-1.892
-0.526
3.361
37.598
C
C
16
17
6.968
D
D
28
27
3.456
4.469
-0.305
-0.729
CC_DC16DC17:DG27DG28_DD
15
-4.851
7.564
37.036
-1.742
-0.190
3.235
33.136
C
C
17
18
10.284
D
D
27
26
3.405
5.801
0.342
-0.720
CC_DC17DC18:DG26DG27_DD
16
6.440
-11.419
32.013
-2.272
0.520
3.092
34.248
C
C
18
19
20.089
D
D
26
25
3.196
11.592
-0.004
0.270
CC_DC18DG19:DC25DG26_DD
17
3.242
-5.618
32.123
-1.355
0.514
3.309
31.211
C
C
19
20
11.565
D
D
25
24
3.476
6.181
0.133
-0.534
CC_DG19DG20:DC24DC25_DD
18
1.180
-2.209
30.585
-2.224
-0.012
3.081
33.229
C
C
20
21
10.749
D
D
24
23
3.165
6.113
0.265
-0.136
CC_DG20DA21:DT23DC24_DD
19
-0.986
1.733
32.663
-1.222
-0.623
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Advisory
Version format compliance
Refinement description
Database references
Derived calculations
Data collection
1
0
2006-12-12
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2021-10-20
1
5
2024-02-14
_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
Engrailed Homeodomain Q50K mutant bound to the same DNA but unmodified
RCSB
Y
RCSB
2006-07-16
REL
REL
P2O
3-PROP-2-YN-1-YL-1,3-OXAZOLIDIN-2-ONE
GOL
GLYCEROL
HOH
water
Solid-phase DNA synthesis
sample
Commercial solid-phase DNA synthesis
sample
P2O
22
4
P2O
P2O
22
C
GOL
201
5
GOL
GOL
201
B
GOL
202
5
GOL
GOL
202
B
HOH
1
6
HOH
HOH
23
C
HOH
9
6
HOH
HOH
24
C
HOH
21
6
HOH
HOH
25
C
HOH
23
6
HOH
HOH
26
C
HOH
26
6
HOH
HOH
27
C
HOH
28
6
HOH
HOH
28
C
HOH
32
6
HOH
HOH
29
C
HOH
33
6
HOH
HOH
30
C
HOH
39
6
HOH
HOH
31
C
HOH
46
6
HOH
HOH
32
C
HOH
49
6
HOH
HOH
33
C
HOH
51
6
HOH
HOH
34
C
HOH
52
6
HOH
HOH
35
C
HOH
54
6
HOH
HOH
36
C
HOH
55
6
HOH
HOH
37
C
HOH
57
6
HOH
HOH
38
C
HOH
60
6
HOH
HOH
39
C
HOH
61
6
HOH
HOH
40
C
HOH
66
6
HOH
HOH
41
C
HOH
69
6
HOH
HOH
42
C
HOH
71
6
HOH
HOH
43
C
HOH
73
6
HOH
HOH
44
C
HOH
79
6
HOH
HOH
45
C
HOH
4
6
HOH
HOH
43
D
HOH
8
6
HOH
HOH
44
D
HOH
10
6
HOH
HOH
45
D
HOH
11
6
HOH
HOH
46
D
HOH
12
6
HOH
HOH
47
D
HOH
14
6
HOH
HOH
48
D
HOH
17
6
HOH
HOH
49
D
HOH
20
6
HOH
HOH
50
D
HOH
24
6
HOH
HOH
51
D
HOH
30
6
HOH
HOH
52
D
HOH
36
6
HOH
HOH
53
D
HOH
37
6
HOH
HOH
54
D
HOH
38
6
HOH
HOH
55
D
HOH
40
6
HOH
HOH
56
D
HOH
47
6
HOH
HOH
57
D
HOH
64
6
HOH
HOH
58
D
HOH
68
6
HOH
HOH
59
D
HOH
70
6
HOH
HOH
60
D
HOH
72
6
HOH
HOH
61
D
HOH
75
6
HOH
HOH
62
D
HOH
77
6
HOH
HOH
63
D
HOH
80
6
HOH
HOH
64
D
HOH
2
6
HOH
HOH
61
A
HOH
3
6
HOH
HOH
62
A
HOH
5
6
HOH
HOH
63
A
HOH
6
6
HOH
HOH
64
A
HOH
25
6
HOH
HOH
65
A
HOH
27
6
HOH
HOH
66
A
HOH
29
6
HOH
HOH
67
A
HOH
35
6
HOH
HOH
68
A
HOH
41
6
HOH
HOH
69
