0.012009
0.006933
0.000000
0.000000
0.013867
0.000000
0.000000
0.000000
0.030488
0.00000
0.00000
0.00000
Xu, S.
Gu, L.
Zhou, Y.
Lin, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
83.270
83.270
32.800
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
C4 H10 O2
90.121
1,4-BUTANEDIOL
non-polymer
Cd 2
112.411
CADMIUM 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
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
C
N
75
N
C
N
76
N
C
N
77
N
C
N
78
N
O
N
79
N
O
N
80
N
H
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
H
N
89
N
H
N
90
N
CD
N
91
N
N
N
92
R
C
N
93
N
C
N
94
N
O
N
95
N
C
N
96
N
S
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
N
N
106
S
C
N
107
N
C
N
108
N
O
N
109
N
C
N
110
N
C
N
111
N
C
N
112
N
O
N
113
N
N
N
114
N
O
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
N
N
126
S
C
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
C
N
131
N
C
N
132
N
O
N
133
N
O
N
134
N
O
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
N
C
N
146
N
C
N
147
N
O
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
N
N
155
S
C
N
156
N
C
N
157
N
O
N
158
N
C
Y
159
N
C
Y
160
N
N
Y
161
N
C
Y
162
N
C
Y
163
N
N
N
164
N
O
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
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
O
N
176
N
H
N
177
N
H
N
178
N
N
N
179
S
C
N
180
N
C
N
181
N
O
N
182
S
C
N
183
N
C
N
184
N
C
N
185
N
C
N
186
N
O
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
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
N
N
201
S
C
N
202
N
C
N
203
N
O
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
O
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
N
N
223
S
C
N
224
N
C
N
225
N
O
N
226
N
C
N
227
N
C
N
228
N
C
N
229
N
C
N
230
N
N
N
231
N
O
N
232
N
H
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
H
N
247
N
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
N
252
N
C
N
253
N
S
N
254
N
C
N
255
N
O
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
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
Y
272
N
C
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
C
N
296
N
C
N
297
N
O
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
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
R
C
N
326
N
O
N
327
N
C
N
328
N
O
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
H
N
337
N
H
N
338
N
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
N
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
N
376
N
O
N
377
N
O
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
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
N
N
390
S
C
N
391
N
C
N
392
N
O
N
393
N
C
N
394
N
C
N
395
N
C
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
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
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
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
doub
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
doub
N
113
N
sing
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
sing
N
123
N
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
doub
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
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
Y
155
N
sing
Y
156
N
doub
Y
157
N
doub
N
158
N
sing
Y
159
N
sing
N
160
N
sing
Y
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
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
doub
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
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
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
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
doub
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
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
doub
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
Y
263
N
doub
Y
264
N
sing
Y
265
N
sing
N
266
N
sing
Y
267
N
doub
N
268
N
sing
Y
269
N
doub
N
270
N
sing
Y
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
sing
N
298
N
doub
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
sing
N
311
N
doub
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
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
Y
337
N
sing
Y
338
N
sing
N
339
N
sing
Y
340
N
sing
Y
341
N
doub
N
342
N
sing
Y
343
N
doub
N
344
N
sing
Y
345
N
sing
N
346
N
sing
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
doub
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
Y
360
N
doub
Y
361
N
sing
Y
362
N
sing
N
363
N
sing
Y
364
N
doub
N
365
N
sing
Y
366
N
doub
N
367
N
sing
Y
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
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
US
Biochem.Biophys.Res.Commun.
BBRCA9
0146
0006-291X
300
271
277
10.1016/S0006-291X(02)02833-4
12504079
Structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas at 1.9A resolutio
2003
UK
J.MOL.BIOL.
