0.017064
0.000000
0.000000
0.000000
0.007160
0.000000
0.000000
0.000000
0.007569
0.00000
0.00000
0.00000
Meinke, G.
Bohm, A.
Bullock, P.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
58.604
139.672
132.112
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
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
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
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
O
N
89
N
P
N
90
N
O
N
91
N
O
N
92
N
O
N
93
N
C
N
94
R
C
N
95
N
O
N
96
S
C
N
97
N
O
N
98
N
C
N
99
R
C
Y
100
N
N
Y
101
N
C
Y
102
N
N
Y
103
N
C
Y
104
N
C
N
105
N
N
Y
106
N
N
Y
107
N
C
Y
108
N
N
Y
109
N
C
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
O
N
125
N
P
N
126
N
O
N
127
N
O
N
128
N
O
N
129
N
C
N
130
R
C
N
131
N
O
N
132
S
C
N
133
N
O
N
134
N
C
N
135
R
C
N
136
N
N
N
137
N
C
N
138
N
O
N
139
N
N
N
140
N
C
N
141
N
N
N
142
N
C
N
143
N
C
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
O
N
159
N
P
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
C
N
164
R
C
N
165
N
O
N
166
S
C
N
167
N
O
N
168
N
C
N
169
R
C
Y
170
N
N
Y
171
N
C
Y
172
N
N
Y
173
N
C
N
174
N
C
N
175
N
O
N
176
N
N
N
177
N
C
N
178
N
N
N
179
N
N
Y
180
N
C
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
O
N
196
N
P
N
197
N
O
N
198
N
O
N
199
N
O
N
200
N
C
N
201
R
C
N
202
N
O
N
203
S
C
N
204
N
O
N
205
N
C
N
206
R
C
N
207
N
N
N
208
N
C
N
209
N
O
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
C
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
O
N
239
N
N
N
240
N
O
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
O
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
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
N
N
271
N
C
N
272
N
C
N
273
N
O
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
N
Y
287
N
C
Y
288
N
C
Y
289
N
N
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
O
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
S
C
N
309
N
C
N
310
N
C
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
N
331
N
C
N
332
N
C
N
333
N
C
N
334
N
O
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
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
C
N
356
N
N
N
357
N
O
N
358
N
H
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
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
S
N
380
N
C
N
381
N
O
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
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
Y
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
N
404
N
O
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
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
N
N
417
S
C
N
418
N
C
N
419
N
O
N
420
N
C
N
421
N
C
N
422
N
C
N
423
N
O
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
N
C
N
438
N
O
N
439
N
O
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
N
N
448
S
C
N
449
N
C
N
450
N
O
N
451
R
C
N
452
N
O
N
453
N
C
N
454
N
O
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
N
N
465
S
C
N
466
N
C
N
467
N
O
N
468
N
C
Y
469
N
C
Y
470
N
C
Y
471
N
C
Y
472
N
C
Y
473
N
C
Y
474
N
C
N
475
N
O
N
476
N
O
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
N
N
489
S
C
N
490
N
C
N
491
N
O
N
492
N
C
N
493
N
C
N
494
N
C
N
495
N
O
N
496
N
H
N
497
N
H
N
498
N
H
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
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
doub
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
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
Y
106
N
sing
Y
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
110
N
sing
Y
111
N
sing
Y
112
N
doub
N
113
N
sing
Y
114
N
doub
N
115
N
sing
N
116
N
sing
Y
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
doub
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
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
sing
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
doub
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
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
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
doub
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
doub
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
doub
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
doub
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
doub
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
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
Y
289
N
sing
Y
290
N
doub
Y
291
N
doub
N
292
N
sing
Y
293
N
sing
N
294
N
sing
Y
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
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
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
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
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
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
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
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
doub
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
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
doub
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
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
doub
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
Y
466
N
doub
Y
467
N
sing
Y
468
N
sing
N
469
N
sing
Y
470
N
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
sing
N
485
N
doub
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
US
J.Virol.
JOVIAM
0825
0022-538X
87
2923
2934
10.1128/JVI.02549-12
23269808
Analysis of the Costructure of the Simian Virus 40 T-Antigen Origin Binding Domain with Site I Reveals a Correlation between GAGGC Spacing and Spiral Assembly.