A
HOH
42
6
HOH
HOH
70
A
HOH
48
6
HOH
HOH
71
A
HOH
56
6
HOH
HOH
72
A
HOH
59
6
HOH
HOH
73
A
HOH
62
6
HOH
HOH
74
A
HOH
63
6
HOH
HOH
75
A
HOH
78
6
HOH
HOH
76
A
HOH
7
6
HOH
HOH
203
B
HOH
13
6
HOH
HOH
204
B
HOH
15
6
HOH
HOH
205
B
HOH
16
6
HOH
HOH
206
B
HOH
18
6
HOH
HOH
207
B
HOH
19
6
HOH
HOH
208
B
HOH
22
6
HOH
HOH
209
B
HOH
31
6
HOH
HOH
210
B
HOH
34
6
HOH
HOH
211
B
HOH
43
6
HOH
HOH
212
B
HOH
44
6
HOH
HOH
213
B
HOH
45
6
HOH
HOH
214
B
HOH
50
6
HOH
HOH
215
B
HOH
53
6
HOH
HOH
216
B
HOH
58
6
HOH
HOH
217
B
HOH
65
6
HOH
HOH
218
B
HOH
67
6
HOH
HOH
219
B
HOH
74
6
HOH
HOH
220
B
HOH
76
6
HOH
HOH
221
B
T
1
n
1
DT
1
C
T
2
n
2
DT
2
C
T
3
n
3
DT
3
C
T
4
n
4
DT
4
C
G
5
n
5
DG
5
C
C
6
n
6
DC
6
C
C
7
n
7
DC
7
C
A
8
n
8
DA
8
C
T
9
n
9
DT
9
C
G
10
n
10
DG
10
C
T
11
n
11
DT
11
C
A
12
n
12
DA
12
C
A
13
n
13
DA
13
C
T
14
n
14
DT
14
C
C
15
n
15
DC
15
C
C
16
n
16
DC
16
C
C
17
n
17
DC
17
C
C
18
n
18
DC
18
C
G
19
n
19
DG
19
C
G
20
n
20
DG
20
C
A
21
n
21
DA
21
C
A
22
n
1
DA
22
D
T
23
n
2
DT
23
D
C
24
n
3
DC
24
D
C
25
n
4
DC
25
D
G
26
n
5
DG
26
D
G
27
n
6
DG
27
D
G
28
n
7
DG
28
D
G
29
n
8
DG
29
D
A
30
n
9
DA
30
D
T
31
n
10
DT
31
D
T
32
n
11
DT
32
D
A
33
n
12
DA
33
D
C
34
n
13
DC
34
D
A
35
n
14
DA
35
D
T
36
n
15
DT
36
D
G
37
n
16
DG
37
D
G
38
n
17
DG
38
D
C
39
n
18
DC
39
D
A
40
n
19
DA
40
D
A
41
n
20
DA
41
D
A
42
n
21
DA
42
D
n
1
-2
A
n
2
-1
A
n
3
0
A
n
4
1
A
n
5
2
A
n
6
3
A
n
7
4
A
ARG
5
n
8
ARG
5
A
THR
6
n
9
THR
6
A
ALA
7
n
10
ALA
7
A
PHE
8
n
11
PHE
8
A
SER
9
n
12
SER
9
A
SER
10
n
13
SER
10
A
GLU
11
n
14
GLU
11
A
GLN
12
n
15
GLN
12
A
LEU
13
n
16
LEU
13
A
ALA
14
n
17
ALA
14
A
ARG
15
n
18
ARG
15
A
LEU
16
n
19
LEU
16
A
LYS
17
n
20
LYS
17
A
ARG
18
n
21
ARG
18
A
GLU
19
n
22
GLU
19
A
PHE
20
n
23
PHE
20
A
ASN
21
n
24
ASN
21
A
GLU
22
n
25
GLU
22
A
ASN
23
n
26
ASN
23
A
ARG
24
n
27
ARG
24
A
TYR
25
n
28
TYR
25
A
LEU
26
n
29
LEU
26
A
THR
27
n
30
THR
27
A
GLU
28
n
31
GLU
28
A
ARG
29
n
32
ARG
29
A
ARG
30
n
33
ARG
30
A
ARG
31
n
34
ARG
31
A
GLN
32
n
35
GLN
32
A
GLN
33
n
36
GLN
33
A
LEU
34
n
37
LEU
34
A
SER
35
n
38
SER
35
A
SER
36
n
39
SER
36
A
GLU
37
n
40
GLU
37
A
LEU
38
n
41
LEU
38
A
GLY
39
n
42
GLY
39
A
LEU
40
n
43
LEU
40
A
ASN
41
n
44
ASN
41
A
GLU
42
n
45
GLU
42
A
ALA
43
n
46
ALA
43
A
GLN
44
n
47
GLN
44
A
VAL
45
n
48
VAL
45
A
LYS
46
n
49
LYS
46
A
GLY
47
n
50
GLY
47
A
TRP
48
n
51
TRP
48
A
PHE
49
n
52
PHE
49
A
LYS
50
n
53
LYS
50
A
ASN
51
n
54
ASN
51
A
MET
52
n
55
MET
52
A
ARG
53
n
56
ARG
53
A
ALA
54
n
57
ALA
54
A
LYS
55
n
58
LYS
55
A
ILE
56
n
59
ILE
56
A
LYS