JMOBAK
0070
0022-2836
255
669
676
10.1006/jmbi.1996.0054
Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution
1996
UK
TOXICON
TOXIA6
2043
0041-0101
36
875
886
10.1016/S0041-0101(97)00169-4
Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide
1998
10.2210/pdb1m8r/pdb
pdb_00001m8r
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
1
AREA DETECTOR
2001-06-14
MARRESEARCH
graphite
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
13956.688
phospholipase A2
3.1.1.4
1
nat
polymer
112.411
CADMIUM ION
1
syn
non-polymer
90.121
1,4-BUTANEDIOL
2
syn
non-polymer
18.015
water
81
nat
water
no
no
SLVQFETLIMKVAKKSGMQWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDP
CKKEICECDRAAAICFRDNLNTYNDKKYWAFGAKNCPQEESEPC
SLVQFETLIMKVAKKSGMQWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDP
CKKEICECDRAAAICFRDNLNTYNDKKYWAFGAKNCPQEESEPC
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
halys viper
Gloydius
sample
8714
Gloydius halys
venom
1
2.35
47.69
VAPOR DIFFUSION, HANGING DROP
7.4
10%(v/v) 1,4-butyldiol, 0.01M CdCl2, 0.1M Na(CH3)2AsO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
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
2003-02-11
1
1
2008-04-28
1
2
2011-07-13
1
3
2023-10-25
_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_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_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
1PSJ contains the same protein at 2.01 Resolution
1BK9 contains the same protein Modified By Pbpb
1M8S contains the same protein, crystal grown at pH 5.9
RCSB
Y
PDBJ
2002-07-25
REL
REL
CD
CADMIUM ION
BU1
1,4-BUTANEDIOL
HOH
water
1PSJ
PDB ENTRY 1PSJ
PDB
experimental model
CD
1001
2
CD
CD
1001
A
BU1
1001
3
BU1
BU1
1002
A
BU1
1002
3
BU1
BU1
1003
A
HOH
1
4
HOH
HOH
1004
A
HOH
2
4
HOH
HOH
1005
A
HOH
3
4
HOH
HOH
1006
A
HOH
4
4
HOH
HOH
1007
A
HOH
5
4
HOH
HOH
1008
A
HOH
6
4
HOH
HOH
1009
A
HOH
7
4
HOH
HOH
1010
A
HOH
8
4
HOH
HOH
1011
A
HOH
9
4
HOH
HOH
1012
A
HOH
10
4
HOH
HOH
1013
A
HOH
11
4
HOH
HOH
1014
A
HOH
12
4
HOH
HOH
1015
A
HOH
13
4
HOH
HOH
1016
A
HOH
14
4
HOH
HOH
1017
A
HOH
15
4
HOH
HOH
1018
A
HOH
16
4
HOH
HOH
1019
A
HOH
17
4
HOH
HOH
1020
A
HOH
18
4
HOH
HOH
1021
A
HOH
19
4
HOH
HOH
1022
A
HOH
20
4
HOH
HOH
1023
A
HOH
21
4
HOH
HOH
1024
A
HOH
22
4
HOH
HOH
1025
A
HOH
23
4
HOH
HOH
1026
A
HOH
24
4
HOH
HOH
1027
A
HOH
25
4
HOH
HOH
1028
A
HOH
26
4
HOH
HOH
1029
A
HOH
27
4
HOH
HOH
1030
A
HOH
28
4
HOH
HOH
1031
A
HOH
29
4
HOH
HOH
1032
A
HOH
30
4
HOH
HOH
1033
A
HOH
31
4
HOH
HOH
1034
A
HOH
32
4
HOH
HOH
1035
A
HOH
33
4
HOH
HOH
1036
A
HOH
34
4
HOH
HOH
1037
A
HOH
35
4
HOH
HOH
1038
A
HOH
36
4
HOH
HOH
1039
A
HOH
37
4
HOH
HOH
1040
A
HOH
38
4
HOH
HOH
1041
A
HOH
39
4
HOH
HOH
1042