2013
10.2210/pdb4fgn/pdb
pdb_00004fgn
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
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.9792
1.0
X29A
NSLS
0.9792
SYNCHROTRON
NSLS BEAMLINE X29A
15240.476
Large T antigen
3.6.4.-
origin binding domain, UNP residues 131-260
2
man
polymer
6963.528
Site I DNA
1
syn
polymer
7158.603
Site I DNA
1
syn
polymer
18.015
water
3
nat
water
LT, LT-AG
no
no
GSKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAI
NNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPE
GSKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAI
NNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPE
A,B
polypeptide(L)
no
no
(DA)(DG)(DG)(DC)(DC)(DT)(DC)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DC)(DC)(DT)(DC)(DC)
(DT)(DC)(DA)
AGGCCTCCAAAAAAGCCTCCTCA
Z
polydeoxyribonucleotide
no
no
(DG)(DA)(DG)(DG)(DA)(DG)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DG)(DA)(DG)(DG)(DC)
(DC)(DT)(DT)
GAGGAGGCTTTTTTGGAGGCCTT
Y
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
SV40
sample
10633
Simian virus 40
469008
Escherichia coli
Bl21 (DE3)
1
3.03
59.41
VAPOR DIFFUSION, HANGING DROP
4.6
0.1M sodium acetate pH 4.6, .2M ammonium sulfate, 30 % Peg 4000, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
-3.003
1
20
Z
1
Y
22
-10.187
Z_DA1:DT22_Y
1
10.378
0.958
0.720
-0.003
20.953
1
19
Z
2
Y
21
-8.330
Z_DG2:DC21_Y
2
7.859
0.727
0.328
0.098
15.207
1
19
Z
3
Y
20
-3.070
Z_DG3:DC20_Y
3
-15.141
0.098
0.764
0.300
0.130
1
19
Z
4
Y
19
-4.802
Z_DC4:DG19_Y
4
-16.534
0.546
0.347
-0.362
-6.545
1
19
Z
5
Y
18
8.520
Z_DC5:DG18_Y
5
0.461
0.680
0.649
-0.298
13.875
1
20
Z
6
Y
17
-9.780
Z_DT6:DA17_Y
6
-0.918
-1.190
0.124
-0.208
8.852
1
19
Z
7
Y
16
-3.820
Z_DC7:DG16_Y
7
-3.808
0.193
-0.407
-0.248
14.391
1
19
Z
8
Y
15
-9.777
Z_DC8:DG15_Y
8
3.329
-0.343
-0.619
0.014
34.447
1
20
Z
9
Y
14
5.065
Z_DA9:DT14_Y
9
-5.531
0.580
0.631
-0.041
17.007
1
20
Z
10
Y
13
0.550
Z_DA10:DT13_Y
10
-2.776
-0.170
-0.395
0.149
11.548
1
20
Z
11
Y
12
3.894
Z_DA11:DT12_Y
11
1.649
-0.197
-0.295
0.194
9.465
1
20
Z
12
Y
11
1.052
Z_DA12:DT11_Y
12
-7.428
-0.051
-0.125
-0.066
11.523
1
20
Z
13
Y
10
4.487
Z_DA13:DT10_Y
13
-14.833
0.073
0.101
-0.032
7.223
1
20
Z
14
Y
9
-6.075
Z_DA14:DT9_Y
14
-3.732
0.244
-0.027
-0.006
-7.013
1
19
Z
15
Y
8
-4.802
Z_DG15:DC8_Y
15
-17.385
-0.667
0.202
-0.176
-5.912
1
19
Z
16
Y
7
-2.382
Z_DC16:DG7_Y
16
-3.874
0.141
0.195
-0.162
-13.740
1
19
Z
17
Y
6
8.338
Z_DC17:DG6_Y
17
14.522
0.473
0.894
0.022
17.433
1
20
Z
18
Y
5
-4.740
Z_DT18:DA5_Y
18
-4.519
-0.293
0.231
-0.050
10.670
1
19
Z
19
Y
4
4.933
Z_DC19:DG4_Y
19
-15.931
1.097
0.315
-0.361
9.206
1
Z
20
Y
3
7.551
Z_DC20:DG3_Y
20
-1.153
-0.024
-0.172
0.485
18.496
1
20
Z
21
Y
2
6.665
Z_DT21:DA2_Y
21
-10.680
0.222
-0.415
-0.061
12.025
Z
22
Y
1
74.235
Z_DC22:DG1_Y
22
10.804
-0.601
-0.413
-4.796
3.048
29.517
Z
Z
1
2
-3.655
Y
Y
22
21
2.952
-1.857
0.660
-0.783
ZZ_DA1DG2:DC21DT22_YY
1
3.272
-6.440
29.282
-1.173
-0.654
3.624
32.283
Z
Z
2
3
-9.821
Y
Y
21
20
3.590
-5.430
0.771
-0.965
ZZ_DG2DG3:DC20DC21_YY
2
-2.703
4.888
31.723
-0.663
-1.920
3.524
39.049
Z
Z
3
4
-2.038
Y
Y
20
19
3.494
-1.356
0.126
-1.735
ZZ_DG3DC4:DG19DC20_YY
3
6.597
-9.916
38.486
-2.420
0.671
3.170
35.654
Z
Z
