0.032006
0.000000
0.000000
0.000000
0.019161
0.000000
0.000000
0.000000
0.017212
0.00000
0.00000
0.00000
Frese, S.
Schubert, W.-D.
Findeis, A.C.
Marquardt, T.
Roske, Y.S.
Stradal, T.E.B.
Heinz, D.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
31.244
52.188
58.100
C2 H4 O
44.053
ACETYL GROUP
non-polymer
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
C3 H8 O
60.095
ISOPROPYL ALCOHOL
2-PROPANOL
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C6 H14 O2
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C9 H12 N O6 P
261.168
n
O-PHOSPHOTYROSINE
PHOSPHONOTYROSINE
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
C
N
2
N
O
N
3
N
C
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
N
N
22
S
C
N
23
N
C
N
24
N
O
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
N
N
29
N
C
N
30
N
N
N
31
N
N
N
32
N
O
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
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
N
N
49
S
C
N
50
N
C
N
51
N
O
N
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
O
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
C
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
N
N
82
R
C
N
83
N
C
N
84
N
O
N
85
N
C
N
86
N
S
N
87
N
O
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
N
N
104
N
O
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
N
N
116
S
C
N
117
N
C
N
118
N
O
N
119
N
C
N
120
N
C
N
121
N
C
N
122
N
O
N
123
N
O
N
124
N
O
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
N
N
135
N
C
N
136
N
C
N
137
N
O
N
138
N
O
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
N
C
Y
149
N
C
Y
150
N
N
Y
151
N
C
Y
152
N
C
Y
153
N
N
N
154
N
O
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
O
N
166
N
H
N
167
N
H
N
168
N
N
N
169
S
C
N
170
N
C
N
171
N
O
N
172
S
C
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
O
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
O
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
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
N
N
225
S
C
N
226
N
C
N
227
N
O
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
N
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
H
N
248
N
H
N
249
N
N
N
250
S
C
N
251
N
C
N
252
N
O
N
253
N
C
N
254
N
C
N
255
N
S
N
256
N
C
N
257
N
O
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
C
N
270
N
C
N
271
N
O
N
272
N
C
N
273
N
C
N
274
S
C
N
275
N
O
N
276
N
C
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
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
N
319
N
C
N
320
N
C
N
321
N
O
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
O
N
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
N
343
N
O
N
344
N
P
N
345
N
O
N
346
N
O
N
347
N
O
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
N
365
N
O
N
366
N
O
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
H
N
374
N
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
R
C
N
379
N
O
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
N
N
392
S
C
N
393
N
C
N
394
N
O
N
395
N
C
Y
396
N
C
Y
397
N
C
Y
398
N
C
Y
399
N
N
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
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
H
N
417
N
H
N
418
N
N
N
419
S
C
N
420
N
C
N
421
N
O
N
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
C
Y
428
N
C
N
429
N
O
N
430
N
O
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
H
N
441
N
H
N
442
N
N
N
443
S
C
N
444
N
C
N
445
N
O
N
446
N
C
N
447
N
C
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
H
N
460
N
H
N
1
N
doub
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
sing
N
12
N
sing
N
13
N
doub
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
N
24
N
sing
N
25
N
doub
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
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
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
doub
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
doub
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
doub
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
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
doub
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
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
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
doub
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
doub
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
Y
146
N
sing
Y
147
N
doub
Y
148
N
doub
N
149
N
sing
Y
150
N
sing
N
151
N
sing
Y
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
doub
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
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
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
doub
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
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
doub
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
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
Y
286
N
doub
Y
287
N
sing
Y
288
N
sing
N
289
N
sing
Y
290
N
doub
N
291
N
sing
Y
292
N
doub
N
293
N
sing
Y
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
doub
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
Y
327
N
doub
Y
328
N
sing
Y
329
N
sing
N
330
N
sing
Y
331
N
doub
N
332
N
sing
Y
333
N
doub
N
334
N
sing
Y
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
doub
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
doub
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
Y
384
N
doub
Y
385
N
sing
Y
386
N
sing
N
387
N
sing
Y
388
N
doub
Y
389
N
sing
Y
390
N
sing
N
391
N
sing
Y
392
N
sing
Y
393
N
doub
N
394
N
sing
Y
395
N
doub
N
396
N
sing
Y
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
sing
N
407
N
doub
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
Y
412
N
doub
Y
413
N
sing
Y
414
N
sing
N
415
N
sing
Y
416
N
doub
N
417
N
sing
Y
418
N
doub
N
419
N
sing
Y
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
doub
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
N
442
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
281
18236
10.1074/JBC.M512917200
16636066
The Phosphotyrosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains.
