0.019366
0.000000
0.000000
0.000000
0.019366
0.000000
0.000000
0.000000
0.005278
0.000000
0.000000
0.000000
Kim, W.M.
Sigalov, A.B.
Stern, L.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
51.638
51.638
189.449
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
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
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
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
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
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
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
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
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
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
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
S
C
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
O
N
153
N
H
N
154
N
H
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
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
C
N
174
N
O
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
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
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
N
N
197
N
O
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
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
N
N
214
S
C
N
215
N
C
N
216
N
O
N
217
N
C
N
218
N
C
N
219
N
S
N
220
N
C
N
221
N
O
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
H
N
232
N
H
N
233
N
N
N
234
S
C
N
235
N
C
N
236
N
O
N
237
N
C
Y
238
N
C
Y
239
N
C
Y
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
N
244
N
O
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
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
N
N
257
S
C
N
258
N
C
N
259
N
O
N
260
N
C
N
261
N
C
N
262
N
C
N
263
N
O
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
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
O
N
279
N
O
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
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
R
C
N
292
N
O
N
293
N
C
N
294
N
O
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
N
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
N
318
N
O
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
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
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
N
342
N
O
N
343
N
O
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
H
N
353
N
H
N
354
N
H
N
355
N
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
N
360
N
C
N
361
N
C
N
362
N
O
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
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
doub
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
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
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
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
doub
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
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
doub
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
sing
N
208
N
sing
N
209
N
doub
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
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
doub
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
Y
233
N
doub
Y
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
sing
