0.013063
0.007542
0.000000
0.000000
0.015084
0.000000
0.000000
0.000000
0.010700
0.00000
0.00000
0.00000
Tyndall, J.D.
Martin, J.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
76.550
76.550
93.460
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
C25 H33 N O3
395.534
6-PHENYL-4(R)-(7-PHENYL-HEPTANOYLAMINO)-HEXANOIC ACID
non-polymer
Ca 2
40.078
CALCIUM ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
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
C
N
75
N
C
N
76
N
C
Y
77
N
C
Y
78
N
C
Y
79
N
C
Y
80
N
C
Y
81
N
C
Y
82
N
C
N
83
N
C
N
84
N
O
N
85
N
C
N
86
N
C
N
87
N
C
N
88
N
N
N
89
N
C
N
90
R
C
N
91
N
C
N
92
N
C
Y
93
N
C
Y
94
N
C
Y
95
N
C
Y
96
N
C
Y
97
N
C
Y
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
H
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
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
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
H
N
135
N
H
N
136
N
CA
N
137
N
N
N
138
R
C
N
139
N
C
N
140
N
O
N
141
N
C
N
142
N
S
N
143
N
O
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
N
N
152
S
C
N
153
N
C
N
154
N
O
N
155
N
C
N
156
N
C
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
O
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
O
N
179
N
O
N
180
N
O
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
N
N
191
N
C
N
192
N
C
N
193
N
O
N
194
N
O
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
N
N
201
S
C
N
202
N
C
N
203
N
O
N
204
N
C
Y
205
N
C
Y
206
N
N
Y
207
N
C
Y
208
N
C
Y
209
N
N
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
O
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
S
C
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
O
N
233
N
H
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
N
N
247
S
C
N
248
N
C
N
249
N
O
N
250
N
C
N
251
N
C
N
252
N
C
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
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
C
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
N
N
277
N
O
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
H
N
292
N
H
N
293
N
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
C
N
299
N
S
N
300
N
C
N
301
N
O
N
302
N
H
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
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
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
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
C
N
342
N
C
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
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
N
358
N
O
N
359
N
O
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
R
C
N
372
N
O
N
373
N
C
N
374
N
O
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
N
N
385
S
C
N
386
N
C
N
387
N
O
N
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
N
395
N
O
N
396
N
O
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
N
N
409
S
C
N
410
N
C
N
411
N
O
N
412
N
C
N
413
N
C
N
414
N
C
N
415
N
O
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
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
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
Y
80
N
doub
Y
81
N
sing
Y
82
N
sing
N
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
doub
N
87
N
sing
Y
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
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
sing
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
sing
N
115
N
sing
Y
116
N
doub
Y
117
N
sing
Y
118
N
sing
N
119
N
sing
Y
120
N
doub
N
121
N
sing
Y
122
N
doub
N
123
N
sing
Y
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
doub
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
doub
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
doub
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
doub
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
Y
203
N
sing
Y
204
N
doub
Y
205
N
doub
N
206
N
sing
Y
207
N
sing
N
208
N
sing
Y
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
doub
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
doub
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
doub
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
Y
311
N
doub
Y
312
N
sing
Y
313
N
sing
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
317
N
doub
N
318
N
sing
Y
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
doub
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
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
doub
N
347
N
sing
N
348
N
sing
N
349
N
sing
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
doub
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
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
doub
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
Y
380
N
doub
Y
381
N
sing
Y
382
N
sing
N
383
N
sing
Y
384
N
doub
N
385
N
sing
Y
386
N
doub
N
387
N
sing
Y
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
doub
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
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
GE
Chembiochem
1439-4227
4
181
185
10.1002/cbic.200390029
12616631
D-Tyrosine as a chiral precusor to potent inhibitors of human nonpancreatic secretory phospholipase A2 (IIa) with antiinflammatory activity.