2006
10.2210/pdb2cia/pdb
pdb_00002cia
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
2 AU COATED X-RAY MIRRORS
CCD
2004-05-17
MARRESEARCH
ROEMO TYPE DOUBLE CRYSTAL MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.050
1.0
BW6
MPG/DESY, HAMBURG
1.050
SYNCHROTRON
MPG/DESY, HAMBURG BEAMLINE BW6
11679.088
CYTOPLASMIC PROTEIN NCK2
SH2-DOMAIN, RESIDUES 284-380
1
man
polymer
THE PEPTIDE WAS SYNTHESIZED CHEMICALLY
1236.201
TRANSLOCATED INTIMIN RECEPTOR
PHOSPHOPEPTIDE LIGAND OF NCK-SH2, RESIDUES 471-480
1
syn
polymer
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
1
syn
non-polymer
60.095
ISOPROPYL ALCOHOL
1
syn
non-polymer
18.015
water
103
nat
water
NCK ADAPTOR PROTEIN 2, SH2/SH3 ADAPTOR PROTEIN NCK-BETA, NCK-2
no
no
GPLGSEWYYGNVTRHQAECALNERGVEGDFLIRDSESSPSDFSVSLKASGKNKHFKVQLVDNVYCIGQRRFHTMDELVEH
YKKAPIFTSEHGEKLYLVRALQ
GPLGSEWYYGNVTRHQAECALNERGVEGDFLIRDSESSPSDFSVSLKASGKNKHFKVQLVDNVYCIGQRRFHTMDELVEH
YKKAPIFTSEHGEKLYLVRALQ
A
polypeptide(L)
no
yes
(ACE)HI(PTR)DEVAADP
XHIYDEVAADP
L
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
HUMAN
sample
9606
HOMO SAPIENS
511693
ESCHERICHIA COLI
BL21
PGEX-6P-1 (AMERSHAM BIOSCIENCES)
1
1.98
37.4
VAPOR DIFFUSION, HANGING DROP
7.00
METHOD: HANGING-DROP, VAPOUR-DIFFUSION PROTEIN CONCENTRATION: 8 MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 50% MPD, 15% ETHANOL, 0.01 M NA2 ACETATE, pH 7.00
exptl_crystal_grow
pdbx_database_proc
pdbx_database_status
struct_biol
struct_conn
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
repository
Initial release
Advisory
Version format compliance
Data collection
Derived calculations
Experimental preparation
Other
Data collection
Database references
Other
Refinement description
1
0
2006-04-24
1
1
2011-07-13
1
2
2019-05-29
1
3
2024-05-01
_exptl_crystal_grow.method
_pdbx_database_status.recvd_author_approval
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
SOLUTION STRUCTURE OF THE SH3 DOMAIN OF THE HUMANCYTOPLASMIC PROTEIN NCK2
STRUCTURAL INSIGHT INTO THE BINDING DIVERSITY BETWEEN THETYR-PHOSPHORYLATED HUMAN EPHRINBS AND NCK2 SH2 DOMAIN
NCK1 SH2-DOMAIN IN COMPLEX WITH A DODECAPHOSPHOPEPTIDE FROM EPEC PROTEIN TIR
HELIX
DETERMINATION METHOD: AUTHOR PROVIDED.
SHEET
DETERMINATION METHOD: AUTHOR PROVIDED.