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
doub
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
doub
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
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
doub
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
Y
302
N
doub
Y
303
N
sing
Y
304
N
sing
N
305
N
sing
Y
306
N
doub
Y
307
N
sing
Y
308
N
sing
N
309
N
sing
Y
310
N
sing
Y
311
N
doub
N
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
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
doub
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
66
163
175
10.1107/S090744490904880X
20124696
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
2010
10.2210/pdb3ioz/pdb
pdb_00003ioz
1
CCD
2008-10-18
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
1.290
1.0
X29A
NSLS
1.290
SYNCHROTRON
NSLS BEAMLINE X29A
16698.676
Protein Nef
1
man
polymer
5279.782
T-cell surface glycoprotein CD3 zeta chain
1
man
polymer
T-cell receptor T3 zeta chain
no
no
GSDDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFG
WLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFGS
GSDDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFG
WLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFGS
A
polypeptide(L)
no
no
GSLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD
GSLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
388909
Simian immunodeficiency virus
469008
Escherichia coli
BL21 (DE3)
human
sample
9606
Homo sapiens
469008
Escherichia coli
BL21 (DE3)
1
2.87
57.19
VAPOR DIFFUSION, HANGING DROP
8.2
15% PEG 3350, 0.15M KF, 0.1M hepes, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Database references
Refinement description
Data collection
Database references
1
0
2010-02-02
1
1
2011-07-13
1
2
2012-03-28
1
3
2017-11-01
1
4
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2009-08-15
REL
REL
53.530
5.000
5.000
28.920
28.920
Phaser MODE: MR_AUTO
n
1
93
A
n
2
94
A
n
3
95
A
n
4
96
A
n
5
97
A
n
6
98
A
n
7
99
A
n
8
100
A
n
9
101
A
n
10
102
A
n
11
103
A
n
12
104
A
n
13
105
A
n
14
106
A
PRO
107
n
15
PRO
107
A
LEU
108
n
16
LEU
108
A
ARG
109
n
17
ARG
109
A
THR
110
n
18
THR
110
A
MET
111
n
19
MET
111
A
SER
112
n
20
SER
112
A
TYR
113
n
21
TYR
113
A
LYS
114
n
22
LYS
114
A
LEU
115
n
23
LEU
115
A
ALA
116
n
24
ALA
116
A
ILE
117
n
25
ILE
117
A
ASP
118
n
26
ASP
118
A
MET
119
n
27
MET
119
A
SER
120
n
28
SER
120
A
HIS
121
n
29
HIS
121
A
PHE
122
n
30
PHE
122
A
ILE
123
n
31
ILE
123
A
LYS
124
n
32
LYS
124
A
GLU
125
n
33
GLU
125
A
LYS
126
n
34
LYS
126
A
GLY
127
n
35
GLY
127
A
GLY
128
n
36
GLY
128
A
LEU
129
n
37
LEU
129
A
GLU
130
n
38
GLU
130
A
GLY
131
n
39
GLY
131
A
ILE
132
n
40
ILE
132
A
TYR
133
n
41
TYR
133
A
TYR
134
n
42
TYR
134
A
SER
135
n
43
SER
135
A
ALA
136
n
44
ALA
136
A
ARG
137
n
45
ARG
137
A
ARG
138
n
46
ARG
138
A
HIS
139
n
47
HIS
139
A
ARG
140
n
48
ARG
140
A
ILE
141
n
49
ILE
141
A
LEU
142
n
50
LEU
142
A
ASP
143
n
51
ASP
143
A
ILE
144
n
52
ILE
144
A
TYR
145
n
53
TYR
145
A
LEU
146
n
54
LEU
146
A
GLU
147
n
55
GLU
147
A
LYS
148
n
56
LYS
148
A
GLU
149
n
57
GLU
149
A
GLU
150
n
58
GLU
150
A
GLY
151
n
59
GLY
151
A
ILE
152
n
60
ILE
152
A
ILE
153
n
61
ILE
153
A
PRO
154
n
62
PRO
154
A
ASP
155
n
63
ASP
155
A
TRP
156
n
64
TRP
156
A
GLN
157
n
65
GLN
157
A
ASP
158
n
66
ASP
158
A
TYR
159
n
67
TYR
159
A
THR
