.017065
.000000
.000000
.000000
.015408
.000000
.000000
.000000
.005682
.00000
.00000
.00000
Julien, J.-P.
Bryson, S.
Pai, E.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
58.600
64.900
176.000
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
C6 H13 N5 O4
219.199
N-OMEGA-NITRO-L-ARGININE
NNA
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
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
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
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
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
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
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
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
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
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
C
N
254
N
C
N
255
N
N
N
256
N
C
N
257
N
N
N
258
N
N
N
259
N
C
N
260
N
O
N
261
N
O
N
262
N
N
N
263
N
O
N
264
N
O
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
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
N
N
279
S
C
N
280
N
C
N
281
N
O
N
282
N
C
Y
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
N
289
N
O
N
290
N
H
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
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
N
C
N
306
N
C
N
307
N
C
N
308
N
O
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
H
N
316
N
H
N
317
N
H
N
318
N
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
N
323
N
O
N
324
N
O
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
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
R
C
N
337
N
O
N
338
N
C
N
339
N
O
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
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
N
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
O
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
374
N
H
N
375
N
H
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
N
387
N
O
N
388
N
O
N
389
N
H
N
390
N
H
N
391
N
H
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
H
N
400
N
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
N
405
N
C
N
406
N
C
N
407
N
O
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
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
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
doub
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
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
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
sing
N
125
N
sing
N
126
N
doub
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
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
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
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
doub
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
sing
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
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
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
E
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
doub
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
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
Y
275
N
doub
Y
276
N
sing
Y
277
N
sing
N
278
N
sing
Y
279
N
doub
N
280
N
sing
Y
281
N
doub
N
282
N
sing
Y
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
doub
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
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
doub
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
doub
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