PDBE
Y
PDBE
2006-03-17
REL
REL
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
IPA
ISOPROPYL ALCOHOL
HOH
water
562
ESCHERICHIA COLI
sample
N-TERMINALLY, RESIDUES GPLGS REMAIN ATTACHED TO NCK2-SH2
FOLLOWING CLEAVAGE OF THE GST-NCK2-SH2 FUSION PROTEIN
NCK1-TIR
other
MPD
1381
3
MPD
MPD
1381
A
IPA
1382
4
IPA
IPA
1382
A
HOH
2001
5
HOH
HOH
2001
A
HOH
2002
5
HOH
HOH
2002
A
HOH
2003
5
HOH
HOH
2003
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2006
5
HOH
HOH
2006
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2008
5
HOH
HOH
2008
A
HOH
2009
5
HOH
HOH
2009
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2011
5
HOH
HOH
2011
A
HOH
2012
5
HOH
HOH
2012
A
HOH
2013
5
HOH
HOH
2013
A
HOH
2014
5
HOH
HOH
2014
A
HOH
2015
5
HOH
HOH
2015
A
HOH
2016
5
HOH
HOH
2016
A
HOH
2017
5
HOH
HOH
2017
A
HOH
2018
5
HOH
HOH
2018
A
HOH
2019
5
HOH
HOH
2019
A
HOH
2020
5
HOH
HOH
2020
A
HOH
2021
5
HOH
HOH
2021
A
HOH
2022
5
HOH
HOH
2022
A
HOH
2023
5
HOH
HOH
2023
A
HOH
2024
5
HOH
HOH
2024
A
HOH
2025
5
HOH
HOH
2025
A
HOH
2026
5
HOH
HOH
2026
A
HOH
2027
5
HOH
HOH
2027
A
HOH
2028
5
HOH
HOH
2028
A
HOH
2029
5
HOH
HOH
2029
A
HOH
2030
5
HOH
HOH
2030
A
HOH
2031
5
HOH
HOH
2031
A
HOH
2032
5
HOH
HOH
2032
A
HOH
2033
5
HOH
HOH
2033
A
HOH
2034
5
HOH
HOH
2034
A
HOH
2035
5
HOH
HOH
2035
A
HOH
2036
5
HOH
HOH
2036
A
HOH
2037
5
HOH
HOH
2037
A
HOH
2038
5
HOH
HOH
2038
A
HOH
2039
5
HOH
HOH
2039
A
HOH
2040
5
HOH
HOH
2040
A
HOH
2041
5
HOH
HOH
2041
A
HOH
2042
5
HOH
HOH
2042
A
HOH
2043
5
HOH
HOH
2043
A
HOH
2044
5
HOH
HOH
2044
A
HOH
2045
5
HOH
HOH
2045
A
HOH
2046
5
HOH
HOH
2046
A
HOH
2047
5
HOH
HOH
2047
A
HOH
2048
5
HOH
HOH
2048
A
HOH
2049
5
HOH
HOH
2049
A
HOH
2050
5
HOH
HOH
2050
A
HOH
2051
5
HOH
HOH
2051
A
HOH
2052
5
HOH
HOH
2052
A
HOH
2053
5
HOH
HOH
2053
A
HOH
2054
5
HOH
HOH
2054
A
HOH
2055
5
HOH
HOH
2055
A
HOH
2056
5
HOH
HOH
2056
A
HOH
2057
5
HOH
HOH
2057
A
HOH
2058
5
HOH
HOH
2058
A
HOH
2059
5
HOH
HOH
2059
A
HOH
2060
5
HOH
HOH
2060
A
HOH
2061
5
HOH
HOH
2061
A
HOH
2062
5
HOH
HOH
2062
A
HOH
2063
5
HOH
HOH
2063
A
HOH
2064
5
HOH
HOH
2064
A
HOH
2065
5
HOH
HOH
2065
A
HOH
2066
5
HOH
HOH
2066
A
HOH
2067
5
HOH
HOH
2067
A
HOH
2068
5
HOH
HOH
2068
A
HOH
2069
5
HOH
HOH
2069
A
HOH
2070
5
HOH
HOH
2070
A
HOH
2071
5
HOH
HOH
2071
A
HOH
2072
5
HOH
HOH
2072
A
HOH
2073
5
HOH
HOH
2073
A
HOH
2074
5
HOH
HOH
2074
A
HOH
2075
5
HOH
HOH
2075
A
HOH
2076
5
