0.024004
0.000000
0.000000
0.000000
0.022676
0.000000
0.000000
0.000000
0.016906
0.00000
0.00000
0.00000
Schubert, C.
Sakurai, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.660
44.100
59.150
C4 H7 N O2
101.104
n
1-AMINOCYCLOPROPANECARBOXYLIC ACID
peptide linking
C11 H11 Cl N2 O2
238.670
n
6-CHLORO-L-TRYPTOPHAN
L-peptide linking
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C4 H9 N O2
103.120
n
ALPHA-AMINOISOBUTYRIC ACID
L-peptide linking
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
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
C10 H14 N O5 P
259.196
n
2-AMINO-3-(4-PHOSPHONOMETHYL-PHENYL)-PROPIONIC ACID
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
C
N
2
N
C
N
3
N
C
N
4
N
C
N
5
N
O
N
6
N
O
N
7
N
N
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
H
N
15
N
N
N
16
S
C
N
17
N
C
Y
18
N
C
Y
19
N
C
Y
20
N
C
Y
21
N
C
Y
22
N
N
Y
23
N
C
Y
24
N
C
Y
25
N
C
N
26
N
CL
Y
27
N
C
N
28
N
C
N
29
N
O
N
30
N
O
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
H
N
42
N
C
N
43
N
O
N
44
N
C
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
N
N
50
N
C
N
51
N
C
N
52
N
O
N
53
N
O
N
54
N
C
N
55
N
C
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
O
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
C
N
85
N
N
N
86
N
C
N
87
N
N
N
88
N
N
N
89
N
O
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
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
N
N
106
S
C
N
107
N
C
N
108
N
O
N
109
N
C
N
110
N
C
N
111
N
O
N
112
N
N
N
113
N
O
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
N
N
123
S
C
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
O
N
129
N
O
N
130
N
O
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
N
N
139
R
C
N
140
N
C
N
141
N
O
N
142
N
C
N
143
N
S
N
144
N
O
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
N
N
153
S
C
N
154
N
C
N
155
N
O
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
O
N
160
N
N
N
161
N
O
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
N
N
173
S
C
N
174
N
C
N
175
N
O
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
O
N
180
N
O
N
181
N
O
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
N
N
192
N
C
N
193
N
C
N
194
N
O
N
195
N
O
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
Y
206
N
C
Y
207
N
N
Y
208
N
C
Y
209
N
C
Y
210
N
N
N
211
N
O
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
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
O
N
223
N
H
N
224
N
H
N
225
N
N
N
226
S
C
N
227
N
C
N
228
N
O
N
229
S
C
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
O
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
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
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
N
252
N
C
N
253
N
C
N
254
N
C
N
255
N
O
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
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
N
N
270
S
C
N
271
N
C
N
272
N
O
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
N
N
278
N
O
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
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
N
N
295
S
C
N
296
N
C
N
297
N
O
N
298
N
C
N
299
N
C
N
300
N
S
N
301
N
C
N
302
N
O
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
H
N
313
N
H
N
314
N
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
N
325
N
O
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
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
N
346
N
C
N
347
N
P
N
348
N
O
N
349
N
O
N
350
N
O
N
351
N
C
N
352
N
O
N
353
N
O
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
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
N
N
369
S
C
N
370
N
C
N
371
N
O
N
372
N
C
N
373
N
C
N
374
N
C
N
375
N
O
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
N
C
N
390
N
O
N
391
N
O
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
N
N
400
S
C
N
401
N
C
N
402
N
O
N
403
R
C
N
404
N
O
N
405
N
C
N
406
N
O
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
Y
421
N
C
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
N
427
N
O
N
428
N
O
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
N
445
N
C
N
446
N
C
N
447
N
O
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
H
N
456
N
H
N
457
N
H
N
458
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
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
doub
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
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
Y
24
N
sing
Y
25
N
doub
Y
26
N
doub
Y
27
N
sing
Y
28
N
sing
N
29
N
sing
Y
30
N
sing
Y
31
N
doub
Y
32
N
sing
N
33
N
sing
N
34
N
sing
Y
35
N
sing
N
36
N
sing
N
37
N
sing
Y
38
N
doub
N
39
N
sing
N
40
N
doub
N
41
N
sing
N
42
N
sing
N
43
N
doub
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
doub
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
doub
N
71
N
sing
N
72
N
sing
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
doub
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
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
doub
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
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
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
doub
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
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
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
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
doub
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
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
doub
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
doub
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
Y
203
N
sing
Y
204
N
doub
Y
205
N
doub
N
206
N
sing
Y
207
N
sing
N
208
N
sing
Y
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
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
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
doub
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
doub
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
sing
N
287
N
doub
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
doub
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
Y
311
N
doub
Y
312
N
sing
Y
313
N
sing
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
317
N
doub
N
318
N
sing
Y
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
Y
332
N
sing
Y
333
N
doub
Y
334
N
doub
N
335
N
sing
Y
336
N
sing
N
337
N
sing
Y
338
N
sing
N
339
N
sing
Y
340
N
doub
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
doub
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
doub
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
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
doub
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
doub
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
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
doub
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
Y
411
N
doub
Y
412
N
sing
Y
413
N
sing
N
414
N
sing
Y
415
N
doub
N
416
N
sing
Y
417
N
doub
N
418
N
sing
Y
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
doub
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
sing
N
441
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
128
11000
11001
10.1021/ja063102j
16925398
Crystallographic Analysis of an 8-mer p53 Peptide Analogue Complexed with MDM2.