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
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
Y
344
N
doub
Y
345
N
sing
Y
346
N
sing
N
347
N
sing
Y
348
N
doub
Y
349
N
sing
Y
350
N
sing
N
351
N
sing
Y
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
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
doub
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
Y
372
N
doub
Y
373
N
sing
Y
374
N
sing
N
375
N
sing
Y
376
N
doub
N
377
N
sing
Y
378
N
doub
N
379
N
sing
Y
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
doub
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
US
J.Virol.
JOVIAM
0825
0022-538X
83
11862
11875
10.1128/JVI.01604-09
19740978
Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.
2009
10.2210/pdb3idm/pdb
pdb_00003idm
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
100
1
IMAGE PLATE
2005-06-14
MAR scanner 345 mm plate
Xenocs optics
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU
23363.844
2F5 Fab light chain
1
nat
polymer
25245.703
2F5 Fab heavy chain
1
nat
polymer
920.924
gp41 MPER peptide analog
1
syn
polymer
18.015
water
222
nat
water
no
no
ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRP
EDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGEC
ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRP
EDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGEC
A
polypeptide(L)
no
no
RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQV
VLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPSSKSTSGGTAALGCL
VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEPKSCDK
RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQV
VLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPSSKSTSGGTAALGCL
VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEPKSCDK
B
polypeptide(L)
no
yes
ELD(NRG)WAS
ELDXWAS
C
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
9606
Homo sapiens
sample
9606
Homo sapiens
1
3.38
63.59
VAPOR DIFFUSION, HANGING DROP
5.6
0.1 M sodium acetate, pH 5.6, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
software
atom_site
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Refinement description
Atomic model
Data collection
Database references
Derived calculations
1
0
2010-02-02
1
1
2011-07-13
1
2
2017-11-01
2
0
2023-11-15
_software.name
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
Same Monoclonal Antibody 2F5 in complex with gp41 Peptide ALDKWNQ
Same Monoclonal Antibody 2F5 in complex with gp41 Peptide analog ELD(Orn)WAS
Same Monoclonal Antibody 2F5 in complex with gp41 Peptide ALDKWD
Same Monoclonal Antibody 2F5 in complex with gp41 Peptide analog ELD(Paf)WAS
RCSB
Y
RCSB
2009-07-21
REL
REL
HOH
water
TIP
6
4
HOH
HOH
215
A
TIP
11
4
HOH
HOH
216
A
TIP
217
4
HOH
HOH
217
A
TIP
12
4
HOH
HOH
218
A
TIP
14
4
HOH
HOH
219
A
TIP
18
4
HOH
HOH
220
A
TIP
21
4
HOH
HOH
221
A
TIP
23
4
HOH
HOH
222
A
TIP
26
4
HOH
HOH
223
A
TIP
27
4
HOH
HOH
224
A
TIP
29
4
HOH
HOH
225
A
TIP
31
4
HOH
HOH
226
A
TIP
33
4
HOH
HOH
227
A
TIP
34
4
HOH
HOH
228
A
TIP
37
4
HOH
HOH
229
A
TIP
38
4
HOH
HOH
230
A
TIP
40
4
HOH
HOH
231
A
TIP
47
4
HOH
HOH
232
A
TIP
49
4
HOH
HOH
233
A
TIP
52
4
HOH
HOH
234
A
TIP
53
4
HOH
HOH
235
A
TIP
55
4
HOH
HOH
236
A
TIP
56
4
HOH
HOH
237
A
TIP
57
4
HOH
HOH
238
A
TIP
60
4
HOH
HOH
239
A
TIP
61
4
HOH
HOH
240
A
TIP
62
4
HOH
HOH
241
A
TIP
63
4
HOH
HOH
242
A
TIP
64
4
HOH
HOH
243
A
TIP
65
4
HOH
HOH
244
A
TIP
67
4
HOH
HOH
245
A
TIP
68
4
HOH
HOH
246
A
TIP
69
4
HOH
HOH
247
A
TIP
74
4
HOH
HOH
248
A
TIP
76
4
HOH
HOH
249
A
TIP
77
4
HOH
HOH
250
A
TIP
78
4
HOH
HOH
251
A
TIP
79
4
HOH
HOH
252
A