2003
GE
Chembiochem
1439-4227
4
181
185
10.1002/cbic.200390029
D-Tyrosine as a Chiral Precusor to Potent Inhibitors of Human Nonpancreatic Secretory Phospholipase A2 (IIa) with Antiinflammatory Activity
2003
10.2210/pdb1kqu/pdb
pdb_00001kqu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
YALE MIRRORS
IMAGE PLATE
1999-01-04
RIGAKU RAXIS IIC
Ni FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU RU200
13945.012
Phospholipase A2, membrane associated
3.1.1.4
1
man
polymer
40.078
CALCIUM ION
2
syn
non-polymer
395.534
6-PHENYL-4(R)-(7-PHENYL-HEPTANOYLAMINO)-HEXANOIC ACID
1
syn
non-polymer
18.015
water
75
nat
water
Phosphatidylcholine 2-acylhydrolase, Group IIA phospholipase A2, GIIC sPLA2, Non-pancreatic secretory phospholipase A2, NPS-PLA2
no
no
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ
DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ
DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
1
2.83
56.60
VAPOR DIFFUSION, SITTING DROP
7.8
sodium Chloride, Calcium Chloride, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
293.0
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-11-11
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR
HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR
HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR
RCSB
Y
RCSB
2002-01-07
REL
CA
CALCIUM ION
BR4
6-PHENYL-4(R)-(7-PHENYL-HEPTANOYLAMINO)-HEXANOIC ACID
HOH
water
1POD
PDB ENTRY 1POD
PDB
experimental model
CA
301
2
CA
CA
301
A
CA
302
2
CA
CA
302
A
BR4
501
3
BR4
BR4
501
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
207
4
HOH
HOH
207
A
HOH
208
4
HOH
HOH
208
A
HOH
209
4
HOH
HOH
209
A
HOH
210
4
HOH
HOH
210
A
HOH
211
4
HOH
HOH
211
A
HOH
212
4
HOH
HOH
212
A
HOH
213
4
HOH
HOH
213
A
HOH
214
4
HOH
HOH
214
A
HOH
215
4
HOH
HOH
215
A
HOH
216
4
HOH
HOH
216
A
HOH
217
4
HOH
HOH
217
A
HOH
218
4
HOH
HOH
218
A
HOH
219
4
HOH
HOH
219
A
HOH
220
4
HOH
HOH
220
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
242
4
HOH
HOH
242
A
HOH
243
4
HOH
HOH
243
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
HOH
246
4
HOH
HOH
246
A
HOH
247
4
HOH
HOH
247
A
HOH
248
4
HOH
HOH
248
A
HOH
249
4
HOH
HOH
249
A
HOH
250
4
HOH
HOH
250
A
HOH
251
4
HOH
HOH
251
A
HOH
252
4
HOH
HOH
252
A
HOH
253
4
HOH
HOH
253
A
HOH
254
4
HOH
HOH
254
A
HOH
255
4
HOH
HOH
255
A
HOH
256
4
HOH
HOH
256
A
HOH
257
4
HOH
HOH
257
A
HOH
258
4
HOH
HOH
258
A
HOH
259
4
HOH
HOH
259
A
HOH
260
4
HOH
HOH
260
A
HOH
261
4
HOH
HOH
261
A
HOH
262
4
HOH
HOH
262
A
HOH
263
4
HOH
HOH
263
A
HOH
264
4
HOH
HOH
264
A
HOH
265
4
HOH
HOH
265
A
HOH
266
4
HOH
HOH
266
A
