0.014443
0.000000
0.000000
0.000000
0.014443
0.000000
0.000000
0.000000
0.014443
0.00000
0.00000
0.00000
Segelke, B.W.
Nguyen, D.
Chee, R.
Xuong, H.N.
Dennis, E.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
69.240
69.240
69.240
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
Na 1
22.990
SODIUM ION
non-polymer
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
279
223
232
10.1006/jmbi.1998.1759
9636712
Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing.
1998
10.2210/pdb1a3d/pdb
pdb_00001a3d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
22
1
AREA DETECTOR
1993-01
XUONG-HAMLIN MULTIWIRE
GRAPHITE(002)
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
13357.855
PHOSPHOLIPASE A2
3.1.1.4
1
nat
polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
119
nat
water
no
no
NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKG
DNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKG
DNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
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
Indian cobra
Naja
sample
VENOM SACK
35670
Naja naja
1
2.05
40.
7.5
1.4M (NH4)2SO4, 1% PEG 400, AND 0.1M TRIS PH 7.5 AT 22.5 DEGREES C., temperature 295.5K
295.5
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Database references
Derived calculations
Other
Refinement description
1
0
1998-04-29
1
1
2008-03-24
1
2
2011-07-13
1
3
2011-11-16
1
4
2023-08-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_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.ptnr1_symmetry
_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_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-01-20
REL
NA
SODIUM ION
HOH
water
1PSH
PDB ENTRY 1PSH
PDB
experimental model
NA
200
2
NA
NA
200
A
HOH
201
3
HOH
HOH
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
244
3
HOH
HOH
244
A
HOH
245
3
HOH
HOH
245
A
HOH
246
3
HOH
HOH
246
A
HOH
247
3
HOH
HOH
247
A
HOH
248
3
HOH
HOH
248
A
HOH
249
3
HOH
HOH
249
A
HOH
250
3
HOH
HOH
250
A
HOH
251
3
HOH
HOH
251
A
HOH
252
3
HOH
HOH
252
A
HOH
253
3
HOH
HOH
253
A
HOH
254
3
HOH
HOH
254
A
HOH
255
3
HOH
HOH
255
A
HOH
256
3
HOH
HOH
256
A
HOH
257
3
HOH
HOH
257
A
HOH
258
3
HOH
HOH
258
A
HOH
259
3
HOH
HOH
259
A
HOH
260
3
HOH
HOH
260
A
HOH
261
3
HOH
HOH
261
A
HOH
262
3
HOH
HOH
262
A
HOH
263
3
HOH
HOH
263
A
HOH
264
3
HOH
HOH
264
A
HOH
265
3
HOH
HOH
265
A
HOH
266
3
HOH
HOH
266
A
HOH
267
3
HOH
HOH
267
A
HOH
268
3
HOH
HOH
268
A
HOH
269
3
HOH
HOH
269
A
HOH
270
3
HOH
HOH
270
A
HOH
271
3
HOH
HOH
271
A
HOH
272
3
HOH
HOH
272
A
HOH
273
3
HOH
HOH
273
A
HOH
274
3
HOH
HOH
274
A
HOH
275
3
HOH
HOH
275
A
HOH
276
3
HOH
HOH
276
A
HOH
277
3
HOH
HOH
277
A
HOH
278
3
HOH
HOH
278
A
HOH
279
3
HOH
HOH
279
A
HOH
280
3
HOH
HOH
280
A
HOH
281
3
HOH
HOH
281
A
HOH
282
3
HOH
HOH
282
A
HOH
283
3
HOH
HOH
283
A
HOH
284
3
HOH
HOH
284
A
HOH
285
3
HOH
HOH
285
A
HOH
286
3
HOH
HOH
286
A
HOH
287
3
HOH
HOH
287
A
HOH
288
3
HOH
HOH
288
A
HOH
289
3
HOH
HOH
289
A
HOH
290
3
HOH
HOH
290
A
HOH
291
3
HOH
HOH
291
A
HOH
292
3
HOH
HOH
292
A
HOH
293
3
HOH
HOH
293
A
HOH
294
3
HOH
HOH
294
A
HOH
295
3
HOH
HOH
295
A
HOH
296