TIP
80
4
HOH
HOH
253
A
TIP
81
4
HOH
HOH
254
A
TIP
84
4
HOH
HOH
255
A
TIP
85
4
HOH
HOH
256
A
TIP
89
4
HOH
HOH
257
A
TIP
90
4
HOH
HOH
258
A
TIP
94
4
HOH
HOH
259
A
TIP
98
4
HOH
HOH
260
A
TIP
100
4
HOH
HOH
261
A
TIP
101
4
HOH
HOH
262
A
TIP
102
4
HOH
HOH
263
A
TIP
105
4
HOH
HOH
264
A
TIP
107
4
HOH
HOH
265
A
TIP
108
4
HOH
HOH
266
A
TIP
110
4
HOH
HOH
267
A
TIP
111
4
HOH
HOH
268
A
TIP
113
4
HOH
HOH
269
A
TIP
114
4
HOH
HOH
270
A
TIP
115
4
HOH
HOH
271
A
TIP
119
4
HOH
HOH
272
A
TIP
121
4
HOH
HOH
273
A
TIP
123
4
HOH
HOH
274
A
TIP
125
4
HOH
HOH
275
A
TIP
127
4
HOH
HOH
276
A
TIP
128
4
HOH
HOH
277
A
TIP
129
4
HOH
HOH
278
A
TIP
131
4
HOH
HOH
279
A
TIP
135
4
HOH
HOH
280
A
TIP
138
4
HOH
HOH
281
A
TIP
139
4
HOH
HOH
282
A
TIP
140
4
HOH
HOH
283
A
TIP
141
4
HOH
HOH
284
A
TIP
142
4
HOH
HOH
285
A
TIP
143
4
HOH
HOH
286
A
TIP
145
4
HOH
HOH
287
A
TIP
146
4
HOH
HOH
288
A
TIP
149
4
HOH
HOH
289
A
TIP
152
4
HOH
HOH
290
A
TIP
153
4
HOH
HOH
291
A
TIP
154
4
HOH
HOH
292
A
TIP
155
4
HOH
HOH
293
A
TIP
161
4
HOH
HOH
294
A
TIP
162
4
HOH
HOH
295
A
TIP
165
4
HOH
HOH
296
A
TIP
168
4
HOH
HOH
297
A
TIP
170
4
HOH
HOH
298
A
TIP
177
4
HOH
HOH
299
A
TIP
180
4
HOH
HOH
300
A
TIP
181
4
HOH
HOH
301
A
TIP
186
4
HOH
HOH
302
A
TIP
189
4
HOH
HOH
303
A
TIP
192
4
HOH
HOH
304
A
TIP
195
4
HOH
HOH
305
A
TIP
203
4
HOH
HOH
306
A
TIP
205
4
HOH
HOH
307
A
TIP
207
4
HOH
HOH
308
A
TIP
211
4
HOH
HOH
309
A
TIP
212
4
HOH
HOH
310
A
TIP
148
4
HOH
HOH
311
A
TIP
167
4
HOH
HOH
312
A
TIP
106
4
HOH
HOH
313
A
TIP
219
4
HOH
HOH
219
B
TIP
220
4
HOH
HOH
220
B
TIP
221
4
HOH
HOH
221
B
TIP
222
4
HOH
HOH
222
B
TIP
223
4
HOH
HOH
223
B
TIP
1
4
HOH
HOH
224
B
TIP
2
4
HOH
HOH
225
B
TIP
3
4
HOH
HOH
226
B
TIP
4
4
HOH
HOH
227
B
TIP
5
4
HOH
HOH
228
B
TIP
7
4
HOH
HOH
229
B
TIP
8
4
HOH
HOH
230
B
TIP
10
4
HOH
HOH
231
B
TIP
13
4
HOH
HOH
232
B
TIP
15
4
HOH
HOH
233
B
TIP
16
4
HOH
HOH
234
B
TIP
17
4
HOH
HOH
235
B
TIP
19
4
HOH
HOH
236
B
TIP
20
4
HOH
HOH
237
B
TIP
22
4
HOH
HOH
238
B
TIP
24
4
HOH
HOH
239
B
TIP
25
4
HOH
HOH
240
B
TIP
28
4
HOH
HOH
241
B
TIP
30
4
HOH
HOH
242
B
TIP
32
4
HOH
HOH
243
B
TIP
35
4
HOH
HOH
244
B
TIP
36
4
HOH
HOH
245
B
TIP
39
4
HOH
HOH
246
B
TIP
41
4
HOH
HOH
247
B
TIP
42
4
HOH
HOH
248
B
TIP
43
4
HOH
HOH
249
B
TIP
44
4
HOH
HOH
250
B
TIP
45
4
HOH
HOH
251
B
TIP
46
4
HOH
HOH
252
B
TIP
48
4
HOH
HOH
253
B
TIP
50
4
HOH
HOH
254
B
TIP
51
4
HOH
HOH
255
B
TIP
54
4
HOH
HOH
256
B
TIP
58
4
HOH
HOH
257
B
TIP
59
4
HOH
HOH
258
B
TIP
66
4
HOH
HOH
259
B
TIP
70
4
HOH
HOH
260
B
TIP
71
4
HOH
HOH
261
B
TIP
72
4
HOH
HOH
262
B
TIP
73
4
HOH
HOH
263
B
TIP
75
4
HOH
HOH
264
B
TIP
82
4
HOH
HOH
265
B
TIP
83
4
HOH
HOH
266
B
TIP
86
4
HOH
HOH
267
B
TIP
87
4
HOH
HOH
268
B
TIP
88
4
HOH
HOH
269
B
TIP
91
4
HOH
HOH
270
B
TIP
92
4
HOH
HOH
271
B
TIP
93
4
HOH
HOH
272
B
TIP
95
4
HOH
HOH
273
B
TIP
96
4
HOH
HOH
274
B
TIP
97
4
HOH
HOH
275
B
TIP
99
4
HOH
HOH
276
B
TIP
103
4
HOH
HOH
277
B
TIP
104
4
HOH
HOH
278
B
TIP
109
4
HOH
HOH
279
B
TIP
112
4
HOH
HOH
280
B
TIP
116
4
HOH
HOH
281
B
TIP
117
4
HOH
HOH
282
B
TIP
118
4
HOH
HOH
283
B
TIP
120
4
HOH
HOH
284
B
TIP
122
4
HOH
HOH
285
B
TIP
124
4
HOH
HOH
286
B
TIP
126
4
HOH
HOH
287
B
TIP
130
4
HOH
HOH
288
B
TIP
132
4
HOH
HOH
289
B
TIP
133
4
HOH
HOH
290
B
TIP
134
4
HOH
HOH
291
B
TIP
137
4
HOH
HOH
292
B
TIP
147
4
HOH
HOH
293
B
TIP
224
4
HOH
HOH
294
B
TIP
150
4
HOH
HOH
295
B
TIP
151
4
HOH
HOH
296
B
TIP
156
4
HOH
HOH
297
B
TIP
157
4
HOH
HOH
298
B
TIP
158
4
HOH
HOH
299
B
TIP
159
4
HOH
HOH
300
B
TIP
160
4
HOH
HOH
301
B
TIP
163
4
HOH
HOH
302
B
TIP
164
4
HOH
HOH
303
B
TIP
166
4
HOH
HOH
304
B
TIP
169
4
HOH
HOH
306
B
TIP
171
4
HOH