4
5
8.950
Y
Y
19
18
3.229
5.452
1.495
-1.007
ZZ_DC4DC5:DG18DG19_YY
4
3.447
-5.659
35.084
-2.425
-1.949
1.905
24.008
Z
Z
5
6
17.893
Y
Y
18
17
2.863
7.226
-1.763
-0.724
ZZ_DC5DT6:DA17DG18_YY
5
6.795
-16.827
21.890
-3.523
5.915
3.280
38.493
Z
Z
6
7
3.442
Y
Y
17
16
3.301
2.265
0.126
-0.258
ZZ_DT6DC7:DG16DA17_YY
6
3.370
-5.120
38.286
-0.675
0.230
3.245
33.837
Z
Z
7
8
7.653
Y
Y
16
15
3.166
4.441
0.565
0.680
ZZ_DC7DC8:DG15DG16_YY
7
1.314
-2.264
33.527
0.463
-0.761
2.976
45.317
Z
Z
8
9
10.863
Y
Y
15
14
2.905
8.232
-0.233
0.892
ZZ_DC8DA9:DT14DG15_YY
8
-12.254
16.170
42.965
0.480
-0.706
3.731
20.987
Z
Z
9
10
0.684
Y
Y
14
13
3.796
0.248
-0.072
-0.764
ZZ_DA9DA10:DT13DT14_YY
9
3.247
-8.949
20.736
-2.218
1.789
3.354
39.502
Z
Z
10
11
-6.480
Y
Y
13
12
3.389
-4.366
-0.069
0.096
ZZ_DA10DA11:DT12DT13_YY
10
-3.463
5.139
39.123
0.675
-0.320
3.289
39.779
Z
Z
11
12
-0.272
Y
Y
12
11
3.275
-0.185
-0.396
-0.244
ZZ_DA11DA12:DT11DT12_YY
11
-1.630
2.396
39.747
-0.337
0.392
3.229
36.549
Z
Z
12
13
-12.421
Y
Y
11
10
3.238
-7.735
0.255
-0.297
ZZ_DA12DA13:DT10DT11_YY
12
-0.143
0.229
35.748
0.594
-0.426
3.221
36.829
Z
Z
13
14
-0.344
Y
Y
10
9
3.219
-0.217
-0.060
-0.651
ZZ_DA13DA14:DT9DT10_YY
13
0.516
-0.816
36.825
-1.001
0.164
3.768
33.972
Z
Z
14
15
-7.413
Y
Y
9
8
3.688
-4.315
0.017
-0.983
ZZ_DA14DG15:DC8DT9_YY
14
-2.756
4.734
33.595
-0.890
-0.534
2.872
37.215
Z
Z
15
16
7.712
Y
Y
8
7
3.055
4.908
-0.562
-1.226
ZZ_DG15DC16:DG7DC8_YY
15
0.164
-0.257
36.901
-2.515
0.900
3.511
40.735
Z
Z
16
17
-3.094
Y
Y
7
6
3.605
-2.150
1.174
-0.480
ZZ_DC16DC17:DG6DG7_YY
16
-3.648
5.249
40.524
-0.431
-2.126
2.010
24.588
Z
Z
17
18
-27.447
Y
Y
6
5
2.622
-10.918
-1.077
-0.757
ZZ_DC17DT18:DA5DG6_YY
17
9.943
-24.996
19.715
0.873
4.943
3.626
43.735
Z
Z
18
19
-5.288
Y
Y
5
4
3.503
-3.926
1.469
0.043
ZZ_DT18DC19:DG4DA5_YY
18
5.042
-6.791
43.288
0.469
-1.444
2.780
34.148
Z
Z
19
20
22.023
Y
Y
4
3
2.976
12.576
0.023
0.128
ZZ_DC19DC20:DG3DG4_YY
19
5.992
-10.492
31.255
-1.618
0.835
2.911
31.618
Z
Z
20
21
14.023
Y
Y
3
2
2.981
7.564
-0.535
0.242
ZZ_DC20DT21:DA2DG3_YY
20
2.233
-4.141
30.643
-0.838
1.360
0.433
-178.882
Z
Z
21
22
-4.524
Y
Y
2
1
1.128
9.037
-1.989
-3.848
ZZ_DT21DC22:DG1DA2_YY
21
-176.563
-88.382
-139.154
1.917
-1.135
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Database references
Data collection
Database references
Refinement description
1
0
2013-01-23
1
1
2013-02-27
1
2
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
apo-large T-antigen origin binding domain
large T-antigen origin binding domain in complex with subset of Site II DNA (P1, P3)
large T-antigen origin binding domain in complex with Site II DNA (P1-P4)
RCSB
Y
RCSB
2012-06-04
REL
REL
HOH
water
This DNA sequence is termed Site 1 in SV40
10633
Simian virus 40
sample
This DNA sequence is from sv40 site I
10633
Simian virus 40
sample
2NTC
PDB
experimental model
HOH
1
4
HOH
HOH
301
A
HOH
2
4
HOH
HOH
302
A
HOH
3
4
HOH
HOH
301
B
n
1
129
A
n
2
130
A
n
3
131
A
n
4
132
A
GLU
133
n
5
GLU
133
A
ASP
134
n
6
ASP
134
A
PRO
135
n
7
PRO
135
A
LYS
136
n
8
LYS
136
A
ASP
137
n
9
ASP
137
A
PHE
138
n
10
PHE
138
A
PRO
139
n
11
PRO
139
A
SER
140
n
12
SER
140
A
GLU
141
n
13
GLU
141
A
LEU
142
n
14
LEU
142
A
LEU
143
n
15