57
n
60
LYS
57
A
LYS
58
n
61
LYS
58
A
SER
59
n
62
SER
59
A
THR
60
n
63
THR
60
A
n
1
-2
B
n
2
-1
B
n
3
0
B
n
4
1
B
LYS
2
n
5
LYS
2
B
ARG
3
n
6
ARG
3
B
PRO
4
n
7
PRO
4
B
ARG
5
n
8
ARG
5
B
THR
6
n
9
THR
6
B
ALA
7
n
10
ALA
7
B
PHE
8
n
11
PHE
8
B
SER
9
n
12
SER
9
B
SER
10
n
13
SER
10
B
GLU
11
n
14
GLU
11
B
GLN
12
n
15
GLN
12
B
LEU
13
n
16
LEU
13
B
ALA
14
n
17
ALA
14
B
ARG
15
n
18
ARG
15
B
LEU
16
n
19
LEU
16
B
LYS
17
n
20
LYS
17
B
ARG
18
n
21
ARG
18
B
GLU
19
n
22
GLU
19
B
PHE
20
n
23
PHE
20
B
ASN
21
n
24
ASN
21
B
GLU
22
n
25
GLU
22
B
ASN
23
n
26
ASN
23
B
ARG
24
n
27
ARG
24
B
TYR
25
n
28
TYR
25
B
LEU
26
n
29
LEU
26
B
THR
27
n
30
THR
27
B
GLU
28
n
31
GLU
28
B
ARG
29
n
32
ARG
29
B
ARG
30
n
33
ARG
30
B
ARG
31
n
34
ARG
31
B
GLN
32
n
35
GLN
32
B
GLN
33
n
36
GLN
33
B
LEU
34
n
37
LEU
34
B
SER
35
n
38
SER
35
B
SER
36
n
39
SER
36
B
GLU
37
n
40
GLU
37
B
LEU
38
n
41
LEU
38
B
GLY
39
n
42
GLY
39
B
LEU
40
n
43
LEU
40
B
ASN
41
n
44
ASN
41
B
GLU
42
n
45
GLU
42
B
ALA
43
n
46
ALA
43
B
GLN
44
n
47
GLN
44
B
VAL
45
n
48
VAL
45
B
LYS
46
n
49
LYS
46
B
GLY
47
n
50
GLY
47
B
TRP
48
n
51
TRP
48
B
PHE
49
n
52
PHE
49
B
LYS
50
n
53
LYS
50
B
ASN
51
n
54
ASN
51
B
MET
52
n
55
MET
52
B
ARG
53
n
56
ARG
53
B
ALA
54
n
57
ALA
54
B
LYS
55
n
58
LYS
55
B
ILE
56
n
59
ILE
56
B
LYS
57
n
60
LYS
57
B
LYS
58
n
61
LYS
58
B
SER
59
n
62
SER
59
B
n
63
60
B
2.6828
-.6772
-.2233
12.3002
1.7250
5.5397
.0198
.0077
-.0476
-.7935
-.0620
-.7270
-.0140
.2685
.0422
.0214
-.0269
.1143
-.1818
.0115
-.2091
refined
17.1870
29.3670
33.0710
X-RAY DIFFRACTION
3.2291
-.7342
-1.6442
9.7122
-.8750
3.0486
-.1014
-.0168
-.0182
.1202
.0717
.1865
.0554
-.0798
.0297
-.1070
-.0255
.0476
-.2200
-.0075
-.2351
refined
-4.0500
20.2410
62.3060
X-RAY DIFFRACTION
10.0942
1.7600
-.5841
.3092
-.0971
.0438
-.3632
-.1037
-.5070
-.0403
.2098
-.3674
-.0539
.2261
.1534
.0351
-.1352
-.0793
.3027
.0454
.1206
refined
25.0810
28.3670
48.0200
X-RAY DIFFRACTION
A
5
C
8
A
60
C
63
X-RAY DIFFRACTION
1
B
2
D
5
B
59
D
62
X-RAY DIFFRACTION
2
C
1
A
1
C
21
A
21
X-RAY DIFFRACTION
3
D
22
B
1
D
42
B
21
X-RAY DIFFRACTION
3
author_defined_assembly
4
tetrameric
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
A
CD
GLU
11
C
CD
GLU
14
1
Y
1
A
OE1
GLU
11
C
OE1
GLU
14
1
Y
1
A
OE2
GLU
11
C
OE2
GLU
14
1
Y
1
A
CD
GLU
22
C
CD
GLU
25
1
Y
1
A
OE1
GLU
22
C
OE1
GLU
25
1
Y
1
A
OE2
GLU
22
C
OE2
GLU
25
1
Y
1
A
CD
ARG
29
C
CD
ARG
32
1
Y
1
A
NE
ARG
29
C
NE
ARG
32
1
Y
1
A
CZ
ARG
29
C
CZ
ARG
32
1
Y
1
A
NH1
ARG
29
C
NH1
ARG
32
1
Y
1
A
NH2