HOH
307
B
TIP
172
4
HOH
HOH
308
B
TIP
173
4
HOH
HOH
309
B
TIP
174
4
HOH
HOH
310
B
TIP
175
4
HOH
HOH
311
B
TIP
176
4
HOH
HOH
312
B
TIP
178
4
HOH
HOH
313
B
TIP
179
4
HOH
HOH
314
B
TIP
182
4
HOH
HOH
315
B
TIP
183
4
HOH
HOH
316
B
TIP
184
4
HOH
HOH
317
B
TIP
185
4
HOH
HOH
318
B
TIP
188
4
HOH
HOH
319
B
TIP
190
4
HOH
HOH
320
B
TIP
191
4
HOH
HOH
321
B
TIP
193
4
HOH
HOH
322
B
TIP
194
4
HOH
HOH
323
B
TIP
196
4
HOH
HOH
324
B
TIP
197
4
HOH
HOH
325
B
TIP
198
4
HOH
HOH
326
B
TIP
199
4
HOH
HOH
327
B
TIP
200
4
HOH
HOH
328
B
TIP
201
4
HOH
HOH
329
B
TIP
202
4
HOH
HOH
330
B
TIP
204
4
HOH
HOH
331
B
TIP
206
4
HOH
HOH
332
B
TIP
208
4
HOH
HOH
333
B
TIP
209
4
HOH
HOH
334
B
TIP
210
4
HOH
HOH
335
B
TIP
213
4
HOH
HOH
336
B
TIP
214
4
HOH
HOH
337
B
TIP
215
4
HOH
HOH
338
B
TIP
218
4
HOH
HOH
339
B
TIP
9
4
HOH
HOH
9
C
TIP
187
4
HOH
HOH
187
C
TIP
225
4
HOH
HOH
225
C
ALA
1
n
1
ALA
1
A
LEU
2
n
2
LEU
2
A
GLN
3
n
3
GLN
3
A
LEU
4
n
4
LEU
4
A
THR
5
n
5
THR
5
A
GLN
6
n
6
GLN
6
A
SER
7
n
7
SER
7
A
PRO
8
n
8
PRO
8
A
SER
9
n
9
SER
9
A
SER
10
n
10
SER
10
A
LEU
11
n
11
LEU
11
A
SER
12
n
12
SER
12
A
ALA
13
n
13
ALA
13
A
SER
14
n
14
SER
14
A
VAL
15
n
15
VAL
15
A
GLY
16
n
16
GLY
16
A
ASP
17
n
17
ASP
17
A
ARG
18
n
18
ARG
18
A
ILE
19
n
19
ILE
19
A
THR
20
n
20
THR
20
A
ILE
21
n
21
ILE
21
A
THR
22
n
22
THR
22
A
CYS
23
n
23
CYS
23
A
ARG
24
n
24
ARG
24
A
ALA
25
n
25
ALA
25
A
SER
26
n
26
SER
26
A
GLN
27
n
27
GLN
27
A
GLY
28
n
28
GLY
28
A
VAL
29
n
29
VAL
29
A
THR
30
n
30
THR
30
A
SER
31
n
31
SER
31
A
ALA
32
n
32
ALA
32
A
LEU
33
n
33
LEU
33
A
ALA
34
n
34
ALA
34
A
TRP
35
n
35
TRP
35
A
TYR
36
n
36
TYR
36
A
ARG
37
n
37
ARG
37
A
GLN
38
n
38
GLN
38
A
LYS
39
n
39
LYS
39
A
PRO
40
n
40
PRO
40
A
GLY
41
n
41
GLY
41
A
SER
42
n
42
SER
42
A
PRO
43
n
43
PRO
43
A
PRO
44
n
44
PRO
44
A
GLN
45
n
45
GLN
45
A
LEU
46
n
46
LEU
46
A
LEU
47
n
47
LEU
47
A
ILE
48
n
48
ILE
48
A
TYR
49
n
49
TYR
49
A
ASP
50
n
50
ASP
50
A
ALA
51
n
51
ALA
51
A
SER
52
n
52
SER
52
A
SER
53
n
53
SER
53
A
LEU
54
n
54
LEU
54
A
GLU
55
n
55
GLU
55
A
SER
56
n
56
SER
56
A
GLY
57
n
57
GLY
57
A
VAL
58
n
58
VAL
58
A
PRO
59
n
59
PRO
59
A
SER
60
n
60
SER
60
A
ARG
61
n
61
ARG
61
A
PHE
62
n
62
PHE
62
A
SER
63
n
63
SER
63
A
GLY
64
n
64
GLY
64
A
SER
65
n
65
SER
65
A
GLY
66
n
66
GLY
66
A
SER
67
n
67
SER
67
A
GLY
68
n
68
GLY
68
A
THR
69
n
69
THR
69
A
GLU
70
n
70
GLU
70
A
PHE
71
n
71
PHE
71
A
THR
72
n
72
THR
72
A
LEU
73
n
73
LEU
73
A
THR
74
n
74
THR
74
A
ILE
75
n
75
ILE
75
A
SER
76
n
76
SER
76
A
THR
77
n
77
THR
77
A
LEU
78
n
78
LEU
78
A
ARG
79
n
79
ARG
79
A
PRO
80
n
80
PRO
80
A
GLU
81
n
81
GLU
81
A
ASP
82
n
82
ASP
82
A
PHE
83
n
83
PHE
83
A
ALA
84
n
84
ALA
84
A
THR
85
n
85
THR
85
A
TYR
86
n
86
TYR
86
A
TYR
87
n
87
TYR
87
A
CYS
88
n
88
CYS
88
A
GLN
89
n
89
GLN
89
A
GLN
90
n
90
GLN
90
A
LEU
91
n
91
LEU
91
A
HIS
92
n
92
HIS
92
A
PHE
93
n
93
PHE
93
A
TYR
94
n
94
TYR
94
A
PRO
95
n
95
PRO
95
A
HIS
96
n
96
HIS
96
A
THR
97
n
97
THR
97
A
PHE
98
n
98
PHE
98
A
GLY
99
n
99
GLY
99
A
GLY
100
n
100
GLY
100
A
GLY
101
n
101
GLY
101
A
THR
102
n
102
THR
102
A
ARG
103
n
103
ARG
103
A
VAL
104
n
104
VAL
104
A
ASP
105
n
105
ASP
105
A
VAL
106
n
106
VAL
106
A
ARG
107
n
107
ARG
107
A
ARG
108
n
108
ARG
108
A
THR
109
n
109
THR
109
A
VAL
110
n
110
VAL
110
A
ALA
111
n
111
ALA
111
A
ALA
112
n
112
ALA
112
A
PRO
113
n
113
PRO
113
A
SER
114
n
114
SER
114
A
VAL
115
n
115
VAL
115
A
PHE
116
n
116
PHE
116
A
ILE
117
n
117
ILE
117
A
PHE
118
n
118
PHE
118
A
PRO
119
n
119
PRO
119
A
PRO
120
n
120
PRO
120
A
SER
121
n
121
SER
121
A
ASP
122
n
122
ASP
122
A
GLU
123
n
123
GLU
123
A
GLN
124
n
124
GLN
124
A