2006
10.2210/pdb2gv2/pdb
pdb_00002gv2
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
Insertion Device, undulator
CCD
2002-06-01
ADSC QUANTUM 210
Si(111) double-crystal
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
17-ID
APS
1.0
SYNCHROTRON
APS BEAMLINE 17-ID
12592.401
E3 ubiquitin-protein ligase Mdm2
p53 binding domain (Residues: 17-125)
1
man
polymer
1194.723
8-MER P53 PEPTIDE ANALOGUE
1
syn
polymer
18.015
water
93
nat
water
no
no
GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKE
HRKIYTMIYRNLVVVNQQESSDSGTSVSEN
GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKE
HRKIYTMIYRNLVVVNQQESSDSGTSVSEN
A
polypeptide(L)
no
yes
(ACE)FM(AIB)(PM3)(6CW)E(1AC)L
XFMAFWEXL
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
1
110
MDM2
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.01
38.74
VAPOR DIFFUSION, HANGING DROP
9.5
2 M (NH4)2SO4, 100 mM Bicine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
entity
entity_name_com
entity_src_gen
pdbx_entity_src_syn
pdbx_initial_refinement_model
struct_conn
struct_ref
struct_ref_seq
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
Source and taxonomy
Structure summary
Data collection
1
0
2006-09-05
1
1
2008-05-01
1
2
2011-07-13
1
3
2023-08-30
1
4
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_entity.pdbx_ec
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
_entity_src_gen.pdbx_seq_type
_pdbx_entity_src_syn.pdbx_beg_seq_num
_pdbx_entity_src_syn.pdbx_end_seq_num
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
mdm2 in complex with a wild-type p53 peptide
mdm2 in complex with an optimized p53 peptide
mdm2 in complex with a small molecule inhibitor
mdm2 in complex with a small molecule inhibitor
RCSB
Y
RCSB
2006-05-02
REL
REL
HOH
water
Synthetic peptide
sample
1
9
1T4F
PDB
experimental model
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
132
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
HOH
135
3
HOH
HOH
135
A
HOH
136
3
HOH
HOH
136
A
HOH
137
3
HOH
HOH
137
A
HOH
138
3
HOH
HOH
138
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
141
3
HOH
HOH
141
A
HOH
142
3
HOH
HOH
142
A
HOH
143
3
HOH
HOH
143
A
HOH
144
3
HOH
HOH
144
A
HOH
145
3
HOH
HOH
145
A
HOH
146
3
HOH
HOH
146
A
HOH
147
3
HOH
HOH
147
A
HOH
148
3
HOH
HOH
148
A
HOH
149
3
HOH
HOH