ARG
29
C
NH2
ARG
32
1
Y
1
A
CD
LYS
57
C
CD
LYS
60
1
Y
1
A
CE
LYS
57
C
CE
LYS
60
1
Y
1
A
NZ
LYS
57
C
NZ
LYS
60
1
Y
1
A
CD
LYS
58
C
CD
LYS
61
1
Y
1
A
CE
LYS
58
C
CE
LYS
61
1
Y
1
A
NZ
LYS
58
C
NZ
LYS
61
1
Y
1
A
CB
THR
60
C
CB
THR
63
1
Y
1
A
OG1
THR
60
C
OG1
THR
63
1
Y
1
A
CG2
THR
60
C
CG2
THR
63
1
Y
1
B
OE1
GLU
11
D
OE1
GLU
14
1
Y
1
B
OE2
GLU
11
D
OE2
GLU
14
1
Y
1
B
CZ
ARG
29
D
CZ
ARG
32
1
Y
1
B
NH1
ARG
29
D
NH1
ARG
32
1
Y
1
B
NH2
ARG
29
D
NH2
ARG
32
1
Y
1
B
CG
LYS
57
D
CG
LYS
60
1
Y
1
B
CD
LYS
57
D
CD
LYS
60
1
Y
1
B
CE
LYS
57
D
CE
LYS
60
1
Y
1
B
NZ
LYS
57
D
NZ
LYS
60
1
Y
1
A
GLY
-2
C
GLY
1
1
Y
1
A
SER
-1
C
SER
2
1
Y
1
A
ASP
0
C
ASP
3
1
Y
1
A
GLU
1
C
GLU
4
1
Y
1
A
LYS
2
C
LYS
5
1
Y
1
A
ARG
3
C
ARG
6
1
Y
1
A
PRO
4
C
PRO
7
1
Y
1
B
GLY
-2
D
GLY
1
1
Y
1
B
SER
-1
D
SER
2
1
Y
1
B
ASP
0
D
ASP
3
1
Y
1
B
GLU
1
D
GLU
4
1
Y
1
B
THR
60
D
THR
63
1
Y
1
4.61
0.30
108.30
112.91
C
C
C
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
3.79
0.30
108.30
112.09
C
C
C
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
-6.55
1.00
110.10
103.55
C
C
C
C1'
O4'
C4'
DT
DT
DT
4
4
4
N
1
3.64
0.30
108.30
111.94
C
C
C
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
8.17
1.20
119.70
127.87
C
C
C
C3'
O3'
P
DC
DC
DC
6
6
7
Y
1
4.01
0.30
108.30
112.31
C
C
C
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-5.46
0.80
102.40
96.94
C
C
C
C3'
C2'
C1'
DT
DT
DT
11
11
11
N
1
3.96
0.30
108.30
112.26
C
C
C
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
1.84
0.30
108.30
110.14
C
C
C
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
4.75
0.30
108.30
113.05
C
C
C
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
-3.03
0.40
104.50
101.47
C
C
C
O4'
C4'
C3'
DC
DC
DC
17
17
17
N
1
2.75
0.30
108.30
111.05
C
C
C
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
1.82
0.30
108.30
110.12
C
C
C
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
4.95
0.30
108.30
113.25
C
C
C
O4'
C1'
N9
DA
DA
DA
21
21
21
N
1
4.39
0.30
108.30
112.69
D
D
D
O4'
C1'
N9
DA
DA
DA
22
22
22
N
1
2.28
0.30
108.30
110.58
D
D
D
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
4.18
0.30
108.30
112.48
D
D
D
O4'
C1'
N1
DC
DC
DC
24
24
24
N
1
4.33
0.30
108.30
112.63
D
D
D
O4'
C1'
N9
DG
DG
DG
26
26
26
N
1
5.08
0.30
108.30
113.38
D
D
D
O4'
C1'
N9
DG
DG
DG
27
27
27
N
1
2.62
0.30
108.30
110.92
D
D
D
O4'
C1'
N9
DG
DG
DG
29
29
29
N
1
2.11
0.30
108.30
110.41
D
D
D
O4'
C1'
N1
DT
DT
DT
31
31
31
N
1
4.57
0.30
108.30
112.87
D
D
D
O4'
C1'
N1
DC
DC
DC
34
34
34
N
1
3.50
0.30
108.30