LEU
143
A
SER
144
n
16
SER
144
A
PHE
145
n
17
PHE
145
A
LEU
146
n
18
LEU
146
A
SER
147
n
19
SER
147
A
HIS
148
n
20
HIS
148
A
ALA
149
n
21
ALA
149
A
VAL
150
n
22
VAL
150
A
PHE
151
n
23
PHE
151
A
SER
152
n
24
SER
152
A
ASN
153
n
25
ASN
153
A
ARG
154
n
26
ARG
154
A
THR
155
n
27
THR
155
A
LEU
156
n
28
LEU
156
A
ALA
157
n
29
ALA
157
A
CYS
158
n
30
CYS
158
A
PHE
159
n
31
PHE
159
A
ALA
160
n
32
ALA
160
A
ILE
161
n
33
ILE
161
A
TYR
162
n
34
TYR
162
A
THR
163
n
35
THR
163
A
THR
164
n
36
THR
164
A
LYS
165
n
37
LYS
165
A
GLU
166
n
38
GLU
166
A
LYS
167
n
39
LYS
167
A
ALA
168
n
40
ALA
168
A
ALA
169
n
41
ALA
169
A
LEU
170
n
42
LEU
170
A
LEU
171
n
43
LEU
171
A
TYR
172
n
44
TYR
172
A
LYS
173
n
45
LYS
173
A
LYS
174
n
46
LYS
174
A
ILE
175
n
47
ILE
175
A
MET
176
n
48
MET
176
A
GLU
177
n
49
GLU
177
A
LYS
178
n
50
LYS
178
A
TYR
179
n
51
TYR
179
A
SER
180
n
52
SER
180
A
VAL
181
n
53
VAL
181
A
THR
182
n
54
THR
182
A
PHE
183
n
55
PHE
183
A
ILE
184
n
56
ILE
184
A
SER
185
n
57
SER
185
A
ARG
186
n
58
ARG
186
A
HIS
187
n
59
HIS
187
A
ASN
188
n
60
ASN
188
A
SER
189
n
61
SER
189
A
TYR
190
n
62
TYR
190
A
ASN
191
n
63
ASN
191
A
HIS
192
n
64
HIS
192
A
ASN
193
n
65
ASN
193
A
ILE
194
n
66
ILE
194
A
LEU
195
n
67
LEU
195
A
PHE
196
n
68
PHE
196
A
PHE
197
n
69
PHE
197
A
LEU
198
n
70
LEU
198
A
THR
199
n
71
THR
199
A
PRO
200
n
72
PRO
200
A
HIS
201
n
73
HIS
201
A
ARG
202
n
74
ARG
202
A
HIS
203
n
75
HIS
203
A
ARG
204
n
76
ARG
204
A
VAL
205
n
77
VAL
205
A
SER
206
n
78
SER
206
A
ALA
207
n
79
ALA
207
A
ILE
208
n
80
ILE
208
A
ASN
209
n
81
ASN
209
A
ASN
210
n
82
ASN
210
A
TYR
211
n
83
TYR
211
A
ALA
212
n
84
ALA
212
A
GLN
213
n
85
GLN
213
A
LYS
214
n
86
LYS
214
A
LEU
215
n
87
LEU
215
A
CYS
216
n
88
CYS
216
A
THR
217
n
89
THR
217
A
PHE
218
n
90
PHE
218
A
SER
219
n
91
SER
219
A
PHE
220
n
92
PHE
220
A
LEU
221
n
93
LEU
221
A
ILE
222
n
94
ILE
222
A
CYS
223
n
95
CYS
223
A
LYS
224
n
96
LYS
224
A
GLY
225
n
97
GLY
225
A
VAL
226
n
98
VAL
226
A
ASN
227
n
99
ASN
227
A
LYS
228
n
100
LYS
228
A
GLU
229
n
101
GLU
229
A
TYR
230
n
102
TYR
230
A
LEU
231
n
103
LEU
231
A
MET
232
n
104
MET
232
A
TYR
233
n
105
TYR
233
A
SER
234
n
106
SER
234
A
ALA
235
n
107
ALA
235
A
LEU
236
n
108
LEU
236
A
THR
237
n
109
THR
237
A
ARG
238
n
110
ARG
238
A
ASP
239
n
111
ASP
239
A
PRO
240
n
112
PRO
240
A
PHE
241
n
113
PHE
241
A
SER
242
n
114
SER
242
A
VAL
243
n
115
VAL
243
A
ILE
244
n
116
ILE
244
A
GLU
245
n
117
GLU
245
A
GLU
246
n
118
GLU
246
A
SER
247
n
119
SER
247
A
LEU
248
n
120
LEU
248
A
PRO
249
n
121
PRO
249
A
GLY
250
n
122
GLY
250
A
GLY
251
n
123
GLY
251
A
LEU
252
n
124
LEU
252
A
LYS
253
n
125
LYS
253
A
GLU
254
n
126
GLU
254
A
HIS
255
n
127
HIS
255
A
ASP
256
n
128
ASP
256
A
PHE
257
n
129
PHE
257
A
ASN
258
n
130
ASN
258
A
n
131
259
A
n
132
260
A
n
1
129
B
n
2
130
B
n
3
131
B
n
4
132
B
n
5
133
B
ASP
134
n
6
ASP
134
B
PRO
135
n
7
PRO
135
B
LYS
136
n
8
LYS
136
B
ASP
137
n
9
ASP
137
B
PHE
138
n
10
PHE
138
B
PRO
139
n
11
PRO
139
B
SER
140
n
12
SER
140
B
GLU
141
n
13
GLU
141
B
LEU
142
n
14
LEU
142
B
LEU
143
n
15
LEU
143
B
SER
144
n
16
SER
144
B
PHE
145
n
17
PHE
145
B
LEU
146
n
18
LEU
146
B
SER
147
n
19
SER
147
B
HIS
148
n
20
HIS
148
B
ALA
149
n
21
ALA
149
B
VAL
150
n
22
VAL
150
B
PHE
151
n
23
PHE
151
B