149
A
HOH
150
3
HOH
HOH
150
A
HOH
151
3
HOH
HOH
151
A
HOH
152
3
HOH
HOH
152
A
HOH
153
3
HOH
HOH
153
A
HOH
154
3
HOH
HOH
154
A
HOH
155
3
HOH
HOH
155
A
HOH
156
3
HOH
HOH
156
A
HOH
157
3
HOH
HOH
157
A
HOH
158
3
HOH
HOH
158
A
HOH
159
3
HOH
HOH
159
A
HOH
160
3
HOH
HOH
160
A
HOH
161
3
HOH
HOH
161
A
HOH
162
3
HOH
HOH
162
A
HOH
163
3
HOH
HOH
163
A
HOH
164
3
HOH
HOH
164
A
HOH
165
3
HOH
HOH
165
A
HOH
166
3
HOH
HOH
166
A
HOH
167
3
HOH
HOH
167
A
HOH
168
3
HOH
HOH
168
A
HOH
169
3
HOH
HOH
169
A
HOH
170
3
HOH
HOH
170
A
HOH
171
3
HOH
HOH
171
A
HOH
172
3
HOH
HOH
172
A
HOH
173
3
HOH
HOH
173
A
HOH
174
3
HOH
HOH
174
A
HOH
175
3
HOH
HOH
175
A
HOH
176
3
HOH
HOH
176
A
HOH
177
3
HOH
HOH
177
A
HOH
178
3
HOH
HOH
178
A
HOH
179
3
HOH
HOH
179
A
HOH
180
3
HOH
HOH
180
A
HOH
181
3
HOH
HOH
181
A
HOH
182
3
HOH
HOH
182
A
HOH
183
3
HOH
HOH
183
A
HOH
184
3
HOH
HOH
184
A
HOH
185
3
HOH
HOH
185
A
HOH
186
3
HOH
HOH
186
A
HOH
187
3
HOH
HOH
187
A
HOH
188
3
HOH
HOH
188
A
HOH
189
3
HOH
HOH
189
A
HOH
190
3
HOH
HOH
190
A
HOH
191
3
HOH
HOH
191
A
HOH
192
3
HOH
HOH
192
A
HOH
193
3
HOH
HOH
193
A
HOH
194
3
HOH
HOH
194
A
HOH
195
3
HOH
HOH
195
A
HOH
10
3
HOH
HOH
10
B
HOH
11
3
HOH
HOH
11
B
HOH
12
3
HOH
HOH
12
B
HOH
13
3
HOH
HOH
13
B
HOH
14
3
HOH
HOH
14
B
HOH
15
3
HOH
HOH
15
B
HOH
16
3
HOH
HOH
16
B
HOH
17
3
HOH
HOH
17
B
HOH
18
3
HOH
HOH
18
B
HOH
19
3
HOH
HOH
19
B
HOH
20
3
HOH
HOH
20
B
HOH
21
3
HOH
HOH
21
B
HOH
22
3
HOH
HOH
22
B
HOH
23
3
HOH
HOH
23
B
HOH
24
3
HOH
HOH
24
B
HOH
25
3
HOH
HOH
25
B
HOH
26
3
HOH
HOH
26
B
HOH
27
3
HOH
HOH
27
B
HOH
28
3
HOH
HOH
28
B
HOH
29
3
HOH
HOH
29
B
HOH
30
3
HOH
HOH
30
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
n
1
16
A
n
2
17
A
n
3
18
A
n
4
19
A
n
5
20
A
n
6
21
A
n
7
22
A
n
8
23
A
n
9
24
A
GLU
25
n
10
GLU
25
A
THR
26
n
11
THR
26
A
LEU
27
n
12
LEU
27
A
VAL
28
n
13
VAL
28
A
ARG
29
n
14
ARG
29
A
PRO
30
n
15
PRO
30
A
LYS
31
n
16
LYS
31
A
PRO
32
n
17
PRO
32
A
LEU
33
n
18
LEU
33
A
LEU
34
n
19
LEU
34
A
LEU
35
n
20
LEU
35
A
LYS
36
n
21
LYS
36
A
LEU
37
n
22
LEU
37
A
LEU
38
n
23
LEU
38
A
LYS
39
n
24
LYS
39
A
SER
40
n
25
SER
40
A
VAL
41
n
26
VAL
41
A
GLY
42
n
27
GLY
42
A
ALA
43
n
28
ALA
43
A
GLN
44
n
29
GLN
44
A
LYS
45
n
30
LYS
45
A
ASP
46
n
31
ASP
46
A
THR
47
n
32
THR
47
A
TYR
48
n
33
TYR
48
A
THR
49
n
34
THR
49
A
MET
50
n
35
MET
50
A
LYS
51
n
36