111.80
D
D
D
O4'
C1'
N1
DT
DT
DT
36
36
36
N
1
-5.73
0.80
102.40
96.67
D
D
D
C3'
C2'
C1'
DC
DC
DC
39
39
39
N
1
3.66
0.30
108.30
111.96
D
D
D
O4'
C1'
N1
DC
DC
DC
39
39
39
N
38.424
-1.08
.00
-.01
.33
.00
.73
.935
.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25448
0.22206
0.22424
2.19
34.88
1183
15927
6.9
89.09
9.875
.134
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
.246
.205
.80
.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.19
34.88
80
1893
21
854
938
.010
.021
1926
1.660
2.518
2756
4.870
5.000
112
30.250
22.000
50
13.987
15.000
197
17.408
15.000
15
.078
.200
295
.005
.020
1163
.180
.200
601
.296
.200
1185
.167
.200
110
.205
.200
45
.149
.200
9
.632
1.500
585
1.032
2.000
895
1.512
3.000
1817
2.440
4.500
1861
0.4
0.276
2.247
57
832
20
62.92
2.190
50.000
2HOT
18302
0.04
1
13.800
3.000
95.200
0.293
2.19
2.27
1
2.40
76.30
0.288
2.27
2.36
1
2.70
85.80
0.251
2.36
2.47
1
2.80
93.30
0.211
2.47
2.60
1
3.00
98.80
0.143
2.60
2.76
1
3.10
100.00
0.094
2.76
2.97
1
3.10
100.00
0.052
2.97
3.27
1
3.10
99.90
0.032
3.27
3.74
1
3.10
99.80
0.023
3.74
4.72
1
3.10
99.60
0.022
4.72
50.00
1
3.00
98.40
data reduction
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
DENZO
package
data scaling
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
SCALEPACK
package
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
April. 3, 2006
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
2.000
data reduction
HKL-2000
data scaling
HKL-2000
Phage selected homeodomain bound to modified DNA
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
5
N
N
6
N
N
6
N
N
6
N
N
6
N
N
A
SER
9
C
SER
12
HELX_P
A
ASN
23
C
ASN
26
1
1
15
A
THR
27
C
THR
30
HELX_P
A
GLY
39
C
GLY
42
1
2
13
A
ASN
41
C
ASN
44
HELX_P
A
THR
60
C
THR
63
1
3
20
B
SER
9
D
SER
12
HELX_P
B
ASN
21
D
ASN
24
1
4
13
B
THR
27
D
THR
30
HELX_P
B
GLY
39
D
GLY
42
1
5
13
B
ASN
41
D
ASN
44
HELX_P
B
SER
59
D
SER
62
1
6
19
covale
1.451
none
C
DT
14
A
C5
DT
14
1_555
C
P2O
22
E
C7
P2O
1_555
hydrog
WATSON-CRICK
C
DT
2
A
N3
DT
2
1_555
D
DA
42
B
N1
DA
21
1_555
hydrog
WATSON-CRICK
C
DT
2
A
O4
DT
2
1_555
D
DA
42
B
N6
DA
21
1_555
hydrog
WATSON-CRICK
C
DT
3
A
N3
DT
3
1_555
D
DA
41
B
N1
DA
20
1_555
hydrog
WATSON-CRICK
C
DT
3
A
O4
DT
3
1_555
D
DA
41
B
N6
DA
20
1_555
hydrog
WATSON-CRICK
C
DT
4
A
N3
DT
4
1_555
D
DA
40
B
N1
DA
19
1_555
hydrog
WATSON-CRICK
C
DT
4
A
O4
DT
4
1_555
D
DA
40
B
N6
DA
19
1_555
hydrog
WATSON-CRICK
C
DG
5
A
N1
DG
5
1_555
D
DC
39
B
N3
DC
18
1_555
hydrog
WATSON-CRICK