LEU
125
n
125
LEU
125
A
LYS
126
n
126
LYS
126
A
SER
127
n
127
SER
127
A
GLY
128
n
128
GLY
128
A
THR
129
n
129
THR
129
A
ALA
130
n
130
ALA
130
A
SER
131
n
131
SER
131
A
VAL
132
n
132
VAL
132
A
VAL
133
n
133
VAL
133
A
CYS
134
n
134
CYS
134
A
LEU
135
n
135
LEU
135
A
LEU
136
n
136
LEU
136
A
ASN
137
n
137
ASN
137
A
ASN
138
n
138
ASN
138
A
PHE
139
n
139
PHE
139
A
TYR
140
n
140
TYR
140
A
PRO
141
n
141
PRO
141
A
ARG
142
n
142
ARG
142
A
GLU
143
n
143
GLU
143
A
ALA
144
n
144
ALA
144
A
LYS
145
n
145
LYS
145
A
VAL
146
n
146
VAL
146
A
GLN
147
n
147
GLN
147
A
TRP
148
n
148
TRP
148
A
LYS
149
n
149
LYS
149
A
VAL
150
n
150
VAL
150
A
ASP
151
n
151
ASP
151
A
ASN
152
n
152
ASN
152
A
ALA
153
n
153
ALA
153
A
LEU
154
n
154
LEU
154
A
GLN
155
n
155
GLN
155
A
SER
156
n
156
SER
156
A
GLY
157
n
157
GLY
157
A
ASN
158
n
158
ASN
158
A
SER
159
n
159
SER
159
A
GLN
160
n
160
GLN
160
A
GLU
161
n
161
GLU
161
A
SER
162
n
162
SER
162
A
VAL
163
n
163
VAL
163
A
THR
164
n
164
THR
164
A
GLU
165
n
165
GLU
165
A
GLN
166
n
166
GLN
166
A
ASP
167
n
167
ASP
167
A
SER
168
n
168
SER
168
A
LYS
169
n
169
LYS
169
A
ASP
170
n
170
ASP
170
A
SER
171
n
171
SER
171
A
THR
172
n
172
THR
172
A
TYR
173
n
173
TYR
173
A
SER
174
n
174
SER
174
A
LEU
175
n
175
LEU
175
A
SER
176
n
176
SER
176
A
SER
177
n
177
SER
177
A
THR
178
n
178
THR
178
A
LEU
179
n
179
LEU
179
A
THR
180
n
180
THR
180
A
LEU
181
n
181
LEU
181
A
SER
182
n
182
SER
182
A
LYS
183
n
183
LYS
183
A
ALA
184
n
184
ALA
184
A
ASP
185
n
185
ASP
185
A
TYR
186
n
186
TYR
186
A
GLU
187
n
187
GLU
187
A
LYS
188
n
188
LYS
188
A
HIS
189
n
189
HIS
189
A
LYS
190
n
190
LYS
190
A
VAL
191
n
191
VAL
191
A
TYR
192
n
192
TYR
192
A
GLU
193
n
193
GLU
193
A
CYS
194
n
194
CYS
194
A
GLU
195
n
195
GLU
195
A
VAL
196
n
196
VAL
196
A
THR
197
n
197
THR
197
A
HIS
198
n
198
HIS
198
A
GLN
199
n
199
GLN
199
A
GLY
200
n
200
GLY
200
A
LEU
201
n
201
LEU
201
A
SER
202
n
202
SER
202
A
SER
203
n
203
SER
203
A
PRO
204
n
204
PRO
204
A
VAL
205
n
205
VAL
205
A
THR
206
n
206
THR
206
A
LYS
207
n
207
LYS
207
A
SER
208
n
208
SER
208
A
PHE
209
n
209
PHE
209
A
ASN
210
n
210
ASN
210
A
ARG
211
n
211
ARG
211
A
GLY
212
n
212
GLY
212
A
GLU
213
n
213
GLU
213
A
CYS
214
n
214
CYS
214
A
ARG
1
n
1
ARG
1
B
ILE
2
n
2
ILE
2
B
THR
3
n
3
THR
3
B
LEU
4
n
4
LEU
4
B
LYS
5
n
5
LYS
5
B
GLU
6
n
6
GLU
6
B
SER
7
n
7
SER
7
B
GLY
8
n
8
GLY
8
B
PRO
9
n
9
PRO
9
B
PRO
10
n
10
PRO
10
B
LEU
11
n
11
LEU
11
B
VAL
12
n
12
VAL
12
B
LYS
13
n
13
LYS
13
B
PRO
14
n
14
PRO
14
B
THR
15
n
15
THR
15
B
GLN
16
n
16
GLN
16
B
THR
17
n
17
THR
17
B
LEU
18
n
18
LEU
18
B
THR
19
n
19
THR
19
B
LEU
20
n
20
LEU
20
B
THR
21
n
21
THR
21
B
CYS
22
n
22
CYS
22
B
SER
23
n
23
SER
23
B
PHE
24
n
24
PHE
24
B
SER
25
n
25
SER
25
B
GLY
26
n
26
GLY
26
B
PHE
27
n
27
PHE
27
B
SER
28
n
28
SER
28
B
LEU
29
n
29
LEU
29
B
SER
30
n
30
SER
30
B
ASP
31
n
31
ASP
31
B
PHE
32
n
32
PHE
32
B
GLY
33
n
33
GLY
33
B
VAL
34
n
34
VAL
34
B
GLY
35
n
35
GLY
35
B
VAL
35
n
36
A
VAL
35
B
GLY
35
n
37
B
GLY
35
B
TRP
36
n
38
TRP
36
B
ILE
37
n
39
ILE
37
B
ARG
38
n
40
ARG
38
B
GLN
39
n
41
GLN
39
B
PRO
40
n
42
PRO
40
B
PRO
41
n
43
PRO
41
B
GLY
42
n
44
GLY
42
B
LYS
43
n
45
LYS
43
B
ALA
44
n
46
ALA
44
B
LEU
45
n
47
LEU
45
B
GLU
46
n
48
GLU
46
B
TRP
47
n
49
TRP
47
B
LEU
48
n
50
LEU
48
B
ALA
49
n
51
ALA
49
B
ILE
50
n
52
ILE
50
B
ILE
51
n
53
ILE
51
B
TYR
52
n
54
TYR
52
B
SER
53
n
55
SER
53
B
ASP
54
n
56
ASP
54
B
ASP
55
n
57
ASP
55
B
ASP
56
n
58
ASP
56
B
LYS
57
n
59
LYS
57
B
ARG
58
n
60
ARG
58
B
TYR
59
n
61
TYR
59
B
SER
60
n
62
SER
60
B
PRO
61
n
63
PRO
61
B
SER
62
n
64
SER
62
B
LEU
63
n
65
LEU
63