LYS
51
A
GLU
52
n
37
GLU
52
A
VAL
53
n
38
VAL
53
A
LEU
54
n
39
LEU
54
A
PHE
55
n
40
PHE
55
A
TYR
56
n
41
TYR
56
A
LEU
57
n
42
LEU
57
A
GLY
58
n
43
GLY
58
A
GLN
59
n
44
GLN
59
A
TYR
60
n
45
TYR
60
A
ILE
61
n
46
ILE
61
A
MET
62
n
47
MET
62
A
THR
63
n
48
THR
63
A
LYS
64
n
49
LYS
64
A
ARG
65
n
50
ARG
65
A
LEU
66
n
51
LEU
66
A
TYR
67
n
52
TYR
67
A
ASP
68
n
53
ASP
68
A
GLU
69
n
54
GLU
69
A
LYS
70
n
55
LYS
70
A
GLN
71
n
56
GLN
71
A
GLN
72
n
57
GLN
72
A
HIS
73
n
58
HIS
73
A
ILE
74
n
59
ILE
74
A
VAL
75
n
60
VAL
75
A
TYR
76
n
61
TYR
76
A
CYS
77
n
62
CYS
77
A
SER
78
n
63
SER
78
A
ASN
79
n
64
ASN
79
A
ASP
80
n
65
ASP
80
A
LEU
81
n
66
LEU
81
A
LEU
82
n
67
LEU
82
A
GLY
83
n
68
GLY
83
A
ASP
84
n
69
ASP
84
A
LEU
85
n
70
LEU
85
A
PHE
86
n
71
PHE
86
A
GLY
87
n
72
GLY
87
A
VAL
88
n
73
VAL
88
A
PRO
89
n
74
PRO
89
A
SER
90
n
75
SER
90
A
PHE
91
n
76
PHE
91
A
SER
92
n
77
SER
92
A
VAL
93
n
78
VAL
93
A
LYS
94
n
79
LYS
94
A
GLU
95
n
80
GLU
95
A
HIS
96
n
81
HIS
96
A
ARG
97
n
82
ARG
97
A
LYS
98
n
83
LYS
98
A
ILE
99
n
84
ILE
99
A
TYR
100
n
85
TYR
100
A
THR
101
n
86
THR
101
A
MET
102
n
87
MET
102
A
ILE
103
n
88
ILE
103
A
TYR
104
n
89
TYR
104
A
ARG
105
n
90
ARG
105
A
ASN
106
n
91
ASN
106
A
LEU
107
n
92
LEU
107
A
VAL
108
n
93
VAL
108
A
VAL
109
n
94
VAL
109
A
VAL
110
n
95
VAL
110
A
ASN
111
n
96
ASN
111
A
GLN
112
n
97
GLN
112
A
n
98
113
A
n
99
114
A
n
100
115
A
n
101
116
A
n
102
117
A
n
103
118
A
n
104
119
A
n
105
120
A
n
106
121
A
n
107
122
A
n
108
123
A
n
109
124
A
n
110
125
A
ACE
1
n
1
ACE
1
B
PHE
2
n
2
PHE
2
B
MET
3
n
3
MET
3
B
AIB
4
n
4
AIB
4
B
PM3
5
n
5
PM3
5
B
6CW
6
n
6
6CW
6
B
GLU
7
n
7
GLU
7
B
1AC
8
n
8
1AC
8
B
LEU
9
n
9
LEU
9
B
author_and_software_defined_assembly
PISA
2
dimeric
1560
-15
5830
B
AIB
4
ALPHA-AMINOISOBUTYRIC ACID
B
AIB
4
ALA
B
PM3
5
B
PM3
5
PHE
B
6CW
6
6-CHLORO-L-TRYPTOPHAN
B
6CW
6
TRP
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
TYR
48
A
O
TYR
33
A
N
VAL
28
A
N
VAL
13
A
N
ARG
29
A
N
ARG
14
A
O
VAL
108
A
O
VAL
93
A
N
VAL
75
A
N
VAL
60
A
O
PHE
91
A
O
PHE
76
1
A
GLY
16
A
GLY
1
1
Y
1
A
SER
17
A
SER
2
1
Y
1
A
GLN
18
A
GLN
3
1
Y
1
A
ILE
19
A
ILE
4
1
Y
1
A
PRO
20
A
PRO
5
1
Y
1
A
ALA
21
A
ALA
6
1
Y
1
A
SER
22
A
SER
7
1
Y
1
A
GLU
23
A
GLU
8
1
Y
1
A
GLN
24
A
GLN
9
1
Y
1
A
GLN
113
A
GLN
98
1
Y
1
A
GLU
114
A
GLU
99
1
Y
1
A
SER
115
A
SER
100