C
DG
5
A
N2
DG
5
1_555
D
DC
39
B
O2
DC
18
1_555
hydrog
WATSON-CRICK
C
DG
5
A
O6
DG
5
1_555
D
DC
39
B
N4
DC
18
1_555
hydrog
WATSON-CRICK
C
DC
6
A
N3
DC
6
1_555
D
DG
38
B
N1
DG
17
1_555
hydrog
WATSON-CRICK
C
DC
6
A
N4
DC
6
1_555
D
DG
38
B
O6
DG
17
1_555
hydrog
WATSON-CRICK
C
DC
6
A
O2
DC
6
1_555
D
DG
38
B
N2
DG
17
1_555
hydrog
WATSON-CRICK
C
DC
7
A
N3
DC
7
1_555
D
DG
37
B
N1
DG
16
1_555
hydrog
WATSON-CRICK
C
DC
7
A
N4
DC
7
1_555
D
DG
37
B
O6
DG
16
1_555
hydrog
WATSON-CRICK
C
DC
7
A
O2
DC
7
1_555
D
DG
37
B
N2
DG
16
1_555
hydrog
WATSON-CRICK
C
DA
8
A
N1
DA
8
1_555
D
DT
36
B
N3
DT
15
1_555
hydrog
WATSON-CRICK
C
DA
8
A
N6
DA
8
1_555
D
DT
36
B
O4
DT
15
1_555
hydrog
WATSON-CRICK
C
DT
9
A
N3
DT
9
1_555
D
DA
35
B
N1
DA
14
1_555
hydrog
WATSON-CRICK
C
DT
9
A
O4
DT
9
1_555
D
DA
35
B
N6
DA
14
1_555
hydrog
WATSON-CRICK
C
DG
10
A
N1
DG
10
1_555
D
DC
34
B
N3
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
10
A
N2
DG
10
1_555
D
DC
34
B
O2
DC
13
1_555
hydrog
WATSON-CRICK
C
DG
10
A
O6
DG
10
1_555
D
DC
34
B
N4
DC
13
1_555
hydrog
WATSON-CRICK
C
DT
11
A
N3
DT
11
1_555
D
DA
33
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
C
DT
11
A
O4
DT
11
1_555
D
DA
33
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
C
DA
12
A
N1
DA
12
1_555
D
DT
32
B
N3
DT
11
1_555
hydrog
WATSON-CRICK
C
DA
12
A
N6
DA
12
1_555
D
DT
32
B
O4
DT
11
1_555
hydrog
WATSON-CRICK
C
DA
13
A
N1
DA
13
1_555
D
DT
31
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
C
DA
13
A
N6
DA
13
1_555
D
DT
31
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
C
DT
14
A
N3
DT
14
1_555
D
DA
30
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
C
DT
14
A
O4
DT
14
1_555
D
DA
30
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
C
DC
15
A
N3
DC
15
1_555
D
DG
29
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
C
DC
15
A
N4
DC
15
1_555
D
DG
29
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
C
DC
15
A
O2
DC
15
1_555
D
DG
29
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
C
DC
16
A
N3
DC
16
1_555
D
DG
28
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
C
DC
16
A
N4
DC
16
1_555
D
DG
28
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
C
DC
16
A
O2
DC
16
1_555
D
DG
28
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
C
DC
17
A
N3
DC
17
1_555
D
DG
27
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
17
A
N4
DC
17
1_555
D
DG
27
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
17
A
O2
DC
17
1_555
D
DG
27