HOH
267
4
HOH
HOH
267
A
HOH
268
4
HOH
HOH
268
A
HOH
269
4
HOH
HOH
269
A
HOH
270
4
HOH
HOH
270
A
HOH
271
4
HOH
HOH
271
A
HOH
272
4
HOH
HOH
272
A
HOH
273
4
HOH
HOH
273
A
HOH
274
4
HOH
HOH
274
A
HOH
275
4
HOH
HOH
275
A
ASN
1
n
1
ASN
1
A
LEU
2
n
2
LEU
2
A
VAL
3
n
3
VAL
3
A
ASN
4
n
4
ASN
4
A
PHE
5
n
5
PHE
5
A
HIS
6
n
6
HIS
6
A
ARG
7
n
7
ARG
7
A
MET
8
n
8
MET
8
A
ILE
9
n
9
ILE
9
A
LYS
10
n
10
LYS
10
A
LEU
11
n
11
LEU
11
A
THR
12
n
12
THR
12
A
THR
13
n
13
THR
13
A
GLY
14
n
14
GLY
14
A
LYS
15
n
15
LYS
15
A
GLU
16
n
16
GLU
16
A
ALA
17
n
17
ALA
17
A
ALA
18
n
18
ALA
18
A
LEU
19
n
19
LEU
19
A
SER
20
n
20
SER
20
A
TYR
21
n
21
TYR
21
A
GLY
22
n
22
GLY
22
A
PHE
23
n
23
PHE
23
A
TYR
24
n
24
TYR
24
A
GLY
25
n
25
GLY
25
A
CYS
26
n
26
CYS
26
A
HIS
27
n
27
HIS
27
A
CYS
28
n
28
CYS
28
A
GLY
29
n
29
GLY
29
A
VAL
30
n
30
VAL
30
A
GLY
31
n
31
GLY
31
A
GLY
32
n
32
GLY
32
A
ARG
33
n
33
ARG
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
PRO
36
n
36
PRO
36
A
LYS
37
n
37
LYS
37
A
ASP
38
n
38
ASP
38
A
ALA
39
n
39
ALA
39
A
THR
40
n
40
THR
40
A
ASP
41
n
41
ASP
41
A
ARG
42
n
42
ARG
42
A
CYS
43
n
43
CYS
43
A
CYS
44
n
44
CYS
44
A
VAL
45
n
45
VAL
45
A
THR
46
n
46
THR
46
A
HIS
47
n
47
HIS
47
A
ASP
48
n
48
ASP
48
A
CYS
49
n
49
CYS
49
A
CYS
50
n
50
CYS
50
A
TYR
51
n
51
TYR
51
A
LYS
52
n
52
LYS
52
A
ARG
53
n
53
ARG
53
A
LEU
54
n
54
LEU
54
A
GLU
55
n
55
GLU
55
A
ALA
56
n
56
LYS
56
A
ARG
57
n
57
ARG
57
A
GLY
58
n
58
GLY
58
A
CYS
59
n
59
CYS
59
A
GLY
60
n
60
GLY
60
A
THR
61
n
61
THR
61
A
LYS
62
n
62
LYS
62
A
PHE
63
n
63
PHE
63
A
LEU
64
n
64
LEU
64
A
SER
65
n
65
SER
65
A
TYR
66
n
66
TYR
66
A
LYS
67
n
67
LYS
67
A
PHE
68
n
68
PHE
68
A
SER
69
n
69
SER
69
A
ASN
70
n
70
ASN
70
A
SER
71
n
71
SER
71
A
GLY
72
n
72
GLY
72
A
SER
73
n
73
SER
73
A
ALA
74
n
74
ARG
74
A
ILE
75
n
75
ILE
75
A
THR
76
n
76
THR
76
A
CYS
77
n
77
CYS
77
A
ALA
78
n
78
ALA
78
A
ALA
79
n
79
LYS
79
A
GLN
80
n
80
GLN
80
A
ASP
81
n
81
ASP
81
A
SER
82
n
82
SER
82
A
CYS
83
n
83
CYS
83
A
ARG
84
n
84
ARG
84
A
SER
85
n
85
SER
85
A
GLN
86
n
86
GLN
86
A
LEU
87
n
87
LEU
87
A
CYS
88
n
88
CYS
88
A
GLU
89
n
89
GLU
89
A
CYS
90
n
90
CYS
90
A
ASP
91
n
91
ASP
91
A
LYS
92
n
92
LYS
92
A
ALA
93
n
93
ALA
93
A
ALA
94
n
94
ALA
94
A
ALA
95
n
95
ALA
95
A
THR
96
n
96
THR
96
A
CYS
97
n
97
CYS
97
A
PHE
98
n
98
PHE
98
A
ALA
99
n
99
ALA
99
A
ARG
100
n
100
ARG
100
A
ASN
101
n
101
ASN
101
A
LYS
102
n
102
LYS
102
A
THR
103
n
103
THR
103
A
THR
104
n
104
THR
104
A
TYR
105
n
105
TYR
105
A
ASN
106
n
106
ASN
106
A
LYS
107
n
107
LYS
107
A
ALA
108
n
108
LYS
108
A
TYR
109
n
109
TYR
109
A
GLN
110
n
110
GLN
110
A
TYR
111