160
n
68
THR
160
A
SER
161
n
69
SER
161
A
GLY
162
n
70
GLY
162
A
PRO
163
n
71
PRO
163
A
GLY
164
n
72
GLY
164
A
ILE
165
n
73
ILE
165
A
ARG
166
n
74
ARG
166
A
TYR
167
n
75
TYR
167
A
PRO
168
n
76
PRO
168
A
LYS
169
n
77
LYS
169
A
THR
170
n
78
THR
170
A
PHE
171
n
79
PHE
171
A
GLY
172
n
80
GLY
172
A
TRP
173
n
81
TRP
173
A
LEU
174
n
82
LEU
174
A
TRP
175
n
83
TRP
175
A
LYS
176
n
84
LYS
176
A
LEU
177
n
85
LEU
177
A
VAL
178
n
86
VAL
178
A
PRO
179
n
87
PRO
179
A
VAL
180
n
88
VAL
180
A
n
89
181
A
n
90
182
A
n
91
183
A
n
92
184
A
n
93
185
A
n
94
186
A
n
95
187
A
n
96
188
A
n
97
189
A
n
98
190
A
n
99
191
A
n
100
192
A
n
101
193
A
n
102
194
A
n
103
195
A
n
104
196
A
n
105
197
A
n
106
198
A
n
107
199
A
THR
200
n
108
THR
200
A
SER
201
n
109
SER
201
A
GLN
202
n
110
GLN
202
A
TRP
203
n
111
TRP
203
A
ASP
204
n
112
ASP
204
A
ASP
205
n
113
ASP
205
A
PRO
206
n
114
PRO
206
A
TRP
207
n
115
TRP
207
A
GLY
208
n
116
GLY
208
A
GLU
209
n
117
GLU
209
A
VAL
210
n
118
VAL
210
A
LEU
211
n
119
LEU
211
A
ALA
212
n
120
ALA
212
A
TRP
213
n
121
TRP
213
A
LYS
214
n
122
LYS
214
A
PHE
215
n
123
PHE
215
A
ASP
216
n
124
ASP
216
A
PRO
217
n
125
PRO
217
A
THR
218
n
126
THR
218
A
LEU
219
n
127
LEU
219
A
ALA
220
n
128
ALA
220
A
TYR
221
n
129
TYR
221
A
THR
222
n
130
THR
222
A
TYR
223
n
131
TYR
223
A
GLU
224
n
132
GLU
224
A
ALA
225
n
133
ALA
225
A
TYR
226
n
134
TYR
226
A
VAL
227
n
135
VAL
227
A
ARG
228
n
136
ARG
228
A
TYR
229
n
137
TYR
229
A
PRO
230
n
138
PRO
230
A
GLU
231
n
139
GLU
231
A
GLU
232
n
140
GLU
232
A
PHE
233
n
141
PHE
233
A
GLY
234
n
142
GLY
234
A
n
143
235
A
n
1
49
B
n
2
50
B
n
3
51
B
n
4
52
B
n
5
53
B
n
6
54
B
n
7
55
B
n
8
56
B
n
9
57
B
n
10
58
B
n
11
59
B
n
12
60
B
n
13
61
B
n
14
62
B
ALA
63
n
15
ALA
63
B
TYR
64
n
16
TYR
64
B
GLN
65
n
17
GLN
65
B
GLN
66
n
18
GLN
66
B
GLY
67
n
19
GLY
67
B
GLN
68
n
20
GLN
68
B
ASN
69
n
21
ASN
69
B
GLN
70
n
22
GLN
70
B
LEU
71
n
23
LEU
71
B
TYR
72
n
24
TYR
72
B
ASN
73
n
25
ASN
73
B
GLU
74
n
26
GLU
74
B
LEU
75
n
27
LEU
75
B
ASN
76
n
28
ASN
76
B
LEU
77
n
29
LEU
77
B
GLY
78
n
30
GLY
78
B
n
31
79
B
n
32
80
B
n
33
81
B
n
34
82
B
n
35
83
B
n
36
84
B
n
37
85
B
n
38
86
B
n
39
87
B
n
40
88
B
n
41
89
B
n
42
90
B
n
43
91
B
n
44
92
B
n
45
93
B
software_defined_assembly
PISA
2
dimeric
1040
-6
7380
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
LYS
176
A
N
LYS
84
A
O
LYS
214
A
O
LYS
122
1
A
GLY
93
A
GLY
1
1
Y
1
A
SER
94
A
SER
2
1
Y
1
A
ASP
95
A
ASP
3
1
Y
1
A
ASP
96
A
ASP
4
1
Y
1
A
LEU
97
A
LEU
5
1
Y
1
A
VAL
98
A
VAL
6
1
Y
1
A
GLY
99
A
GLY
7
1
Y
1
A
VAL
100
A
VAL
8
1
Y
1
A
SER
101
A
SER
9
1
Y
1
A
VAL
102
A
VAL
10
1
Y
1
A
ARG
103
A
ARG
11
1
Y
1
A
PRO
104
A
PRO
12
1
Y
1
A
LYS
105
A
LYS
13
1
Y
1
A
VAL
106
A
VAL
14
1
Y
1
A
ASN
181
A
ASN
89
1
Y
1
A
VAL
182
A
VAL
90
1
Y
1
A
SER
183
A
SER
91
1
Y
1
A
ASP
184
A
ASP
92
1
Y
1
A
GLU
185
A
GLU
93
1
Y
1
A
ALA
186
A
ALA
94
1
Y
1
A
GLN
187
A
GLN
95
1
Y
1
A
GLU
188
A
GLU
96
1
Y
1
A
ASP
189
A
ASP
97
1
Y
1
A
GLU
190
A
GLU
98
1
Y
1
A
GLU
191
A
GLU
99
1
Y
1
A
HIS
192
A
HIS
100
1
Y
1
A
TYR
193
A
TYR
101
1
Y
1
A
LEU
194
A
LEU
102
1
Y
1
A
MET
195
A
MET
103
1
Y
1
A
HIS
196
A
HIS
104
1
Y
1
A
PRO
197
A
PRO
105
1
Y
1
A
ALA
198
A
ALA
106
1
Y
1
A
GLN
199
A
GLN
107
1
Y
1
A
SER
235
A
SER
143
1
Y
1
B
GLY
49
B
GLY
1
1
Y
1
B
SER
50
B
SER
2
1
Y
1
B
LEU
51
B
LEU
3
1
Y
1
B
ARG
52
B
ARG
4
1
Y
1
B
VAL
53