B
ASN
64
n
66
ASN
64
B
THR
65
n
67
THR
65
B
ARG
66
n
68
ARG
66
B
LEU
67
n
69
LEU
67
B
THR
68
n
70
THR
68
B
ILE
69
n
71
ILE
69
B
THR
70
n
72
THR
70
B
LYS
71
n
73
LYS
71
B
ASP
72
n
74
ASP
72
B
THR
73
n
75
THR
73
B
SER
74
n
76
SER
74
B
LYS
75
n
77
LYS
75
B
ASN
76
n
78
ASN
76
B
GLN
77
n
79
GLN
77
B
VAL
78
n
80
VAL
78
B
VAL
79
n
81
VAL
79
B
LEU
80
n
82
LEU
80
B
VAL
81
n
83
VAL
81
B
MET
82
n
84
MET
82
B
THR
82
n
85
A
THR
82
B
ARG
82
n
86
B
ARG
82
B
VAL
82
n
87
C
VAL
82
B
SER
83
n
88
SER
83
B
PRO
84
n
89
PRO
84
B
VAL
85
n
90
VAL
85
B
ASP
86
n
91
ASP
86
B
THR
87
n
92
THR
87
B
ALA
88
n
93
ALA
88
B
THR
89
n
94
THR
89
B
TYR
90
n
95
TYR
90
B
PHE
91
n
96
PHE
91
B
CYS
92
n
97
CYS
92
B
ALA
93
n
98
ALA
93
B
HIS
94
n
99
HIS
94
B
ARG
95
n
100
ARG
95
B
ARG
96
n
101
ARG
96
B
GLY
97
n
102
GLY
97
B
PRO
98
n
103
PRO
98
B
THR
99
n
104
THR
99
B
THR
100
n
105
THR
100
B
LEU
100
n
106
A
LEU
100
B
PHE
100
n
107
B
PHE
100
B
GLY
100
n
108
C
GLY
100
B
VAL
100
n
109
D
VAL
100
B
PRO
100
n
110
E
PRO
100
B
ILE
100
n
111
F
ILE
100
B
ALA
100
n
112
G
ALA
100
B
ARG
100
n
113
H
ARG
100
B
GLY
100
n
114
I
GLY
100
B
PRO
100
n
115
J
PRO
100
B
VAL
100
n
116
K
VAL
100
B
ASN
100
n
117
L
ASN
100
B
ALA
100
n
118
M
ALA
100
B
MET
100
n
119
N
MET
100
B
ASP
101
n
120
ASP
101
B
VAL
102
n
121
VAL
102
B
TRP
103
n
122
TRP
103
B
GLY
104
n
123
GLY
104
B
GLN
105
n
124
GLN
105
B
GLY
106
n
125
GLY
106
B
ILE
107
n
126
ILE
107
B
THR
108
n
127
THR
108
B
VAL
109
n
128
VAL
109
B
THR
110
n
129
THR
110
B
ILE
111
n
130
ILE
111
B
SER
112
n
131
SER
112
B
SER
113
n
132
SER
113
B
THR
114
n
133
THR
114
B
SER
115
n
134
SER
115
B
THR
116
n
135
THR
116
B
LYS
117
n
136
LYS
117
B
GLY
118
n
137
GLY
118
B
PRO
119
n
138
PRO
119
B
SER
120
n
139
SER
120
B
VAL
121
n
140
VAL
121
B
PHE
122
n
141
PHE
122
B
PRO
123
n
142
PRO
123
B
LEU
124
n
143
LEU
124
B
ALA
125
n
144
ALA
125
B
PRO
126
n
145
PRO
126
B
SER
127
n
146
SER
127
B
n
147
128
B
n
148
129
B
n
149
130
B
n
150
131
B
n
151
132
B
n
152
133
B
GLY
134
n
153
GLY
134
B
ALA
135
n
154
THR
135
B
ALA
136
n
155
ALA
136
B
ALA
137
n
156
ALA
137
B
LEU
138
n
157
LEU
138
B
GLY
139
n
158
GLY
139
B
CYS
140
n
159
CYS
140
B
LEU
141
n
160
LEU
141
B
VAL
142
n
161
VAL
142
B
LYS
143
n
162
LYS
143
B
ASP
144
n
163
ASP
144
B
TYR
145
n
164
TYR
145
B
PHE
146
n
165
PHE
146
B
PRO
147
n
166
PRO
147
B
GLU
148
n
167
GLU
148
B
PRO
149
n
168
PRO
149
B
VAL
150
n
169
VAL
150
B
THR
151
n
170
THR
151
B
VAL
152
n
171
VAL
152
B
SER
153
n
172
SER
153
B
TRP
154
n
173
TRP
154
B
ASN
155
n
174
ASN
155
B
SER
156
n
175
SER
156
B
GLY
157
n
176
GLY
157
B
ALA
158
n
177
ALA
158
B
LEU
159
n
178
LEU
159
B
THR
160
n
179
THR
160
B
SER
161
n
180
SER
161
B
GLY
162
n
181
GLY
162
B
VAL
163
n
182
VAL
163
B
HIS
164
n
183
HIS
164
B
THR
165
n
184
THR
165
B
PHE
166
n
185
PHE
166
B
PRO
167
n
186
PRO
167
B
ALA
168
n
187
ALA
168
B
VAL
169
n
188
VAL
169
B
LEU
170
n
189
LEU
170
B
GLN
171
n
190
GLN
171
B
SER
172
n
191
SER
172
B
SER
173
n
192
SER
173
B
GLY
174
n
193
GLY
174
B
LEU
175
n
194
LEU
175
B
TYR
176
n
195
TYR
176
B
SER
177
n
196
SER
177
B
LEU
178
n
197
LEU
178
B
SER
179
n
198
SER
179
B
SER
180
n
199
SER
180
B
VAL
181
n
200
VAL
181
B
VAL
182
n
201
VAL
182
B
THR
183
n
202
THR
183
B
VAL
184
n
203
VAL
184
B
PRO
185
n
204
PRO
185
B
SER
186
n
205
SER
186
B
SER
187
n
206
SER
187
B
SER
188
n
207
SER
188
B
n
208
189
B
n
209
190
B
THR
191
n
210
THR
191
B
GLN
192
n
211
GLN
192
B
THR
193
n
212
THR
193
B
TYR
194
n
213
TYR
194
B
THR
195
n
214
THR
195
B
CYS
196
n
215
CYS
196
B
ASN
197
n
216
ASN
197
B
VAL
198
n
217
VAL
198
B
ASN
199
n
218
ASN
199