A
HOH
40
4
HOH
HOH
1043
A
HOH
41
4
HOH
HOH
1044
A
HOH
42
4
HOH
HOH
1045
A
HOH
43
4
HOH
HOH
1046
A
HOH
44
4
HOH
HOH
1047
A
HOH
45
4
HOH
HOH
1048
A
HOH
46
4
HOH
HOH
1049
A
HOH
47
4
HOH
HOH
1050
A
HOH
48
4
HOH
HOH
1051
A
HOH
49
4
HOH
HOH
1052
A
HOH
50
4
HOH
HOH
1053
A
HOH
51
4
HOH
HOH
1054
A
HOH
52
4
HOH
HOH
1055
A
HOH
53
4
HOH
HOH
1056
A
HOH
54
4
HOH
HOH
1057
A
HOH
55
4
HOH
HOH
1058
A
HOH
56
4
HOH
HOH
1059
A
HOH
57
4
HOH
HOH
1060
A
HOH
58
4
HOH
HOH
1061
A
HOH
59
4
HOH
HOH
1062
A
HOH
60
4
HOH
HOH
1063
A
HOH
61
4
HOH
HOH
1064
A
HOH
62
4
HOH
HOH
1065
A
HOH
63
4
HOH
HOH
1066
A
HOH
64
4
HOH
HOH
1067
A
HOH
65
4
HOH
HOH
1068
A
HOH
66
4
HOH
HOH
1069
A
HOH
67
4
HOH
HOH
1070
A
HOH
68
4
HOH
HOH
1071
A
HOH
69
4
HOH
HOH
1072
A
HOH
70
4
HOH
HOH
1073
A
HOH
71
4
HOH
HOH
1074
A
HOH
72
4
HOH
HOH
1075
A
HOH
73
4
HOH
HOH
1076
A
HOH
74
4
HOH
HOH
1077
A
HOH
75
4
HOH
HOH
1078
A
HOH
76
4
HOH
HOH
1079
A
HOH
77
4
HOH
HOH
1080
A
HOH
78
4
HOH
HOH
1081
A
HOH
79
4
HOH
HOH
1082
A
HOH
80
4
HOH
HOH
1083
A
HOH
81
4
HOH
HOH
1084
A
SER
1
n
1
SER
1
A
LEU
2
n
2
LEU
2
A
VAL
3
n
3
VAL
3
A
GLN
4
n
4
GLN
4
A
PHE
5
n
5
PHE
5
A
GLU
6
n
6
GLU
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
ILE
9
n
9
ILE
9
A
MET
10
n
10
MET
10
A
LYS
11
n
11
LYS
11
A
VAL
12
n
12
VAL
12
A
ALA
13
n
13
ALA
13
A
LYS
14
n
14
LYS
14
A
LYS
16
n
15
LYS
16
A
SER
17
n
16
SER
17
A
GLY
18
n
17
GLY
18
A
MET
19
n
18
MET
19
A
GLN
20
n
19
GLN
20
A
TRP
21
n
20
TRP
21
A
TYR
22
n
21
TYR
22
A
SER
23
n
22
SER
23
A
ASN
24
n
23
ASN
24
A
TYR
25
n
24
TYR
25
A
GLY
26
n
25
GLY
26
A
CYS
27
n
26
CYS
27
A
TYR
28
n
27
TYR
28
A
CYS
29
n
28
CYS
29
A
GLY
30
n
29
GLY
30
A
TRP
31
n
30
TRP
31
A
GLY
32
n
31
GLY
32
A
GLY
33
n
32
GLY
33
A
GLN
34
n
33
GLN
34
A
GLY
35
n
34
GLY
35
A
ARG
36
n
35
ARG
36
A
PRO
37
n
36
PRO
37
A
GLN
38
n
37
GLN
38
A
ASP
39
n
38
ASP
39
A
ALA
40
n
39
ALA
40
A
THR
41
n
40
THR
41
A
ASP
42
n
41
ASP
42
A
ARG
43
n
42
ARG
43
A
CYS
44
n
43
CYS
44
A
CYS
45
n
44
CYS
45
A
PHE
46
n
45
PHE
46
A
VAL
47
n
46
VAL
47
A
HIS
48
n
47
HIS
48
A
ASP
49
n
48
ASP
49
A
CYS
50
n
49
CYS
50
A
CYS
51
n
50
CYS
51
A
TYR
52
n
51
TYR
52
A
GLY
53
n
52
GLY
53
A
LYS
54
n
53
LYS
54
A
VAL
55
n
54
VAL
55
A
THR
56
n
55
THR
56
A
GLY
59
n
56
GLY
59
A
CYS
61
n
57
CYS
61
A
ASP
67
n
58
ASP
67
A
PRO
68
n
59
PRO
68
A
LYS
69
n
60
LYS
69
A
MET
70
n
61
MET
70
A
ASP
71
n
62
ASP
71
A
VAL
72
n
63
VAL
72
A
TYR
73
n
64
TYR
73
A
SER
74
n
65
SER
74
A
PHE
75
n
66
PHE
75
A
SER
76
n
67
SER
76
A
GLU
77
n
68
GLU
77
A
GLU
78
n
69
GLU
78
A
ASN
79
n
70
ASN
79
A
GLY
80
n
71
GLY
80
A
ASP
81
n
72
ASP
81
A
ILE
82
n
73
ILE
82
A
VAL
83
n
74
VAL
83
A
CYS
84
n
75
CYS
84
A
GLY
85
n
76
GLY
85
A
GLY
86
n
77
GLY
86
A
ASP
88
n
78
ASP
88
A
ASP
89
n
79
ASP
89
A