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
18
A
N3
DC
18
1_555
D
DG
26
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
C
DC
18
A
N4
DC
18
1_555
D
DG
26
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
C
DC
18
A
O2
DC
18
1_555
D
DG
26
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
C
DG
19
A
N1
DG
19
1_555
D
DC
25
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
C
DG
19
A
N2
DG
19
1_555
D
DC
25
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
C
DG
19
A
O6
DG
19
1_555
D
DC
25
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
C
DG
20
A
N1
DG
20
1_555
D
DC
24
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
C
DG
20
A
N2
DG
20
1_555
D
DC
24
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
C
DG
20
A
O6
DG
20
1_555
D
DC
24
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
C
DA
21
A
N1
DA
21
1_555
D
DT
23
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
C
DA
21
A
N6
DA
21
1_555
D
DT
23
B
O4
DT
2
1_555
transcription/DNA
Homeodomain, Phage display, transcription-DNA COMPLEX
HMEN_DROME
UNP
3
453
P02836
2HOT
PDB
1
2HOT
2HOT
PDB
2
2HOT
453
513
2HOT
0
60
P02836
A
1
3
63
453
513
2HOT
0
60
P02836
B
1
3
63
1
21
2HOT
1
21
2HOT
C
2
1
21
22
42
2HOT
22
42
2HOT
D
3
1
21
1
cloning artifact
GLY
-2
2HOT
A
P02836
UNP
1
1
cloning artifact
SER
-1
2HOT
A
P02836
UNP
2
1
ILE
engineered mutation
VAL
45
2HOT
A
P02836
UNP
498
48
1
ILE
engineered mutation
GLY
47
2HOT
A
P02836
UNP
500
50
1
GLN
engineered mutation
LYS
50
2HOT
A
P02836
UNP
503
53
1
LYS
engineered mutation
MET
52
2HOT
A
P02836
UNP
505
55
2
cloning artifact
GLY
-2
2HOT
B
P02836
UNP
1
2
cloning artifact
SER
-1
2HOT
B
P02836
UNP
2
2
ILE
engineered mutation
VAL
45
2HOT
B
P02836
UNP
498
48
2
ILE
engineered mutation
GLY
47
2HOT
B
P02836
UNP
500
50
2
GLN
engineered mutation
LYS
50
2HOT
B
P02836
UNP
503
53
2
LYS
engineered mutation
MET
52
2HOT
B
P02836
UNP
505
55
BINDING SITE FOR RESIDUE P2O C 22
C
P2O
22
Software
6
BINDING SITE FOR RESIDUE GOL B 201
B
GOL
201
Software
4
BINDING SITE FOR RESIDUE GOL B 202
B
GOL
202
Software
7
A
ALA
43
C
ALA
46
6
1_555
A
LYS
46
C
LYS
49
6
1_555
A
GLY
47
C
GLY
50
6
1_555
A
LYS
50
C
LYS
53
6
1_555
C
DA
13
A
DA
13
6
1_555
C
DT
14
A
DT
14
6
1_555
B
PHE
20
D
PHE
23
4
4_547
B
ASN
21
D
ASN
24
4
4_547
B
ARG
24
D
ARG
27
4
4_547
B
ASN
41
D
ASN
44
4
1_555
B
SER
9
D
SER
12
7
1_555
B
GLU
11
D
GLU
14
7
1_555
B
GLN
12
D
GLN
15
7
1_555
B
TYR
25
D
TYR
28
7
4_547
B
HOH
219
K
HOH
7
1_555
C
DC
18
A
DC
18
7
4_547
C
HOH
23
H
HOH
7
4_547
5
C 1 2 1