SER
152
n
24
SER
152
B
ASN
153
n
25
ASN
153
B
ARG
154
n
26
ARG
154
B
THR
155
n
27
THR
155
B
LEU
156
n
28
LEU
156
B
ALA
157
n
29
ALA
157
B
CYS
158
n
30
CYS
158
B
PHE
159
n
31
PHE
159
B
ALA
160
n
32
ALA
160
B
ILE
161
n
33
ILE
161
B
TYR
162
n
34
TYR
162
B
THR
163
n
35
THR
163
B
THR
164
n
36
THR
164
B
LYS
165
n
37
LYS
165
B
GLU
166
n
38
GLU
166
B
LYS
167
n
39
LYS
167
B
ALA
168
n
40
ALA
168
B
ALA
169
n
41
ALA
169
B
LEU
170
n
42
LEU
170
B
LEU
171
n
43
LEU
171
B
TYR
172
n
44
TYR
172
B
LYS
173
n
45
LYS
173
B
LYS
174
n
46
LYS
174
B
ILE
175
n
47
ILE
175
B
MET
176
n
48
MET
176
B
GLU
177
n
49
GLU
177
B
LYS
178
n
50
LYS
178
B
TYR
179
n
51
TYR
179
B
SER
180
n
52
SER
180
B
VAL
181
n
53
VAL
181
B
THR
182
n
54
THR
182
B
PHE
183
n
55
PHE
183
B
ILE
184
n
56
ILE
184
B
SER
185
n
57
SER
185
B
ARG
186
n
58
ARG
186
B
HIS
187
n
59
HIS
187
B
ASN
188
n
60
ASN
188
B
SER
189
n
61
SER
189
B
TYR
190
n
62
TYR
190
B
ASN
191
n
63
ASN
191
B
HIS
192
n
64
HIS
192
B
ASN
193
n
65
ASN
193
B
ILE
194
n
66
ILE
194
B
LEU
195
n
67
LEU
195
B
PHE
196
n
68
PHE
196
B
PHE
197
n
69
PHE
197
B
LEU
198
n
70
LEU
198
B
THR
199
n
71
THR
199
B
PRO
200
n
72
PRO
200
B
HIS
201
n
73
HIS
201
B
ARG
202
n
74
ARG
202
B
HIS
203
n
75
HIS
203
B
ARG
204
n
76
ARG
204
B
VAL
205
n
77
VAL
205
B
SER
206
n
78
SER
206
B
ALA
207
n
79
ALA
207
B
ILE
208
n
80
ILE
208
B
ASN
209
n
81
ASN
209
B
ASN
210
n
82
ASN
210
B
TYR
211
n
83
TYR
211
B
ALA
212
n
84
ALA
212
B
GLN
213
n
85
GLN
213
B
LYS
214
n
86
LYS
214
B
LEU
215
n
87
LEU
215
B
CYS
216
n
88
CYS
216
B
THR
217
n
89
THR
217
B
PHE
218
n
90
PHE
218
B
SER
219
n
91
SER
219
B
PHE
220
n
92
PHE
220
B
LEU
221
n
93
LEU
221
B
ILE
222
n
94
ILE
222
B
CYS
223
n
95
CYS
223
B
LYS
224
n
96
LYS
224
B
GLY
225
n
97
GLY
225
B
VAL
226
n
98
VAL
226
B
ASN
227
n
99
ASN
227
B
LYS
228
n
100
LYS
228
B
GLU
229
n
101
GLU
229
B
TYR
230
n
102
TYR
230
B
LEU
231
n
103
LEU
231
B
MET
232
n
104
MET
232
B
TYR
233
n
105
TYR
233
B
SER
234
n
106
SER
234
B
ALA
235
n
107
ALA
235
B
LEU
236
n
108
LEU
236
B
THR
237
n
109
THR
237
B
ARG
238
n
110
ARG
238
B
ASP
239
n
111
ASP
239
B
PRO
240
n
112
PRO
240
B
PHE
241
n
113
PHE
241
B
SER
242
n
114
SER
242
B
VAL
243
n
115
VAL
243
B
ILE
244
n
116
ILE
244
B
GLU
245
n
117
GLU
245
B
GLU
246
n
118
GLU
246
B
SER
247
n
119
SER
247
B
LEU
248
n
120
LEU
248
B
PRO
249
n
121
PRO
249
B
GLY
250
n
122
GLY
250
B
GLY
251
n
123
GLY
251
B
LEU
252
n
124
LEU
252
B
LYS
253
n
125
LYS
253
B
GLU
254
n
126
GLU
254
B
HIS
255
n
127
HIS
255
B
ASP
256
n
128
ASP
256
B
PHE
257
n
129
PHE
257
B
n
130
258
B
n
131
259
B
n
132
260
B
DA
1
n
1
DA
1
Z
DG
2
n
2
DG
2
Z
DG
3
n
3
DG
3
Z
DC
4
n
4
DC
4
Z
DC
5
n
5
DC
5
Z
DT
6
n
6
DT
6
Z
DC
7
n
7
DC
7
Z
DC
8
n
8
DC
8
Z
DA
9
n
9
DA
9
Z
DA
10
n
10
DA
10
Z
DA
11
n
11
DA
11
Z
DA
12
n
12
DA
12
Z
DA
13
n
13
DA
13
Z
DA
14
n
14
DA
14
Z
DG
15
n
15
DG
15
Z
DC
16
n
16
DC
16
Z
DC
17
n
17
DC
17
Z
DT
18
n
18
DT
18
Z
DC
19
n
19
DC
19
Z
DC
20
n
20
DC
20
Z
DT
21
n
21
DT
21
Z
DC
22
n
22
DC
22
Z
DA
23
n
23
DA
23
Z
DG
1
n
1
DG
1
Y
DA
2
n
2
DA
2
Y
DG
3
n
3
DG
3
Y
DG
4
n
4
DG
4
Y
DA
5
n
5
DA
5
Y
DG
6
n
6
DG
6
Y
DG
7
n
7
DG
7
Y
DC
8
n
8
DC
8
Y
DT
9
n
9
DT
9
Y
DT
10
n
10
DT
10
Y
DT
11
n
11
DT
11
Y
DT
12
n
12
DT
12
Y
DT
13
n
13
DT
13
Y
DT
14
n
14
DT
14
Y
DG
15
n
15
DG
15