PRO
90
n
80
PRO
90
A
CYS
91
n
81
CYS
91
A
LYS
92
n
82
LYS
92
A
LYS
93
n
83
LYS
93
A
GLU
94
n
84
GLU
94
A
ILE
95
n
85
ILE
95
A
CYS
96
n
86
CYS
96
A
GLU
97
n
87
GLU
97
A
CYS
98
n
88
CYS
98
A
ASP
99
n
89
ASP
99
A
ARG
100
n
90
ARG
100
A
ALA
101
n
91
ALA
101
A
ALA
102
n
92
ALA
102
A
ALA
103
n
93
ALA
103
A
ILE
104
n
94
ILE
104
A
CYS
105
n
95
CYS
105
A
PHE
106
n
96
PHE
106
A
ARG
107
n
97
ARG
107
A
ASP
108
n
98
ASP
108
A
ASN
109
n
99
ASN
109
A
LEU
110
n
100
LEU
110
A
ASN
111
n
101
ASN
111
A
THR
112
n
102
THR
112
A
TYR
113
n
103
TYR
113
A
ASN
114
n
104
ASN
114
A
ASP
115
n
105
ASP
115
A
LYS
116
n
106
LYS
116
A
LYS
117
n
107
LYS
117
A
TYR
118
n
108
TYR
118
A
TRP
119
n
109
TRP
119
A
ALA
120
n
110
ALA
120
A
PHE
121
n
111
PHE
121
A
GLY
122
n
112
GLY
122
A
ALA
123
n
113
ALA
123
A
LYS
124
n
114
LYS
124
A
ASN
125
n
115
ASN
125
A
CYS
126
n
116
CYS
126
A
PRO
127
n
117
PRO
127
A
GLN
128
n
118
GLN
128
A
GLU
129
n
119
GLU
129
A
GLU
130
n
120
GLU
130
A
SER
131
n
121
SER
131
A
GLU
132
n
122
GLU
132
A
PRO
133
n
123
PRO
133
A
CYS
134
n
124
CYS
134
A
author_defined_assembly
1
monomeric
A
TYR
28
A
O
TYR
27
1_555
A
CD
1001
B
CD
CD
1_555
A
GLY
30
A
O
GLY
29
1_555
87.9
A
TYR
28
A
O
TYR
27
1_555
A
CD
1001
B
CD
CD
1_555
A
GLY
32
A
O
GLY
31
1_555
101.2
A
GLY
30
A
O
GLY
29
1_555
A
CD
1001
B
CD
CD
1_555
A
GLY
32
A
O
GLY
31
1_555
90.4
A
TYR
28
A
O
TYR
27
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD1
ASP
48
1_555
117.3
A
GLY
30
A
O
GLY
29
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD1
ASP
48
1_555
120.6
A
GLY
32
A
O
GLY
31
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD1
ASP
48
1_555
129.6
A
TYR
28
A
O
TYR
27
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD2
ASP
48
1_555
110.7
A
GLY
30
A
O
GLY
29
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD2
ASP
48
1_555
160.5
A
GLY
32
A
O
GLY
31
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD2
ASP
48
1_555
91.8
A
ASP
49
A
OD1
ASP
48
1_555
A
CD
1001
B
CD
CD
1_555
A
ASP
49
A
OD2
ASP
48
1_555
46.0
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
O
GLU
78
A
O
GLU
69
A
N
ASP
81
A
N
ASP
72
1
A
CG
LYS
54
A
CG
LYS
53
1
Y
1
A
CD
LYS
54
A
CD
LYS
53
1
Y
1
A
CE
LYS
54
A
CE
LYS
53
1
Y
1
A
NZ
LYS
54
A
NZ
LYS
53
1
Y
1
A
CG
GLU
78
A
CG
GLU
69
1
Y
1
A
CD
GLU
78
A
CD
GLU
69
1
Y
1
A
OE1
GLU
78
A
OE1
GLU
69
1
Y
1
A
OE2
GLU
78
A
OE2
GLU
69
1
Y
1
A
CB
LYS
124
A
CB
LYS
114
1
Y
1
A
CG
LYS
124
A
CG
LYS
114
1
Y
1
A
CD
LYS
124
A
CD
LYS
114
1
Y
1
A
CE
LYS
124
A
CE
LYS
114
1
Y
1
A
NZ
LYS
124
A
NZ
LYS
114
1
Y
1
A
ASN
24
-156.70
55.91
PROTEIN_REP.PARAM
PROTEIN.TOP
ION.PARAM
ION.TOP
WATER.PARAM
WATER.TOP
BBO.PARAM
BBO.TOP
25.7
0.89
0.81
0.00
0.89
0.00
-1.78
0.21
0.006
0.193
0.193
0.193
1.90
