0.013742
0.000000
0.000000
0.000000
0.013742
0.000000
0.000000
0.000000
0.013742
0.00000
0.00000
0.00000
Shu, W.
Ji, H.
Lu, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
72.77
72.77
72.77
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
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
N
238
N
O
N
239
N
O
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
R
C
N
252
N
O
N
253
N
C
N
254
N
O
N
255
N
H
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
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
N
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
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
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
O
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
H
N
315
N
N
N
316
S
C
N
317
N
C
N
318
N
O
N
319
N
C
N
320
N
C
N
321
N
C
N
322
N
O
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
H
N
332
N
H
N
333
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
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
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
Y
262
N
doub
Y
263
N
sing
Y
264
N
sing
N
265
N
sing
Y
266
N
doub
Y
267
N
sing
Y
268
N
sing
N
269
N
sing
Y
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
273
N
doub
N
274
N
sing
Y
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
doub
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
Y
290
N
doub
Y
291
N
sing
Y
292
N
sing
N
293
N
sing
Y
294
N
doub
N
295
N
sing
Y
296
N
doub
N
297
N
sing
Y
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
sing
N
308
N
sing
N
309
N
doub
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
275
1839
1845
10.1074/jbc.275.3.1839
10636883
Interactions between HIV-1 gp41 core and detergents and their implications for membrane fusion.
2000
10.2210/pdb1df5/pdb
pdb_00001df5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
130.0
1
IMAGE PLATE
1998-03-19
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
7879.753
HIV-1 ENVELOPE GLYCOPROTEIN GP41
RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
1
man
polymer
no
no
SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARSGGRGGWMEWDREINNYTSLIHSLIEESQNQQEK
SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARSGGRGGWMEWDREINNYTSLIHSLIEESQNQQEK
A
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
Lentivirus
Escherichia
sample
1
RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
34
11676
Human immunodeficiency virus 1
562
Escherichia coli
Lentivirus
Escherichia
sample
41
RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
68
11676
Human immunodeficiency virus 1
562
Escherichia coli
1
2.04
39.64
VAPOR DIFFUSION, HANGING DROP
7.5
Potassium sodium tartrate, SDS, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
entity_src_gen
software
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Refinement description
Source and taxonomy
Data collection
Database references
1
0
1999-11-24
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-08-09
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
1999-11-17
REL
IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES
546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - 40 IS AN
ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES
628 - 655.
SER
1
n
1
SER
1
A
GLY
2
n
2
GLY
2
A
ILE
3
n
3
ILE
3
A
VAL
4
n
4
VAL
4
A
GLN
5
n
5
GLN
5
A
GLN
6
n
6
GLN
6
A
GLN
7
n
7
GLN
7
A
ASN
8
n
8
ASN
8
A
ASN
9
n
9
ASN
9
A
LEU
10
n
10
LEU
10
A
LEU
11
n
11
LEU
11
A
ARG
12
n
12
ARG
12
A
ALA
13
n
13
ALA
13
A
ILE
14
n
14
ILE
14
A
GLU
15
n
15
GLU
15
A
ALA
16
n
16
ALA
16
A
GLN
17
n
17
GLN
17
A
GLN
18
n
18
GLN
18
A
HIS
19
n
19
HIS
19
A
LEU
20
n
20
LEU
20
A
LEU
21
n
21
LEU
21
A
GLN
22
n
22
GLN
22
A
LEU
23
n
23
LEU
23
A
THR
24
n
24
THR
24
A
VAL
25
n
25
VAL
25
A
TRP
26
n
26
TRP
26
A
GLY
27
n
27
GLY
27
A
ILE
28
n
28
ILE
28
A
LYS
29
n
29
LYS
29
A
GLN
30
n
30
GLN
30
A
LEU
31
n
31
LEU
31
A
GLN
32
n
32
GLN
32
A
ALA
33
n
33
ALA
33
A
ARG
34
n
34
ARG
34
A
SER
35
n
35
SER
35
A
GLY
36
n
36
GLY
36
A
GLY
37
n
37
GLY
37
A
ARG
38
n
38
ARG
38
A
GLY
39
n
39
GLY
39
A
GLY
40
n
40
GLY
40
A
TRP
41
n
41
TRP
41
A
MET
42
n
42
MET
42
A
GLU
43
n
43
GLU
43
A
TRP
44
n
44
TRP
44
A
ASP
45
n
45
ASP
45
A
ARG
46
n
46
ARG
46
A
GLU
47
n
47
GLU
47
A
ILE
48
n
48
ILE
48
A
ASN
49
n
49
ASN
49
A
ASN
50
n
50
ASN
50
A
TYR
51
n
51
TYR
51
A
THR
52
n
52
THR
52
A
SER
53
n
53
SER
53
A
LEU
54
n
54
LEU
54
A
ILE
55
n
55
ILE
55
A
HIS
56
n
56
HIS
56
A
SER
57
n
57
SER
57
A
LEU
58
n
58
LEU
58
A
ILE
59
n
59
ILE
59
A
GLU
60
n
60
GLU
60
A
GLU
61
n
61
GLU
61
A
SER
62
n
62
SER
62
A
GLN
63
n
63
GLN
63
A
ASN
64
n
64
ASN
64
A
GLN
65
n
65
GLN
65
A
GLN
66
n
66
GLN
66
A
GLU
67
n
67
GLU
67
A
LYS
68
n
68
LYS
68
A
author_and_software_defined_assembly
PISA,PQS
3
trimeric
6610
-63
10780
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
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
5_546
z,x-1,y+1
crystal symmetry operation
0.0000000000
-72.7700000000
72.7700000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
9_645
y+1,z-1,x
crystal symmetry operation
72.7700000000
-72.7700000000
0.0000000000
1
A
ILE
3
65.83
108.64
1
A
GLN
66
-178.56
-13.01
0.3150000
0.1830000
2.7
8.0
86
1726
1726
99.9
RANDOM
1
0
0
Engh & Huber
2.7
8.0
0
555
0
0
555
0.004
0.8
2.70
30.0
1DF5
1859
1859
0
0
0.0460000
1
21.0
5.6
99.9
0.1020000
2.70
2.80
186
1
5.8
100.0
phasing
AMoRE
refinement
X-PLOR
3.1
data reduction
DENZO
data scaling
SCALEPACK
INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION
1
N
N
The biological assembly is a homotrimer.
A
VAL
4
A
VAL
4
HELX_P
A
GLY
37
A
GLY
37
1
1
34
A
ARG
38
A
ARG
38
HELX_P
A
GLY
40
A
GLY
40
5
2
3
A
TRP
41
A
TRP
41
HELX_P
A
ASN
64
A
ASN
64
1
3
24
VIRAL PROTEIN
HIV-1, GP41, MEMBRANE FUSION, PROTEIN-DETERGENT INTERACTION, Viral protein
ENV_HV1H2
UNP
1
P04578
546
579
1DF5
1
34
P04578
A
1
1
34
628
655
1DF5
41
68
P04578
A
1
41
68
1
SEE REMARK 999
SER
35
1DF5
A
P04578
UNP
35
1
SEE REMARK 999
GLY
36
1DF5
A
P04578
UNP
36
1
SEE REMARK 999
GLY
37
1DF5
A
P04578
UNP
37
1
SEE REMARK 999
ARG
38
1DF5
A
P04578
UNP
38
1
SEE REMARK 999
GLY
39
1DF5
A
P04578
UNP
39
1
SEE REMARK 999
GLY
40
1DF5
A
P04578
UNP
40
199
I 21 3