Y
DG
16
n
16
DG
16
Y
DA
17
n
17
DA
17
Y
DG
18
n
18
DG
18
Y
DG
19
n
19
DG
19
Y
DC
20
n
20
DC
20
Y
DC
21
n
21
DC
21
Y
DT
22
n
22
DT
22
Y
DT
23
n
23
DT
23
Y
4.3163
-2.8324
-1.0743
14.3332
2.3666
11.8625
0.0745
-0.2827
-0.9794
0.8123
-0.7172
0.6496
0.5555
-0.3503
0.6427
0.3479
-0.0302
0.2384
0.6030
-0.0679
0.8232
refined
1.5594
42.2545
-0.2878
X-RAY DIFFRACTION
10.8722
2.9635
1.3241
11.1175
0.2369
3.7342
0.9076
-0.6183
-0.5681
-0.2245
-0.7337
1.4421
1.6383
-1.9481
-0.1738
1.2112
-0.4074
-0.4374
1.5418
-0.1961
0.7115
refined
3.1383
5.6793
-17.5268
X-RAY DIFFRACTION
4.5856
-5.0544
-0.7161
8.9030
3.2412
3.2417
0.6374
0.3198
0.9739
-1.2909
-0.4605
-1.7934
-0.3216
0.3427
-0.1769
1.0534
0.2711
0.1618
0.6879
-0.0419
0.7649
refined
17.6876
27.3756
-20.0936
X-RAY DIFFRACTION
2.5926
-2.6339
1.4469
4.0713
0.4706
4.1954
0.9031
0.5819
0.0307
-1.4441
-0.7736
0.2976
-0.2765
0.1121
-0.1295
0.9832
0.2006
0.2339
0.6251
-0.0533
0.7814
refined
16.4447
29.9636
-20.6853
X-RAY DIFFRACTION
A
133
A
258
X-RAY DIFFRACTION
1
B
134
B
257
X-RAY DIFFRACTION
2
Z
1
Z
23
X-RAY DIFFRACTION
3
Y
1
Y
23
X-RAY DIFFRACTION
4
author_and_software_defined_assembly
PISA
4
tetrameric
4860
-34
19360
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
O
LYS
224
A
O
LYS
96
A
N
ALA
160
A
N
ALA
32
A
N
LEU
156
A
N
LEU
28
A
O
HIS
203
A
O
HIS
75
A
O
ILE
194
A
O
ILE
66
A
N
HIS
187
A
N
HIS
59
A
N
ARG
186
A
N
ARG
58
A
O
ILE
244
A
O
ILE
116
B
N
LEU
156
B
N
LEU
28
B
O
HIS
203
B
O
HIS
75
B
O
PHE
196
B
O
PHE
68
B
N
SER
185
B
N
SER
57
B
N
ASN
188
B
N
ASN
60
B
O
SER
242
B
O
SER
114
1
B
HOH
301
F
HOH
1
A
CG
LYS
136
A
CG
LYS
8
1
Y
1
A
CD
LYS
136
A
CD
LYS
8
1
Y
1
A
CE
LYS
136
A
CE
LYS
8
1
Y
1
A
NZ
LYS
136
A
NZ
LYS
8
1
Y
1
B
CG
LYS
136
B
CG
LYS
8
1
Y
1
B
CD
LYS
136
B
CD
LYS
8
1
Y
1
B
CE
LYS
136
B
CE
LYS
8
1
Y
1
B
NZ
LYS
136
B
NZ
LYS
8
1
Y
1
B
CG
LYS
167
B
CG
LYS
39
1
Y
1
B
CD
LYS
167
B
CD
LYS
39
1
Y
1
B
CE
LYS
167
B
CE
LYS
39
1
Y
1
B
NZ
LYS
167
B
NZ
LYS
39
1
Y
1
B
CG
LYS
214
B
CG
LYS
86
1
Y
1
B
CD
LYS
214
B
CD
LYS
86
1
Y
1
B
CE
LYS
214
B
CE
LYS
86
1
Y
1
B
NZ
LYS
214
B
NZ
LYS
86
1
Y
1
B
CG
LYS
228
B
CG
LYS
100
1
Y
1
B
CD
LYS
228
B
CD
LYS
100
1
Y
1
B
CE
LYS
228
B
CE
LYS
100
1
Y
1
B
NZ
LYS
228
B
NZ
LYS
100
1
Y
1
A
GLY
129
A
GLY
1
1
Y
1
A
SER
130
A
SER
2
1
Y
1
A
LYS
131
A
LYS
3
1
Y
1
A
VAL
132
A
VAL
4
1
Y
1
A
PRO
259
A
PRO
131
1
Y
1
A
GLU
260
A
GLU
132
1
Y
1
B
GLY
129
B
GLY
1
1
Y
1
B
SER
130
B
SER
2
1
Y
1
B
LYS
131
B
LYS
3
1
Y
1
B
VAL
132
B
VAL
4
1
Y
1
B
GLU
133
B
GLU
5
1
Y
1
B
ASN
258
B
ASN
130
1
Y
1
B
PRO
259
B
PRO
131
1
Y
1
B
GLU
260
B
GLU
132
1
Y
1
A
A
PHE
ASN
257
258
149.86
1
B
B
THR
PHE
217
218
148.93
1
7.83
1.20
119.70
127.53
Z
Z
Z
C3'
O3'
P
DA
DA
DA
9
9
10
Y
1
7.50
1.20
119.70
127.20
Z
Z
Z
C3'
O3'
P
DA
DA
DA
13
13
14
Y
1
9.73
1.20
119.70
129.43
Z
Z
Z
C3'
O3'
P
DA
DA
DG
14
14
15
Y
1
-8.38
1.20
119.70
111.32
Z
Z
Z
C3'
O3'
P
DC
DC
DC
16
16
17
Y
1
-8.10
1.20
119.70
111.60
Y
Y
Y
C3'
O3'
P
DA
DA
DG
2
2
3
Y
1
9.17
1.20
119.70
128.87
Y
Y
Y
C3'
O3'
P
DT
DT
DT
9
9
10
Y
1
A
A
CG
CD2
HIS
HIS
148
148
0.059
0.009
1.354
1.413
N
1
A
PRO
135
-37.48
130.90
1
A
SER
140
-1.63
-66.13
1
A
ALA
149
-52.32
105.22
1
A
PHE
151
-105.55
47.07
1
A
THR
163
-165.28
-167.31
1
A
SER
189
-160.08
98.49
1
A
LEU