B
HIS
200
n
219
HIS
200
B
LYS
201
n
220
LYS
201
B
PRO
202
n
221
PRO
202
B
SER
203
n
222
SER
203
B
ASN
204
n
223
ASN
204
B
THR
205
n
224
THR
205
B
LYS
206
n
225
LYS
206
B
VAL
207
n
226
VAL
207
B
ASP
208
n
227
ASP
208
B
LYS
209
n
228
LYS
209
B
ARG
210
n
229
ARG
210
B
VAL
211
n
230
VAL
211
B
GLU
212
n
231
GLU
212
B
PRO
213
n
232
PRO
213
B
LYS
214
n
233
LYS
214
B
SER
215
n
234
SER
215
B
CYS
216
n
235
CYS
216
B
n
236
217
B
n
237
218
B
GLU
1
n
1
GLU
1
C
LEU
2
n
2
LEU
2
C
ASP
3
n
3
ASP
3
C
NRG
4
n
4
NRG
4
C
TRP
5
n
5
TRP
5
C
ALA
6
n
6
ALA
6
C
SER
7
n
7
SER
7
C
author_and_software_defined_assembly
PISA
3
trimeric
5040
-23
20190
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
THR
5
A
N
THR
5
A
O
ARG
24
A
O
ARG
24
A
N
ILE
21
A
N
ILE
21
A
O
LEU
73
A
O
LEU
73
A
O
THR
74
A
O
THR
74
A
N
SER
63
A
N
SER
63
A
N
LEU
11
A
N
LEU
11
A
O
ARG
103
A
O
ARG
103
A
O
THR
102
A
O
THR
102
A
N
TYR
86
A
N
TYR
86
A
O
THR
85
A
O
THR
85
A
N
GLN
38
A
N
GLN
38
A
N
TRP
35
A
N
TRP
35
A
O
LEU
47
A
O
LEU
47
A
N
TYR
49
A
N
TYR
49
A
O
SER
53
A
O
SER
53
A
N
PHE
118
A
N
PHE
118
A
O
VAL
133
A
O
VAL
133
A
N
VAL
132
A
N
VAL
132
A
O
LEU
179
A
O
LEU
179
A
O
THR
178
A
O
THR
178
A
N
GLN
160
A
N
GLN
160
A
O
ALA
153
A
O
ALA
153
A
N
VAL
150
A
N
VAL
150
A
N
LYS
149
A
N
LYS
149
A
O
GLU
193
A
O
GLU
193
A
N
VAL
196
A
N
VAL
196
A
O
VAL
205
A
O
VAL
205
B
N
LYS
5
B
N
LYS
5
B
O
SER
23
B
O
SER
23
B
N
LEU
18
B
N
LEU
18
B
O
MET
82
B
O
MET
84
B
O
VAL
81
B
O
VAL
83
B
N
THR
68
B
N
THR
70
B
N
VAL
12
B
N
VAL
12
B
O
THR
110
B
O
THR
129
B
O
ILE
107
B
O
ILE
126
B
N
TYR
90
B
N
TYR
95
B
O
PHE
91
B
O
PHE
96
B
N
ILE
37
B
N
ILE
39
B
N
ARG
38
B
N
ARG
40
B
O
GLU
46
B
O
GLU
48
B
N
ILE
50
B
N
ILE
52
B
O
ARG
58
B
O
ARG
60
B
N
VAL
12
B
N
VAL
12
B
O
THR
110
B
O
THR
129
B
O
ILE
107
B
O
ILE
126
B
N
TYR
90
B
N
TYR
95
B
N
HIS
94
B
N
HIS
99
B
O
VAL
102
B
O
VAL
121
B
N
THR
99
B
N
THR
104
F
B
O
ILE
100
B
O
ILE
111
B
N
PHE
122
B
N
PHE
141
B
O
LEU
141
B
O
LEU
160
B
N
TYR
145
B
N
TYR
164
B
O
TYR
176
B
O
TYR
195
B
O
VAL
181
B
O
VAL
200
B
N
HIS
164
B
N
HIS
183
B
N
PHE
122
B
N
PHE
141
B
O
LEU
141
B
O
LEU
160
B
N
TYR
145
B
N
TYR
164
B
O
TYR
176
B
O
TYR
195
B
O
SER
177
B
O
SER
196
B
N
VAL
169
B
N
VAL
188
B
N
SER
153
B
N
SER
172
B
O
ASN
197
B
O
ASN
216
B
N
VAL
198
B
N
VAL
217
B
O
VAL
207
B
O
VAL
226
1
B
OG
SER
127
B
OG
SER
146
1
Y
1
B
OG1
THR
135
B
OG1
THR
154
1
Y
1
B
CG2
THR
135
B
CG2
THR
154
1
Y
1
B
SER
128
B
SER
147
1
Y
1
B
LYS
129
B
LYS
148
1
Y
1
B
SER
130
B
SER
149
1
Y
1
B
THR
131
B
THR
150
1
Y
1
B
SER
132
B
SER
151
1
Y
1
B
GLY
133
B
GLY
152
1
Y
1
B
LEU
189
B
LEU
208
1
Y
1
B
GLY
190
B
GLY
209
1
Y
1
B
ASP
217
B
ASP
236
1
Y
1
B
LYS
218
B
LYS
237
1
Y
1
17.36
2.30
115.30
132.66
B
B
B
CA
CB
CG
LEU
LEU
LEU
178
178
178
N
1
B
B
CE1
CZ
PHE
PHE
27
27
0.138
0.019
1.369
1.507
N
1
A
THR
30
52.36
-130.01
1
A
ALA
51
67.69
-40.36
1
A
THR
77
56.37
85.98
1
A
ALA
84
-163.67
-164.56
1
A
ASN
138
45.35
73.27
1
B
THR
15
79.95
-12.06
M
1
B
ALA
100
169.55
165.49
1
B
PRO
126
-61.87
-90.07
1
B
ASP
144
56.87
70.76
1
B
LYS
214
-56.90
170.32
1
B
SER
215
69.88
85.58
protein_nrg.param
protein_nrg.top
water_rep.param
37.4
-1.00
.00
.00
3.15
.00
-2.16
.236
.006
.229
.229
.229
2.24
60.89
1531
33120
30834
5.0
93.1
RANDOM
885298.40
.000000
1
OVERALL
THROUGHOUT
.0
MOLECULAR REPLACEMENT
FLAT MODEL
18.7883
.356744
.30
.29
5.00
.15
.21
2.24
60.89
222
3634
0
0
3412
.013
1.8
28.5
1.73
1
NONE
1
X-RAY DIFFRACTION
.298
.019
.283
2.38
248
4759
6
5.0
92.7
33.3
2.24
80
3IDM
33120
30834
0
0
0.66
1
93.1
2.24
2.38
0.385
92.7
data collection
MAR345
refinement
CNS
data reduction