25.00
1078
10434
10.3
99.9
RANDOM
2
RESTRAINED
THROUGHOUT
0.0
isomorphous difference Fourier
PDB ENTRY 1PSJ
FLAT MODEL
91.6329
0.401006
0.20
0.06
1.90
25.00
81
1048
13
0
954
0.007
1.3
22.6
0.83
1.59
1.50
2.55
2.00
3.16
2.00
5.08
2.50
0.242
0.015
0.214
2.02
198
1504
6
11.6
100.0
20.4
1.9
25
1M8R
10450
10450
0.0001
0.068
2
26.2
7.7
99.9
0.369
1.90
1.97
5.7
1016
6.9
100
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
A
SER
1
A
SER
1
HELX_P
A
ALA
13
A
ALA
13
1
1
13
A
SER
17
A
SER
16
HELX_P
A
TYR
22
A
TYR
21
1
2
6
A
ASP
89
A
ASP
79
HELX_P
A
ASN
109
A
ASN
99
1
4
21
A
LEU
110
A
LEU
100
HELX_P
A
TYR
113
A
TYR
103
5
5
4
A
ASN
114
A
ASN
104
HELX_P
A
TRP
119
A
TRP
109
1
6
6
A
PRO
127
A
PRO
117
HELX_P
A
SER
131
A
SER
121
5
7
5
disulf
2.034
A
CYS
27
A
SG
CYS
26
1_555
A
CYS
126
A
SG
CYS
116
1_555
disulf
2.029
A
CYS
29
A
SG
CYS
28
1_555
A
CYS
45
A
SG
CYS
44
1_555
disulf
2.041
A
CYS
44
A
SG
CYS
43
1_555
A
CYS
105
A
SG
CYS
95
1_555
disulf
2.034
A
CYS
50
A
SG
CYS
49
1_555
A
CYS
134
A
SG
CYS
124
1_555
disulf
2.028
A
CYS
51
A
SG
CYS
50
1_555
A
CYS
98
A
SG
CYS
88
1_555
disulf
2.036
A
CYS
61
A
SG
CYS
57
1_555
A
CYS
91
A
SG
CYS
81
1_555
disulf
2.032
A
CYS
84
A
SG
CYS
75
1_555
A
CYS
96
A
SG
CYS
86
1_555
metalc
2.265
A
TYR
28
A
O
TYR
27
1_555
A
CD
1001
B
CD
CD
1_555
metalc
2.223
A
GLY
30
A
O
GLY
29
1_555
A
CD
1001
B
CD
CD
1_555
metalc
2.305
A
GLY
32
A
O
GLY
31
1_555
A
CD
1001
B
CD
CD
1_555
metalc
3.031
A
ASP
49
A
OD1
ASP
48
1_555
A
CD
1001
B
CD
CD
1_555
metalc
2.272
A
ASP
49
A
OD2
ASP
48
1_555
A
CD
1001
B
CD
CD
1_555
HYDROLASE
phopholipase a2-metal cation complex, three alpha, two beta, Hydrolase
PA21B_AGKHP
UNP
1
1
P14418
SLIQFETLIMKVAKKSGMFWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDP
CKKEICECDRAAAICFRDNLTLYNDKKYWAFGAKNCPQEESEPC
1
124
1M8R
1
134
P14418
A
1
1
124
1
ILE
SEE REMARK 999
VAL
3
1M8R
A
P14418
UNP
3
3
1
PHE
SEE REMARK 999
GLN
20
1M8R
A
P14418
UNP
19
19
1
THR
SEE REMARK 999
ASN
111
1M8R
A
P14418
UNP
101
101
1
LEU
SEE REMARK 999
THR
112
1M8R
A
P14418
UNP
102
102
2
anti-parallel
A
SER
74
A
SER
65
A
GLU
78
A
GLU
69
A
ASP
81
A
ASP
72
A
GLY
85
A
GLY
76
BINDING SITE FOR RESIDUE CD A 1001
A
CD
1001
Software
4
BINDING SITE FOR RESIDUE BU1 A 1002
A
BU1
1002
Software
4
BINDING SITE FOR RESIDUE BU1 A 1003
A
BU1
1003
Software
7
A
TYR
28
A
TYR
27
4
1_555
A
GLY
30
A
GLY
29
4
1_555
A
GLY
32
A
GLY
31
4
1_555
A
ASP
49
A
ASP
48
4
1_555
A
GLU
6
A
GLU
6
4
1_555
A
MET
19
A
MET
18
4
1_555
A
TYR
22
A
TYR
21
4
1_555
A
CYS
45
A
CYS
44
4
1_555
A
MET
19
A
MET
18
7
1_555
A
GLN
20
A
GLN
19
7
1_555
A
SER
23
A
SER
22
7
1_555
A
PRO
37
A
PRO
36
7
5_564
A
ALA
40
A
ALA
39
7
5_564
A
ARG
43
A
ARG
42
7
5_564
A
HOH
1007
E
HOH
7
5_564
169
P 61