215
-89.57
31.22
1
A
CYS
216
-168.08
98.03
1
A
PHE
218
-137.72
-36.56
1
A
LEU
221
-161.15
119.82
1
A
ILE
244
-126.42
-80.60
1
A
SER
247
-55.44
-86.80
1
B
SER
140
-24.99
-57.72
1
B
ARG
154
-38.27
120.48
1
B
LYS
173
-75.82
-78.88
1
B
ASN
191
46.66
18.05
1
B
HIS
192
-112.28
-154.54
1
B
SER
219
69.93
-117.26
1
B
LEU
221
-174.48
104.98
1
B
CYS
223
-169.79
119.10
1
B
MET
232
-65.00
-72.33
1
B
PRO
249
-34.16
127.40
1
B
LYS
253
-83.48
-128.46
1
B
GLU
254
-106.73
-67.40
1
B
HIS
255
-2.91
-56.43
137.11
-0.22000
0.00000
0.00000
-0.13000
0.00000
0.35000
0.971
0.952
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.267
0.188
0.191
3.20
47.99
444
9305
8841
4.800
99.8
73.091
0.517
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.504
0.80
0.80
1.20
2NTC
MAXIMUM LIKELIHOOD
MASK
3.20
47.99
3
2967
0
937
2027
0.011
0.017
3132
1.767
1.737
4434
8.224
5.000
248
35.384
23.061
98
20.750
15.000
345
26.134
15.000
10
0.102
0.200
448
0.008
0.021
2062
0.2660
0.3020
3.28
29
563
20
97.69
3.200
50.000
4FGN
9304
1.000
1
100.0
3.20
3.31
1
100.0
data collection
CBASS
phasing
PHASER
refinement
REFMAC
5.6.0117
data reduction
HKL-2000
data scaling
SCALEPACK
Crystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
A
GLU
141
A
GLU
13
HELX_P
A
LEU
146
A
LEU
18
5
1
6
A
THR
164
A
THR
36
HELX_P
A
TYR
179
A
TYR
51
1
2
16
A
ARG
204
A
ARG
76
HELX_P
A
LYS
214
A
LYS
86
1
3
11
A
LYS
228
A
LYS
100
HELX_P
A
ARG
238
A
ARG
110
1
4
11
A
GLY
250
A
GLY
122
HELX_P
A
GLU
254
A
GLU
126
5
5
5
B
PRO
139
B
PRO
11
HELX_P
B
LEU
146
B
LEU
18
5
6
8
B
ALA
168
B
ALA
40
HELX_P
B
SER
180
B
SER
52
1
7
13
B
ARG
204
B
ARG
76
HELX_P
B
CYS
216
B
CYS
88
1
8
13
B
LYS
228
B
LYS
100
HELX_P
B
ARG
238
B
ARG
110
1
9
11
hydrog
WATSON-CRICK
Z
DA
1
C
N1
DA
1
1_555
Y
DT
22
D
N3
DT
22
1_555
hydrog
WATSON-CRICK
Z
DA
1
C
N6
DA
1
1_555
Y
DT
22
D
O4
DT
22
1_555
hydrog
WATSON-CRICK
Z
DG
2
C
N1
DG
2
1_555
Y
DC
21
D
N3
DC
21
1_555
hydrog
WATSON-CRICK
Z
DG
2
C
N2
DG
2
1_555
Y
DC
21
D
O2
DC
21
1_555
hydrog
WATSON-CRICK
Z
DG
2
C
O6
DG
2
1_555
Y
DC
21
D
N4
DC
21
1_555
hydrog
WATSON-CRICK
Z
DG
3
C
N1
DG
3
1_555
Y
DC
20
D
N3
DC
20
1_555
hydrog
WATSON-CRICK
Z
DG
3
C
N2
DG
3
1_555
Y
DC
20
D
O2
DC
20
1_555
hydrog
WATSON-CRICK
Z
DG
3
C
O6
DG
3
1_555
Y
DC
20
D
N4
DC
20
1_555
hydrog
WATSON-CRICK
Z
DC
4
C
N3
DC
4
1_555
Y
DG
19
D
N1
DG
19
1_555
hydrog
WATSON-CRICK
Z
DC
4
C
N4
DC
4
1_555
Y
DG
19
D
O6
DG
19
1_555
hydrog
WATSON-CRICK
Z
DC
4
C
O2
DC
4
1_555
Y
DG
19
D
N2
DG
19
1_555
hydrog
WATSON-CRICK
Z
DC
5
C
N3
DC
5
1_555
Y
DG
18
D
N1
DG
18
1_555
hydrog
WATSON-CRICK
Z
DC
5
C
N4
DC
5
1_555
Y
DG
18
D
O6
DG
18
1_555
hydrog
WATSON-CRICK
Z
DC
5
C
O2
DC
5
1_555
Y
DG
18
D
N2
DG
18
1_555
hydrog
WATSON-CRICK
Z
DT
6
C
N3
DT
6
1_555
Y
DA
17
D
N1
DA
17
1_555
hydrog
WATSON-CRICK
Z
DT
6
C
O4
DT
6
1_555
Y
DA
17
D
N6
DA
17
1_555
hydrog
WATSON-CRICK
Z
DC
7
C
N3
DC
7
1_555
Y
DG
16
D
N1
DG
16
1_555
hydrog
WATSON-CRICK
Z
DC
7
C
N4
DC
7
1_555
Y
DG
16
D
O6
DG
16
1_555
hydrog
WATSON-CRICK
Z
DC
7
C
O2
DC
7
1_555
Y
DG
16
D
N2
DG
16
1_555
hydrog
WATSON-CRICK
Z
DC
8
C
N3
DC
8
1_555
Y
DG
15
D
N1
DG
15
1_555
hydrog
WATSON-CRICK
Z
DC
8
C
N4
DC
8
1_555
Y
DG
15
D
O6
DG
15
1_555
hydrog
WATSON-CRICK
Z
DC
8
C
O2
DC
8
1_555
Y
DG
15
D
N2
DG
15
1_555