3
HOH
HOH
296
A
HOH
297
3
HOH
HOH
297
A
HOH
298
3
HOH
HOH
298
A
HOH
299
3
HOH
HOH
299
A
HOH
300
3
HOH
HOH
300
A
HOH
301
3
HOH
HOH
301
A
HOH
302
3
HOH
HOH
302
A
HOH
303
3
HOH
HOH
303
A
HOH
304
3
HOH
HOH
304
A
HOH
305
3
HOH
HOH
305
A
HOH
306
3
HOH
HOH
306
A
HOH
307
3
HOH
HOH
307
A
HOH
308
3
HOH
HOH
308
A
HOH
309
3
HOH
HOH
309
A
HOH
310
3
HOH
HOH
310
A
HOH
311
3
HOH
HOH
311
A
HOH
312
3
HOH
HOH
312
A
HOH
313
3
HOH
HOH
313
A
HOH
314
3
HOH
HOH
314
A
HOH
315
3
HOH
HOH
315
A
HOH
316
3
HOH
HOH
316
A
HOH
317
3
HOH
HOH
317
A
HOH
318
3
HOH
HOH
318
A
HOH
319
3
HOH
HOH
319
A
ASN
1
n
1
ASN
1
A
LEU
2
n
2
LEU
2
A
TYR
3
n
3
TYR
3
A
GLN
4
n
4
GLN
4
A
PHE
5
n
5
PHE
5
A
LYS
6
n
6
LYS
6
A
ASN
7
n
7
ASN
7
A
MET
8
n
8
MET
8
A
ILE
9
n
9
ILE
9
A
LYS
10
n
10
LYS
10
A
CYS
11
n
11
CYS
11
A
THR
12
n
12
THR
12
A
VAL
13
n
13
VAL
13
A
PRO
14
n
14
PRO
14
A
SER
15
n
15
SER
15
A
ARG
16
n
16
ARG
16
A
SER
17
n
17
SER
17
A
TRP
18
n
18
TRP
18
A
TRP
19
n
19
TRP
19
A
ASP
20
n
20
ASP
20
A
PHE
21
n
21
PHE
21
A
ALA
22
n
22
ALA
22
A
ASP
23
n
23
ASP
23
A
TYR
24
n
24
TYR
24
A
GLY
25
n
25
GLY
25
A
CYS
26
n
26
CYS
26
A
TYR
27
n
27
TYR
27
A
CYS
28
n
28
CYS
28
A
GLY
29
n
29
GLY
29
A
ARG
30
n
30
ARG
30
A
GLY
31
n
31
GLY
31
A
GLY
32
n
32
GLY
32
A
SER
33
n
33
SER
33
A
GLY
34
n
34
GLY
34
A
THR
35
n
35
THR
35
A
PRO
36
n
36
PRO
36
A
VAL
37
n
37
VAL
37
A
ASP
38
n
38
ASP
38
A
ASP
39
n
39
ASP
39
A
LEU
40
n
40
LEU
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
GLN
45
n
45
GLN
45
A
VAL
46
n
46
VAL
46
A
HIS
47
n
47
HIS
47
A
ASP
48
n
48
ASP
48
A
ASN
49
n
49
ASN
49
A
CYS
50
n
50
CYS
50
A
TYR
51
n
51
TYR
51
A
ASN
52
n
52
ASN
52
A
GLU
53
n
53
GLU
53
A
ALA
54
n
54
ALA
54
A
GLU
55
n
55
GLU
55
A
LYS
56
n
56
LYS
56
A
ILE
57
n
57
ILE
57
A
SER
58
n
58
SER
58
A
GLY
59
n
59
GLY
59
A
CYS
60
n
60
CYS
60
A
TRP
61
n
61
TRP
61
A
PRO
62
n
62
PRO
62
A
TYR
63
n
63
TYR
63
A
PHE
64
n
64
PHE
64
A
LYS
65
n
65
LYS
65
A
THR
66
n
66
THR
66
A
TYR
67
n
67
TYR
67
A
SER
68
n
68
SER
68
A
TYR
69
n
69
TYR
69
A
GLU
70
n
70
GLU
70
A
CYS
71
n
71
CYS
71
A
SER
72
n
72
SER
72
A
GLN
73
n
73
GLN
73
A
GLY
74
n
74
GLY
74
A
THR
75
n
75
THR
75
A
LEU
76
n
76
LEU
76
A
THR
77
n
77
THR
77
A
CYS
78
n
78
CYS
78
A
LYS
79
n
79
LYS
79
A
GLY
80
n
80
GLY
80
A
ASP
81
n
81
ASP
81
A
ASN
82
n
82
ASN
82
A
ASN
83
n
83
ASN
83
A
ALA
84
n
84
ALA
84
A
CYS
85
n
85
CYS
85
A
ALA
86
n
86
ALA
86
A
ALA
87
n
87
ALA
87
A
SER
88
n
88
SER
88
A
VAL
89
n
89
VAL
89
A
CYS
90
n
90
CYS
90
A
ASP
91
n
91
ASP
91
A
CYS
92
n
92
CYS
92
A
ASP
93
n
93
ASP
93
A
ARG
94
n
94
ARG
94
A
LEU
95
n
95
LEU
95
A
ALA
96
n
96
ALA
96
A
ALA
97
n
97
ALA
97
A
ILE
98
n
98
ILE
98
A
CYS
99
n
99
CYS
99
A
PHE
100
n
100
PHE
100
A
ALA
101
n
101
ALA
101
A
GLY
102
n
102
GLY
102
A
ALA
103
n
103
ALA
103
A
PRO
104
n
104
PRO
104
A
TYR
105
n
105
TYR
105
A
ASN
106
n
106
ASN
106
A
ASP
107
n
107
ASP
107
A
ASN
108
n
108
ASN
108
A
ASN
109
n
109
ASN
109
A
TYR
110
n
110
TYR
110
A
ASN
111
n
111
ASN
111
A
ILE
112
n
112
ILE
112
A
ASP
113
n
113
ASP
113
A
LEU
114
n
114
LEU
114
A
LYS
115
n
115
LYS
115
A
ALA
116
n
116
ALA
116
A
ARG
117
n
117
ARG
117
A
CYS
118
n
118
CYS
118
A