HKL-2000
data scaling
HKL-2000
phasing
CNS
Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
ARG
79
A
ARG
79
HELX_P
A
PHE
83
A
PHE
83
5
1
5
A
SER
121
A
SER
121
HELX_P
A
LYS
126
A
LYS
126
1
2
6
A
LYS
183
A
LYS
183
HELX_P
A
LYS
188
A
LYS
188
1
3
6
B
LEU
63
B
LEU
65
HELX_P
B
THR
65
B
THR
67
5
4
3
B
SER
83
B
SER
88
HELX_P
B
THR
87
B
THR
92
5
5
5
B
ARG
100
B
ARG
113
HELX_P
B
ASN
100
B
ASN
117
5
6
5
H
L
B
SER
156
B
SER
175
HELX_P
B
ALA
158
B
ALA
177
5
7
3
B
LYS
201
B
LYS
220
HELX_P
B
ASN
204
B
ASN
223
5
8
4
disulf
2.037
A
CYS
23
A
SG
CYS
23
1_555
A
CYS
88
A
SG
CYS
88
1_555
disulf
2.022
A
CYS
134
A
SG
CYS
134
1_555
A
CYS
194
A
SG
CYS
194
1_555
disulf
2.044
B
CYS
22
B
SG
CYS
22
1_555
B
CYS
92
B
SG
CYS
97
1_555
disulf
2.028
B
CYS
140
B
SG
CYS
159
1_555
B
CYS
196
B
SG
CYS
215
1_555
covale
1.329
both
C
ASP
3
C
C
ASP
3
1_555
C
NRG
4
C
N
NRG
4
1_555
covale
1.331
both
C
NRG
4
C
C
NRG
4
1_555
C
TRP
5
C
N
TRP
5
1_555
IMMUNE SYSTEM
HIV-1, gp41, MPER, 2F5, IMMUNE SYSTEM
A
SER
7
A
SER
7
1
A
PRO
8
A
PRO
8
-0.29
A
TYR
94
A
TYR
94
1
A
PRO
95
A
PRO
95
0.09
A
TYR
140
A
TYR
140
1
A
PRO
141
A
PRO
141
0.87
B
PHE
146
B
PHE
165
1
B
PRO
147
B
PRO
166
0.07
B
GLU
148
B
GLU
167
1
B
PRO
149
B
PRO
168
0.43
3IDM
PDB
1
3IDM
ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRP
EDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGEC
3IDM
PDB
2
3IDM
RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQV
VLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPSSKSTSGGTAALGCL
VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEPKSCDK
3IDM
PDB
3
3IDM
ELD(NRG)WAS
1
214
3IDM
1
214
3IDM
A
1
1
214
1
218
3IDM
1
218
3IDM
B
2
1
237
1
7
3IDM
1
7
3IDM
C
3
1
7
4
6
4
4
4
6
4
2
4
4
3
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
4
A
LEU
4
A
SER
7
A
SER
7
A
ILE
19
A
ILE
19
A
ALA
25
A
ALA
25
A
GLU
70
A
GLU
70
A
ILE
75
A
ILE
75
A
PHE
62
A
PHE
62
A
SER
67
A
SER
67
A
SER
10
A
SER
10
A
ALA
13
A
ALA
13
A
THR
102
A
THR
102
A
VAL
106
A
VAL
106
A
THR
85
A
THR
85
A
GLN
90
A
GLN
90
A
LEU
33
A
LEU
33
A
GLN
38
A
GLN
38
A
GLN
45
A
GLN
45
A
TYR
49
A
TYR
49
A
SER
53
A
SER
53
A
LEU
54
A
LEU
54
A
SER
114
A
SER
114
A
PHE
118
A
PHE
118
A
THR
129
A
THR
129
A
PHE
139
A
PHE
139
A
TYR
173
A
TYR
173
A
SER
182
A
SER
182
A
SER
159
A
SER
159
A
VAL
163
A
VAL
163
A
ALA
153
A
ALA
153
A
LEU
154
A
LEU
154
A
LYS
145
A
LYS
145
A
VAL
150
A
VAL
150
A
VAL
191
A
VAL
191
A
THR
197
A
THR
197
A
VAL
205
A
VAL
205
A
ASN
210
A
ASN
210
B
THR
3
B
THR
3
B
SER
7
B
SER
7
B
LEU
18
B
LEU
18
B
SER
25
B
SER
25
B
GLN
77
B
GLN
79
B
MET
82
B
MET
84
B
LEU
67
B
LEU
69
B
ASP
72
B
ASP
74
B
LEU
11
B
LEU
11
B
VAL
12
B
VAL
12
B
ILE
107
B
ILE
126
B
ILE
111
B
ILE
130
B
ALA
88
B
ALA
93
B
ARG
95
B
ARG
100
B
GLY
35
B
GLY
35
B
GLN
39
B
GLN
41
B
GLU
46
B
GLU
48
B
TYR
52
B
TYR
54
B
LYS
57
B
LYS
59
B
TYR
59
B
TYR
61
B
LEU
11
B
LEU
11
B
VAL
12
B
VAL
12
B
ILE
107
B
ILE
126
B
ILE
111
B
ILE
130
B
ALA
88
B
ALA
93
B
ARG
95
B
ARG
100
B
VAL
102
B
VAL
121
B
TRP
103
B
TRP
122
B
THR
99
B
THR
104
B
LEU
100
B
LEU
106
A
B
VAL
100
B
VAL
109
B
ALA
100
B
ALA
112
D
G
B
SER
120
B
SER
139
B
LEU
124
B
LEU
143
B
THR
135
B
THR
154
B
TYR
145
B
TYR
164
B
TYR
176
B
TYR
195
B
PRO
185
B
PRO
204
B
VAL
163
B
VAL
182
B
THR
165
B
THR
184
B
SER
120
B
SER
139
B
LEU
124
B
LEU
143
B
THR
135
B
THR
154
B
TYR
145
B
TYR
164
B
TYR
176
B
TYR
195
B
PRO
185
B
PRO
204
B
VAL
169
B
VAL
188
B
LEU
170
B
LEU
189
B
THR
151
B
THR
170
B
TRP
154
B
TRP
173
B
TYR
194
B
TYR
213
B
HIS
200
B
HIS
219
B
THR
205
B
THR
224
B
VAL
211
B
VAL
230
19
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