hydrog
WATSON-CRICK
Z
DA
9
C
N1
DA
9
1_555
Y
DT
14
D
N3
DT
14
1_555
hydrog
WATSON-CRICK
Z
DA
9
C
N6
DA
9
1_555
Y
DT
14
D
O4
DT
14
1_555
hydrog
WATSON-CRICK
Z
DA
10
C
N1
DA
10
1_555
Y
DT
13
D
N3
DT
13
1_555
hydrog
WATSON-CRICK
Z
DA
10
C
N6
DA
10
1_555
Y
DT
13
D
O4
DT
13
1_555
hydrog
WATSON-CRICK
Z
DA
11
C
N1
DA
11
1_555
Y
DT
12
D
N3
DT
12
1_555
hydrog
WATSON-CRICK
Z
DA
11
C
N6
DA
11
1_555
Y
DT
12
D
O4
DT
12
1_555
hydrog
WATSON-CRICK
Z
DA
12
C
N1
DA
12
1_555
Y
DT
11
D
N3
DT
11
1_555
hydrog
WATSON-CRICK
Z
DA
12
C
N6
DA
12
1_555
Y
DT
11
D
O4
DT
11
1_555
hydrog
WATSON-CRICK
Z
DA
13
C
N1
DA
13
1_555
Y
DT
10
D
N3
DT
10
1_555
hydrog
WATSON-CRICK
Z
DA
13
C
N6
DA
13
1_555
Y
DT
10
D
O4
DT
10
1_555
hydrog
WATSON-CRICK
Z
DA
14
C
N1
DA
14
1_555
Y
DT
9
D
N3
DT
9
1_555
hydrog
WATSON-CRICK
Z
DA
14
C
N6
DA
14
1_555
Y
DT
9
D
O4
DT
9
1_555
hydrog
WATSON-CRICK
Z
DG
15
C
N1
DG
15
1_555
Y
DC
8
D
N3
DC
8
1_555
hydrog
WATSON-CRICK
Z
DG
15
C
N2
DG
15
1_555
Y
DC
8
D
O2
DC
8
1_555
hydrog
WATSON-CRICK
Z
DG
15
C
O6
DG
15
1_555
Y
DC
8
D
N4
DC
8
1_555
hydrog
WATSON-CRICK
Z
DC
16
C
N3
DC
16
1_555
Y
DG
7
D
N1
DG
7
1_555
hydrog
WATSON-CRICK
Z
DC
16
C
N4
DC
16
1_555
Y
DG
7
D
O6
DG
7
1_555
hydrog
WATSON-CRICK
Z
DC
16
C
O2
DC
16
1_555
Y
DG
7
D
N2
DG
7
1_555
hydrog
WATSON-CRICK
Z
DC
17
C
N3
DC
17
1_555
Y
DG
6
D
N1
DG
6
1_555
hydrog
WATSON-CRICK
Z
DC
17
C
N4
DC
17
1_555
Y
DG
6
D
O6
DG
6
1_555
hydrog
WATSON-CRICK
Z
DC
17
C
O2
DC
17
1_555
Y
DG
6
D
N2
DG
6
1_555
hydrog
WATSON-CRICK
Z
DT
18
C
N3
DT
18
1_555
Y
DA
5
D
N1
DA
5
1_555
hydrog
WATSON-CRICK
Z
DT
18
C
O4
DT
18
1_555
Y
DA
5
D
N6
DA
5
1_555
hydrog
WATSON-CRICK
Z
DC
19
C
N3
DC
19
1_555
Y
DG
4
D
N1
DG
4
1_555
hydrog
WATSON-CRICK
Z
DC
19
C
N4
DC
19
1_555
Y
DG
4
D
O6
DG
4
1_555
hydrog
WATSON-CRICK
Z
DC
19
C
O2
DC
19
1_555
Y
DG
4
D
N2
DG
4
1_555
hydrog
DC-DG PAIR
Z
DC
20
C
O2
DC
20
1_555
Y
DG
3
D
N2
DG
3
1_555
hydrog
WATSON-CRICK
Z
DT
21
C
N3
DT
21
1_555
Y
DA
2
D
N1
DA
2
1_555
hydrog
WATSON-CRICK
Z
DT
21
C
O4
DT
21
1_555
Y
DA
2
D
N6
DA
2
1_555
hydrog
DC-DG PAIR
Z
DC
22
C
N4
DC
22
1_555
Y
DG
1
D
O6
DG
1
1_555
DNA BINDING PROTEIN/DNA
origin binding domain, DNA BINDING PROTEIN-DNA complex
A
ASP
239
A
ASP
111
1
A
PRO
240
A
PRO
112
12.73
B
ASP
239
B
ASP
111
1
B
PRO
240
B
PRO
112
0.19
LT_SV40
UNP
1
131
P03070
KVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINN
YAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPE
4FGN
PDB
2
4FGN
AGGCCTCCAAAAAAGCCTCCTCA
4FGN
PDB
3
4FGN
GAGGAGGCTTTTTTGGAGGCCTT
131
260
4FGN
131
260
P03070
A
1
3
132
131
260
4FGN
131
260
P03070
B
1
3
132
1
23
4FGN
1
23
4FGN
Z
2
1
23
1
23
4FGN
1
23
4FGN
Y
3
1
23
1
expression tag
GLY
129
4FGN
A
P03070
UNP
1
1
expression tag
SER
130
4FGN
A
P03070
UNP
2
2
expression tag
GLY
129
4FGN
B
P03070
UNP
1
2
expression tag
SER
130
4FGN
B
P03070
UNP
2
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
221
A
LEU
93
A
GLY
225
A
GLY
97
A
LEU
156
A
LEU
28
A
THR
163
A
THR
35
A
ASN
193
A
ASN
65
A
HIS
203
A
HIS
75
A
PHE
183
A
PHE
55
A
ASN
188
A
ASN
60
A
VAL
243
A
VAL
115
A
GLU
246
A
GLU
118
B
LEU
156
B
LEU
28
B
THR
163
B
THR
35
B
ASN
193
B
ASN
65
B
HIS
203
B
HIS
75
B
PHE
183
B
PHE
55
B
ASN
188
B
ASN
60
B
SER
242
B
SER
114
B
GLU
246
B
GLU
118
20
C 2 2 21