B
VAL
5
1
Y
1
B
LYS
54
B
LYS
6
1
Y
1
B
PHE
55
B
PHE
7
1
Y
1
B
SER
56
B
SER
8
1
Y
1
B
ARG
57
B
ARG
9
1
Y
1
B
SER
58
B
SER
10
1
Y
1
B
ALA
59
B
ALA
11
1
Y
1
B
ASP
60
B
ASP
12
1
Y
1
B
ALA
61
B
ALA
13
1
Y
1
B
PRO
62
B
PRO
14
1
Y
1
B
ARG
79
B
ARG
31
1
Y
1
B
ARG
80
B
ARG
32
1
Y
1
B
GLU
81
B
GLU
33
1
Y
1
B
GLU
82
B
GLU
34
1
Y
1
B
TYR
83
B
TYR
35
1
Y
1
B
ASP
84
B
ASP
36
1
Y
1
B
VAL
85
B
VAL
37
1
Y
1
B
LEU
86
B
LEU
38
1
Y
1
B
ASP
87
B
ASP
39
1
Y
1
B
LYS
88
B
LYS
40
1
Y
1
B
ARG
89
B
ARG
41
1
Y
1
B
ARG
90
B
ARG
42
1
Y
1
B
GLY
91
B
GLY
43
1
Y
1
B
ARG
92
B
ARG
44
1
Y
1
B
ASP
93
B
ASP
45
1
Y
1
A
ARG
109
-179.31
136.69
1
A
LEU
115
-63.52
-72.63
1
A
ILE
117
-55.40
-72.75
1
A
LEU
129
77.06
-44.48
1
A
GLU
130
-46.88
107.13
1
A
ASP
143
-39.74
-36.58
1
A
PRO
154
-72.56
29.54
1
A
PRO
163
-75.94
-143.59
1
A
ASP
204
-64.55
-169.67
1
A
ASP
216
-160.53
107.64
1
A
THR
222
-160.25
102.13
1
A
ALA
225
-54.43
-74.72
1
A
GLU
232
-98.42
44.19
1
B
ASN
76
72.72
39.76
251.08
206.485
162.98
28.379
0.000
-0.000
28.379
0.000
-84.592
0.329
0.301
0.302
3.699
35.854
128
2923
4.380
94.440
1.00
1.00
0.577
2.170
1
0.22
MOLECULAR REPLACEMENT
0.900
1.110
ML
FLAT BULK SOLVENT MODEL
143.650
0.314
3.699
35.854
0
1051
0
0
1051
0.003
1088
0.565
1478
0.040
144
0.003
187
13.315
383
0.329
0.301
128
2795
2923
1
94.000
3.700
50.000
3IOZ
3122
0.051
1.037
1
12.800
12.600
99.400
0.393
3.70
3.83
282
1.037
1
12.70
100.00
0.279
3.83
3.99
311
1.007
1
13.10
100.00
0.169
3.99
4.17
293
1.057
1
13.40
100.00
0.158
4.17
4.39
306
1.020
1
13.30
100.00
0.101
4.39
4.66
305
1.057
1
13.10
100.00
0.090
4.66
5.02
305
1.061
1
13.20
100.00
0.072
5.02
5.53
311
1.051
1
12.70
100.00
0.056
5.53
6.32
317
0.986
1
12.50
99.70
0.039
6.32
7.96
325
0.998
1
12.00
100.00
0.030
7.96
50.00
367
1.098
1
10.80
95.10
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Thu Nov 13 11:40:59 2008
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.1.4
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
CBASS
data reduction
HKL-2000
data scaling
HKL-2000
SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)
1
N
N
2
N
N
A
SER
112
A
SER
20
HELX_P
A
GLU
125
A
GLU
33
1
1
14
A
SER
135
A
SER
43
HELX_P
A
GLY
151
A
GLY
59
1
2
17
A
PRO
217
A
PRO
125
HELX_P
A
TYR
221
A
TYR
129
5
3
5
A
TYR
223
A
TYR
131
HELX_P
A
TYR
229
A
TYR
137
1
4
7
B
GLN
65
B
GLN
17
HELX_P
B
GLU
74
B
GLU
26
1
5
10
VIRAL PROTEIN/SIGNALING PROTEIN
Protein-Protein complex, Cell membrane, Lipoprotein, Membrane, Myristate, Viral immunoevasion, Virulence, Disulfide bond, Host-virus interaction, Phosphoprotein, Receptor, Transmembrane, VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX, VIRAL PROTEIN-SIGNALING PROTEIN COMPLEX
A
GLY
162
A
GLY
70
1
A
PRO
163
A
PRO
71
-0.02
Q5QGG3_SIVCZ
UNP
1
95
Q5QGG3
DDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWL
WKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFGS
CD3Z_HUMAN
UNP
2
51
P20963
LRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD
95
235
3IOZ
95
235
Q5QGG3
A
1
3
143
51
93
3IOZ
51
93
P20963
B
2
3
45
1
expression tag
GLY
93
3IOZ
A
Q5QGG3
UNP
1
1
expression tag
SER
94
3IOZ
A
Q5QGG3
UNP
2
2
expression tag
GLY
49
3IOZ
B
P20963
UNP
1
2
expression tag
SER
50
3IOZ
B
P20963
UNP
2
2
anti-parallel
A
TRP
175
A
TRP
83
A
VAL
178
A
VAL
86
A
ALA
212
A
ALA
120
A
PHE
215
A
PHE
123
96
P 43 21 2