HOH
HOH
2076
A
HOH
2077
5
HOH
HOH
2077
A
HOH
2078
5
HOH
HOH
2078
A
HOH
2079
5
HOH
HOH
2079
A
HOH
2080
5
HOH
HOH
2080
A
HOH
2081
5
HOH
HOH
2081
A
HOH
2082
5
HOH
HOH
2082
A
HOH
2083
5
HOH
HOH
2083
A
HOH
2084
5
HOH
HOH
2084
A
HOH
2085
5
HOH
HOH
2085
A
HOH
2086
5
HOH
HOH
2086
A
HOH
2087
5
HOH
HOH
2087
A
HOH
2088
5
HOH
HOH
2088
A
HOH
2089
5
HOH
HOH
2089
A
HOH
2090
5
HOH
HOH
2090
A
HOH
2091
5
HOH
HOH
2091
A
HOH
2092
5
HOH
HOH
2092
A
HOH
2001
5
HOH
HOH
2001
L
HOH
2002
5
HOH
HOH
2002
L
HOH
2003
5
HOH
HOH
2003
L
HOH
2004
5
HOH
HOH
2004
L
HOH
2005
5
HOH
HOH
2005
L
HOH
2006
5
HOH
HOH
2006
L
HOH
2007
5
HOH
HOH
2007
L
HOH
2008
5
HOH
HOH
2008
L
HOH
2009
5
HOH
HOH
2009
L
HOH
2010
5
HOH
HOH
2010
L
HOH
2011
5
HOH
HOH
2011
L
n
1
279
A
n
2
280
A
n
3
281
A
n
4
282
A
SER
283
n
5
SER
283
A
GLU
284
n
6
GLU
284
A
TRP
285
n
7
TRP
285
A
TYR
286
n
8
TYR
286
A
TYR
287
n
9
TYR
287
A
GLY
288
n
10
GLY
288
A
ASN
289
n
11
ASN
289
A
VAL
290
n
12
VAL
290
A
THR
291
n
13
THR
291
A
ARG
292
n
14
ARG
292
A
HIS
293
n
15
HIS
293
A
GLN
294
n
16
GLN
294
A
ALA
295
n
17
ALA
295
A
GLU
296
n
18
GLU
296
A
CYS
297
n
19
CYS
297
A
ALA
298
n
20
ALA
298
A
LEU
299
n
21
LEU
299
A
ASN
300
n
22
ASN
300
A
GLU
301
n
23
GLU
301
A
ARG
302
n
24
ARG
302
A
GLY
303
n
25
GLY
303
A
VAL
304
n
26
VAL
304
A
GLU
305
n
27
GLU
305
A
GLY
306
n
28
GLY
306
A
ASP
307
n
29
ASP
307
A
PHE
308
n
30
PHE
308
A
LEU
309
n
31
LEU
309
A
ILE
310
n
32
ILE
310
A
ARG
311
n
33
ARG
311
A
ASP
312
n
34
ASP
312
A
SER
313
n
35
SER
313
A
GLU
314
n
36
GLU
314
A
SER
315
n
37
SER
315
A
SER
316
n
38
SER
316
A
PRO
317
n
39
PRO
317
A
SER
318
n
40
SER
318
A
ASP
319
n
41
ASP
319
A
PHE
320
n
42
PHE
320
A
SER
321
n
43
SER
321
A
VAL
322
n
44
VAL
322
A
SER
323
n
45
SER
323
A
LEU
324
n
46
LEU
324
A
LYS
325
n
47
LYS
325
A
ALA
326
n
48
ALA
326
A
SER
327
n
49
SER
327
A
GLY
328
n
50
GLY
328
A
LYS
329
n
51
LYS
329
A
ASN
330
n
52
ASN
330
A
LYS
331
n
53
LYS
331
A
HIS
332
n
54
HIS
332
A
PHE
333
n
55
PHE
333
A
LYS
334
n
56
LYS
334
A
VAL
335
n
57
VAL
335
A
GLN
336
n
58
GLN
336
A
LEU
337
n
59
LEU
337
A
VAL
338
n
60
VAL
338
A
ASP
339
n
61
ASP
339
A
ASN
340
n
62
ASN
340
A
VAL
341
n
63
VAL
341
A
TYR
342
n
64
TYR
342
A
CYS
343
n
65
CYS
343
A
ILE
344
n
66
ILE
344
A
GLY
345
n
67
GLY
345
A
GLN
346
n
68
GLN
346
A
ARG
347
n
69
ARG
347
A
ARG
348
n
70
ARG
348
A
PHE
349
n
71
PHE
349
A
HIS
350
n
72
HIS
350
A
THR