n
111
TYR
111
A
TYR
112
n
112
TYR
112
A
SER
113
n
113
SER
113
A
ASN
114
n
114
ASN
114
A
LYS
115
n
115
LYS
115
A
HIS
116
n
116
HIS
116
A
CYS
117
n
117
CYS
117
A
ARG
118
n
118
ARG
118
A
GLY
119
n
119
GLY
119
A
SER
120
n
120
SER
120
A
THR
121
n
121
THR
121
A
PRO
122
n
122
PRO
122
A
ALA
123
n
123
ARG
123
A
CYS
124
n
124
CYS
124
A
author_defined_assembly
1
monomeric
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
A
GLY
25
A
O
GLY
25
1_555
93.2
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
A
TYR
112
A
O
TYR
112
1_555
89.5
A
GLY
25
A
O
GLY
25
1_555
A
CA
302
C
CA
CA
1_555
A
TYR
112
A
O
TYR
112
1_555
90.8
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
A
ASN
114
A
OD1
ASN
114
1_555
173.1
A
GLY
25
A
O
GLY
25
1_555
A
CA
302
C
CA
CA
1_555
A
ASN
114
A
OD1
ASN
114
1_555
86.0
A
TYR
112
A
O
TYR
112
1_555
A
CA
302
C
CA
CA
1_555
A
ASN
114
A
OD1
ASN
114
1_555
97.3
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
225
E
O
HOH
1_555
88.1
A
GLY
25
A
O
GLY
25
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
225
E
O
HOH
1_555
177.0
A
TYR
112
A
O
TYR
112
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
225
E
O
HOH
1_555
91.9
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
225
E
O
HOH
1_555
92.4
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
232
E
O
HOH
1_555
82.4
A
GLY
25
A
O
GLY
25
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
232
E
O
HOH
1_555
86.3
A
TYR
112
A
O
TYR
112
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
232
E
O
HOH
1_555
171.2
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
232
E
O
HOH
1_555
90.7
A
HOH
225
E
O
HOH
1_555
A
CA
302
C
CA
CA
1_555
A
HOH
232
E
O
HOH
1_555
91.2
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
93.9
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
GLY
31
A
O
GLY
31
1_555
86.1
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
A
GLY
31
A
O
GLY
31
1_555
81.8
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD1
ASP
48
1_555
94.9
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD1
ASP
48
1_555
146.4
A
GLY
31
A
O
GLY
31
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD1
ASP
48
1_555
131.1
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
93.1
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
161.6
A
GLY
31
A
O
GLY
31
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
81.8
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
49.3
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
84.7
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
75.3
A
GLY
31
A
O
GLY
31