1
Y
1
A
SER
116
A
SER
101
1
Y
1
A
ASP
117
A
ASP
102
1
Y
1
A
SER
118
A
SER
103
1
Y
1
A
GLY
119
A
GLY
104
1
Y
1
A
THR
120
A
THR
105
1
Y
1
A
SER
121
A
SER
106
1
Y
1
A
VAL
122
A
VAL
107
1
Y
1
A
SER
123
A
SER
108
1
Y
1
A
GLU
124
A
GLU
109
1
Y
1
A
ASN
125
A
ASN
110
1
Y
1
A
GLN
72
-65.16
2.42
1
A
GLN
72
-61.95
2.42
protein_rep_new.param
protein_new.top
water_rep.par
water.top
ion.param
ion.top
19.9
-0.75
0.00
0.00
0.45
0.00
0.30
0.219
0.007
0.192
0.195
0.195
1.80
22.0
976
9370
10.4
88.8
RANDOM
925645.73
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
1T4F
Engh & Huber
FLAT MODEL
54.9142
0.434722
0.23
0.19
5.00
0.18
0.15
1.80
22.0
93
923
3
0
827
0.006
1.6
21.0
0.72
0.301
0.028
0.256
1.91
118
1094
6
9.7
70.9
14.8
1.8
22.0
2GV2
9416
9416
0.0
-3.0
0.065
1
14.8
4.4
88.7
1.8
1.86
2.2
685
0.362
2.2
67.8
refinement
CNX
2005
data collection
ADSC
data scaling
HKL-2000
phasing
CNX
2002
MDM2 in complex with an 8-mer p53 peptide analogue
1
N
N
2
N
N
3
N
N
3
N
N
A
LYS
31
A
LYS
16
HELX_P
A
VAL
41
A
VAL
26
1
1
11
A
MET
50
A
MET
35
HELX_P
A
ARG
65
A
ARG
50
1
2
16
A
ASP
80
A
ASP
65
HELX_P
A
GLY
87
A
GLY
72
1
3
8
A
GLU
95
A
GLU
80
HELX_P
A
ARG
105
A
ARG
90
1
4
11
B
PHE
2
B
PHE
2
HELX_P
B
GLU
7
B
GLU
7
1
5
6
covale
1.332
both
B
ACE
1
B
C
ACE
1
1_555
B
PHE
2
B
N
PHE
2
1_555
covale
1.330
both
B
MET
3
B
C
MET
3
1_555
B
AIB
4
B
N
AIB
4
1_555
covale
1.329
both
B
AIB
4
B
C
AIB
4
1_555
B
PM3
5
B
N
PM3
5
1_555
covale
1.327
both
B
PM3
5
B
C
PM3
5
1_555
B
6CW
6
B
N
6CW
6
1_555
covale
1.327
both
B
6CW
6
B
C
6CW
6
1_555
B
GLU
7
B
N
GLU
7
1_555
LIGASE
Optimized protein-protein interaction. Synthetic peptide. Alpha helix binding protein, Ligase
MDM2_HUMAN
UNP
1
17
Q00987
SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEH
RKIYTMIYRNLVVVNQQESSDSGTSVSEN
2GV2
PDB
2
1
2GV2
17
125
2GV2
17
125
Q00987
A
1
2
110
1
9
2GV2
1
9
2GV2
B
2
1
9
1
expression tag
GLY
16
2GV2
A
Q00987
UNP
1
3
2
anti-parallel
anti-parallel
anti-parallel
A
TYR
48
A
TYR
33
A
THR
49
A
THR
34
A
LEU
27
A
LEU
12
A
PRO
30
A
PRO
15
A
LEU
107
A
LEU
92
A
VAL
109
A
VAL
94
A
ILE
74
A
ILE
59
A
TYR
76
A
TYR
61
A
SER
90
A
SER
75
A
SER
92
A
SER
77
BINDING SITE FOR RESIDUE ACE B 1
B
ACE
1
Software
4
A
GLN
72
A
GLN
57
4
1_555
B
PM3
5
B
PM3
5
4
1_555
B
HOH
13
D
HOH
4
1_555
B
HOH
23
D
HOH
4
1_555
19
P 21 21 21