351
n
73
THR
351
A
MET
352
n
74
MET
352
A
ASP
353
n
75
ASP
353
A
GLU
354
n
76
GLU
354
A
LEU
355
n
77
LEU
355
A
VAL
356
n
78
VAL
356
A
GLU
357
n
79
GLU
357
A
HIS
358
n
80
HIS
358
A
TYR
359
n
81
TYR
359
A
LYS
360
n
82
LYS
360
A
LYS
361
n
83
LYS
361
A
ALA
362
n
84
ALA
362
A
PRO
363
n
85
PRO
363
A
ILE
364
n
86
ILE
364
A
PHE
365
n
87
PHE
365
A
THR
366
n
88
THR
366
A
SER
367
n
89
SER
367
A
GLU
368
n
90
GLU
368
A
HIS
369
n
91
HIS
369
A
GLY
370
n
92
GLY
370
A
GLU
371
n
93
GLU
371
A
LYS
372
n
94
LYS
372
A
LEU
373
n
95
LEU
373
A
TYR
374
n
96
TYR
374
A
LEU
375
n
97
LEU
375
A
VAL
376
n
98
VAL
376
A
ARG
377
n
99
ARG
377
A
ALA
378
n
100
ALA
378
A
LEU
379
n
101
LEU
379
A
GLN
380
n
102
GLN
380
A
ACE
471
n
1
ACE
471
L
HIS
472
n
2
HIS
472
L
ILE
473
n
3
ILE
473
L
PTR
474
n
4
PTR
474
L
ASP
475
n
5
ASP
475
L
GLU
476
n
6
GLU
476
L
VAL
477
n
7
VAL
477
L
ALA
478
n
8
ALA
478
L
ALA
479
n
9
ALA
479
L
ASP
480
n
10
ASP
480
L
n
11
481
L
2.0780
-0.1175
-0.6339
0.9174
0.5820
1.6084
-0.0418
-0.0260
-0.0126
0.0554
0.0112
0.0263
0.0554
-0.0166
0.0306
-0.0530
0.0041
-0.0023
-0.0555
0.0133
-0.0259
refined
9.8110
51.2000
18.6590
X-RAY DIFFRACTION
3.8051
2.5145
-0.5274
10.1891
2.6432
7.0317
0.0061
-0.3238
-0.3674
0.8870
0.0590
-0.8624
0.4510
0.4425
-0.0651
-0.0478
0.0694
-0.0449
-0.0246
0.0715
0.0103
refined
15.7020
47.5640
26.2060
X-RAY DIFFRACTION
A
283
A
380
X-RAY DIFFRACTION
1
L
471
L
479
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PQS
2
dimeric
L
PTR
474
O-PHOSPHOTYROSINE
B
PTR
4
TYR
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
PHE
349
A
N
PHE
71
A
O
TYR
342
A
O
TYR
64
A
N
CYS
343
A
N
CYS
65
A
O
GLN
336
A
O
GLN
58
A
N
VAL
335
A
N
VAL
57
A
O
PHE
320
A
O
PHE
42
A
N
SER
323
A
N
SER
45
A
O
LEU
309
A
O
LEU
31
A
N
PHE
308
A
N
PHE
30
A
O
ARG
377
A
O
ARG
99
A
O
PHE
365
A
O
PHE
87
A
N
LEU
373
A
N
LEU
95
1
A
OG
SER
283
A
OG
SER
5
1
Y
1
L
CA
ASP
480
B
CA
ASP
10
1
Y
1
L
C
ASP
480
B
C
ASP
10
1
Y
1
L
O
ASP
480
B
O
ASP
10
1
Y
1
L
CB
ASP
480
B
CB
ASP
10
1
Y
1
L
CG
ASP
480
B
CG
ASP
10
1
Y
1
L
OD1
ASP
480
B
OD1
ASP
10
1
Y
1
L
OD2
ASP
480
B
OD2
ASP
10
1
Y
1
A
CM
MPD
1381
C
CM
MPD
1
1
N
1
A
O4
MPD
1381
C
O4
MPD
1
1
N
1
A
GLY
279
A
GLY
1
1
Y
1
A
PRO
280
A
PRO
2
1
Y
1
A
LEU
281
A
LEU
3
1
Y
1
A
GLY
282
A
GLY
4
1
Y
1
L
PRO
481
B
PRO
11
1
Y
1
12.90
1.10
114.20
127.10
A
A
A
CA
CB
SG
CYS
CYS
CYS
297
297
297
B
N
1
A
A
CB