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
154.6
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
73.3
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
122.3
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
171.6
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
85.2
A
GLY
31
A
O
GLY
31
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
85.5
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
90.4
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
85.4
A
BR4
501
D
O1
BR4
1_555
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
103.1
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
SER
69
A
N
SER
69
A
O
THR
76
A
O
THR
76
1
A
HOH
268
E
HOH
1
A
CG
LYS
56
A
CG
LYS
56
1
Y
1
A
CD
LYS
56
A
CD
LYS
56
1
Y
1
A
CE
LYS
56
A
CE
LYS
56
1
Y
1
A
NZ
LYS
56
A
NZ
LYS
56
1
Y
1
A
CG
ARG
74
A
CG
ARG
74
1
Y
1
A
CD
ARG
74
A
CD
ARG
74
1
Y
1
A
NE
ARG
74
A
NE
ARG
74
1
Y
1
A
CZ
ARG
74
A
CZ
ARG
74
1
Y
1
A
NH1
ARG
74
A
NH1
ARG
74
1
Y
1
A
NH2
ARG
74
A
NH2
ARG
74
1
Y
1
A
CG
LYS
79
A
CG
LYS
79
1
Y
1
A
CD
LYS
79
A
CD
LYS
79
1
Y
1
A
CE
LYS
79
A
CE
LYS
79
1
Y
1
A
NZ
LYS
79
A
NZ
LYS
79
1
Y
1
A
CG
LYS
108
A
CG
LYS
108
1
Y
1
A
CD
LYS
108
A
CD
LYS
108
1
Y
1
A
CE
LYS
108
A
CE
LYS
108
1
Y
1
A
NZ
LYS
108
A
NZ
LYS
108
1
Y
1
A
CG
ARG
123
A
CG
ARG
123
1
Y
1
A
CD
ARG
123
A
CD
ARG
123
1
Y
1
A
NE
ARG
123
A
NE
ARG
123
1
Y
1
A
CZ
ARG
123
A
CZ
ARG
123
1
Y
1
A
NH1
ARG
123
A
NH1
ARG
123
1
Y
1
A
NH2
ARG
123
A
NH2
ARG
123
1
Y
1
A
THR
61
-132.23
-90.38
1
A
SER
71
-109.43
64.83
1
A
LYS
79
B
-31.33
-74.37
1
A
GLN
80
B
27.70
165.39
1
A
TYR
111
-115.90
56.61
33.4
0.00
0.00
0.00
0.00
0.00
0.00
0.24
0.008
0.209
0.209
2.10
8.00
955
9218
9218
10.4
94.8
RANDOM
10000000.00
0.001000
1
RESTRAINED
THROUGHOUT
0.0
FOURIER SYNTHESIS
PDB ENTRY 1POD
Engh & Huber
0.29
0.25
5.00
0.27
0.27
2.10
8.00
75
1065
31
0
959
0.006
1.2
23.1
1.01
1.36
1.50
2.29
2.00
2.23
2.00
3.37
2.50
0.295
0.024
0.276
2.23
149
1318
6
10.2
92.8
20.8
2.10
50.00
1KQU
9371
9218
0
0.091
1
19.3
5.93
93.8
0.346
2.10
2.18
3.18
898
92.5
data reduction
DENZO
data scaling
SCALEPACK
model building
X-PLOR
refinement
X-PLOR
3.851
phasing
X-PLOR
Human phospholipase A2 complexed with a substrate anologue
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASN
1
A
ASN
1
HELX_P
A
GLY
14
A
GLY
14
1
1
14
A
GLU
16
A
GLU
16
HELX_P
A
TYR
21
A
TYR
21
1
2
6
A
ASP
38
A
ASP
38
HELX_P
A
ARG
57
A
ARG
57
1
3
20
A
ASP
81
A
ASP
81
HELX_P
A
ASN
101
A
ASN
101
1
4
21
A
LYS
102
A
LYS
102
HELX_P
A
TYR
105
A
TYR
105
5
5
4
A
SER
113
A
SER
113
HELX_P
A
CYS
117
A
CYS
117
5
6
5
disulf
2.024
A
CYS
26
A
SG
CYS
26
1_555
A
CYS
117
A
SG
CYS
117
1_555
disulf
2.023
A
CYS
28
A
SG
CYS
28
1_555
A
CYS
44
A
SG
CYS
44
1_555
disulf
2.024
A
CYS
43
A
SG
CYS
43
1_555
A
CYS
97
A
SG
CYS
97
1_555
disulf
2.034
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
124
A
SG
CYS
124
1_555
disulf
2.026
A
CYS
50
A
SG
CYS
50
1_555
A
CYS
90
A
SG
CYS
90
1_555
disulf
2.029
A
CYS
59
A
SG
CYS
59
1_555
A
CYS
83
A
SG
CYS
83
1_555
disulf
2.026
A
CYS
77
A
SG
CYS
77
1_555
A
CYS
88
A
SG
CYS
88
1_555
metalc
2.559
A
PHE
23
A
O
PHE
23
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.454
A
GLY
25
A
O
GLY
25
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.402
A
HIS
27
A
O
HIS
27
1_555
A
CA
301
B
CA
CA
1_555
metalc
2.457
A
GLY
29
A
O
GLY
29
1_555
A
CA
301
B
CA
CA
1_555
metalc
2.450
A
GLY
31
A
O
GLY
31
1_555
A
CA
301
B
CA
CA
1_555
metalc
2.691
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
metalc
2.534
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
301
B
CA
CA
1_555
metalc
2.459
A
TYR
112
A
O
TYR
112
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.449
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.451
A
HOH
225
E
O
HOH
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.329
A
HOH
232
E
O
HOH
1_555
A
CA
302
C
CA
CA
1_555
metalc
2.479
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O1
BR4
1_555
metalc
2.471
A
CA
301
B
CA
CA
1_555
A
BR4
501
D
O2
BR4
1_555
HYDROLASE
Phospholipase A2, Inhibitor, HYDROLASE
PA2GA_HUMAN
UNP
1
1
P14555
MKTLLLLAVIMIFGLLQAHGNLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCG
TKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC
21
144
1KQU
1
124
P14555
A
1
1
124
2
anti-parallel
A
PHE
68
A
PHE
68
A
ASN
70
A
ASN
70
A
ILE
75
A
ILE
75
A
CYS
77
A
CYS
77
BINDING SITE FOR RESIDUE CA A 301
A
CA
301
Software
5
BINDING SITE FOR RESIDUE CA A 302
A
CA
302
Software
6
BINDING SITE FOR RESIDUE BR4 A 501
A
BR4
501
Software
15
A
HIS
27
A
HIS
27
5
1_555
A
GLY
29
A
GLY
29
5
1_555
A
GLY
31
A
GLY
31
5
1_555
A
ASP
48
A
ASP
48
5
1_555
A
BR4
501
D
BR4
5
1_555
A
PHE
23
A
PHE
23
6
1_555
A
GLY
25
A
GLY
25
6
1_555
A
TYR
112
A
TYR
112
6
1_555
A
ASN
114
A
ASN
114
6
1_555
A
HOH
225
E
HOH
6
1_555
A
HOH
232
E
HOH
6
1_555
A
LEU
2
A
LEU
2
15
1_555
A
ALA
17
A
ALA
17
15
1_555
A
LEU
19
A
LEU
19
15
12_556
A
TYR
21
A
TYR
21
15
1_555
A
PHE
23
A
PHE
23
15
12_556
A
HIS
27
A
HIS
27
15
1_555
A
GLY
29
A
GLY
29
15
1_555
A
VAL
30
A
VAL
30
15
1_555
A
GLY
31
A
GLY
31
15
1_555
A
HIS
47
A
HIS
47
15
1_555
A
ASP
48
A
ASP
48
15
1_555
A
TYR
51
A
TYR
51
15
1_555
A
HOH
243
E
HOH
15
1_555
A
HOH
253
E
HOH
15
1_555
A
CA
301
B
CA
15
1_555
178
P 61 2 2