SG
CYS
CYS
297
297
-0.102
0.016
1.812
1.710
B
N
1
A
ASN
289
-91.13
38.72
14.30
0.03000
0.00000
0.00000
-0.01000
0.00000
-0.02000
0.972
0.966
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.170
0.149
0.150
1.45
20.03
879
16142
5.200
98.5
2.162
0.041
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.068
0.066
0.80
0.80
1.40
NCK1-TIR
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.45
20.03
103
984
10
0
871
0.020
0.021
1031
0.004
0.020
706
1.742
1.965
1410
1.907
3.000
1734
4.725
5.000
135
35.841
24.182
55
12.601
15.000
189
19.188
15.000
7
0.113
0.200
148
0.007
0.020
1184
0.003
0.020
218
0.217
0.200
157
0.214
0.200
732
0.195
0.200
484
0.130
0.200
581
0.201
0.200
75
0.197
0.200
15
0.314
0.200
51
0.170
0.200
19
2.285
2.000
625
0.582
2.000
239
3.118
3.000
989
2.785
2.000
465
3.958
3.000
413
0.2270
0.1760
1.49
67
1069
20
95.62
1.450
30.000
2CIA
16143
0.000
0.04000
1
25.1000
3.300
98.4
0.31000
1.45
1.48
3.700
1
2.90
97.0
refinement
REFMAC
5.2.0019
data reduction
DENZO
data scaling
SCALEPACK
phasing
EPMR
human nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
A
THR
291
A
THR
13
HELX_P
A
ASN
300
A
ASN
22
1
1
10
A
THR
351
A
THR
73
HELX_P
A
ALA
362
A
ALA
84
1
2
12
covale
1.364
both
L
ACE
471
B
C
ACE
1
1_555
L
HIS
472
B
N
HIS
2
1_555
covale
1.344
both
L
ILE
473
B
C
ILE
3
1_555
L
PTR
474
B
N
PTR
4
1_555
covale
1.331
both
L
PTR
474
B
C
PTR
4
1_555
L
ASP
475
B
N
ASP
5
1_555
SH2-DOMAIN
SH2-DOMAIN, SH3 DOMAIN, PHOSPHORYLATION, BINDING SPECIFICITY
2CIA
PDB
1
2CIA
NCK2_HUMAN
UNP
1
O43639
2CIA
PDB
2
2CIA
O50190_ECOLI
UNP
2
O50190
279
283
2CIA
279
283
2CIA
A
1
1
5
284
380
2CIA
284
380
O43639
A
2
6
102
471
471
2CIA
471
471
2CIA
L
3
1
1
471
480
2CIA
472
481
O50190
L
4
2
11
6
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
ARG
347
A
ARG
69
A
PHE
349
A
PHE
71
A
VAL
341
A
VAL
63
A
ILE
344
A
ILE
66
A
LYS
329
A
LYS
51
A
VAL
335
A
VAL
57
A
ASP
319
A
ASP
41
A
ALA
326
A
ALA
48
A
ASP
307
A
ASP
29
A
SER
313
A
SER
35
A
ALA
378
A
ALA
100
A
ALA
378
A
ALA
100
A
PHE
365
A
PHE
87
A
SER
367
A
SER
89
A
GLU
371
A
GLU
93
A
LEU
373
A
LEU
95
BINDING SITE FOR RESIDUE MPD A1381
Software
2
BINDING SITE FOR RESIDUE IPA A1382
Software
4
A
GLN
294
A
GLN
16
2
1_555
A
HIS
350
A
HIS
72
2
1_555
A
PHE
320
A
PHE
42
4
1_555
A
TYR
342
A
TYR
64
4
1_555
A
HOH
2054
E
HOH
4
1_555
L
ALA
479
B
ALA
9
4
1_555
19
P 21 21 21