GLN
119
n
119
GLN
119
A
author_defined_assembly
3
trimeric
A
ASP
39
A
OD2
ASP
39
1_555
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD2
ASP
39
10_646
91.6
A
ASP
39
A
OD2
ASP
39
1_555
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD2
ASP
39
7_665
91.6
A
ASP
39
A
OD2
ASP
39
10_646
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD2
ASP
39
7_665
91.6
A
ASP
39
A
OD2
ASP
39
1_555
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD1
ASP
39
1_555
48.3
A
ASP
39
A
OD2
ASP
39
10_646
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD1
ASP
39
1_555
83.4
A
ASP
39
A
OD2
ASP
39
7_665
A
NA
200
B
NA
NA
1_555
A
ASP
39
A
OD1
ASP
39
1_555
139.1
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
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
5_555
z,x,y
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
9_555
y,z,x
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
GLU
70
A
O
GLU
70
A
N
THR
77
A
N
THR
77
1
A
NA
200
B
NA
1
A
HOH
276
C
HOH
1
A
HOH
279
C
HOH
1
7.71
1.10
114.20
121.91
A
A
A
CA
CB
SG
CYS
CYS
CYS
43
43
43
N
1
A
ASP
23
-155.69
72.29
1
A
GLN
73
40.74
97.13
1
A
CYS
118
-105.09
63.74
PARHCSDX.PRO
22.8
0.23
0.007
0.175
0.175
1.8
6.0
1031
10028
10.
95.2
RANDOM
1000000.0
0.001
1
RESTAINED
POST REFINEMENT
2.
MOLECULAR REPLACEMENT
PDB ENTRY 1PSH
0.19
6.0
0.25
1.8
6.0
119
1291
120
0
1052
0.017
1.86
23.2
1.66
0.29
0.024
0.27
1.88
142
978
8
12.4
90.
17.8
1.78
23.06
1A3D
10508
2.
0.06
1
12.6
9.7
98.
1.8
1.88
2.0
0.3
8.5
90.1
data collection
UCSD
SOFTWARE
data reduction
UCSD
SOFTWARE
model building
X-PLOR
3.0
refinement
X-PLOR
3.0
data scaling
UCSD
phasing
X-PLOR
3.0
PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM
1
N
N
2
N
N
3
N
N
A
LEU
2
A
LEU
2
HELX_P
A
THR
12
A
THR
12
1
1
11
A
TRP
18
A
TRP
18
HELX_P
A
PHE
21
A
PHE
21
1
2
4
A
ASP
39
A
ASP
39
HELX_P
A
LYS
56
A
LYS
56
1
3
18
A
ALA
84
A
ALA
84
HELX_P
A
GLY
102
A
GLY
102
1
4
19
A
ASP
107
A
ASP
107
HELX_P
A
ASN
109
A
ASN
109
5
5
3
A
LEU
114
A
LEU
114
HELX_P
A
ARG
117
A
ARG
117
1
6
4
disulf
2.024
A
CYS
11
A
SG
CYS
11
1_555
A
CYS
71
A
SG
CYS
71
1_555
disulf
2.014
A
CYS
26
A
SG
CYS
26
1_555
A
CYS
118
A
SG
CYS
118
1_555
disulf
1.999
A
CYS
28
A
SG
CYS
28
1_555
A
CYS
44
A
SG
CYS
44
1_555
disulf
2.020
A
CYS
43
A
SG
CYS
43
1_555
A
CYS
99
A
SG
CYS
99
1_555
disulf
2.028
A
CYS
50
A
SG
CYS
50
1_555
A
CYS
92
A
SG
CYS
92
1_555
disulf
2.033
A
CYS
60
A
SG
CYS
60
1_555
A
CYS
85
A
SG
CYS
85
1_555
disulf
2.058
A
CYS
78
A
SG
CYS
78
1_555
A
CYS
90
A
SG
CYS
90
1_555
metalc
2.418
A
ASP
39
A
OD2
ASP
39
1_555
A
NA
200
B
NA
NA
1_555
metalc
2.418
A
ASP
39
A
OD2
ASP
39
10_646
A
NA
200
B
NA
NA
1_555
metalc
2.418
A
ASP
39
A
OD2
ASP
39
7_665
A
NA
200
B
NA
NA
1_555
metalc
2.888
A
ASP
39
A
OD1
ASP
39
1_555
A
NA
200
B
NA
NA
1_555
CARBOXYLIC ESTER HYDROLASE
PHOSPHOLIPASE, TRIMER, CALCIUM BINDING, ACTIVATOR SITE, CARBOXYLIC ESTER HYDROLASE
PA2_NAJNA
UNP
1
1
P15445
NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKG
DNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ
1
119
1A3D
1
119
P15445
A
1
1
119
2
anti-parallel
A
TYR
69
A
TYR
69
A
SER
72
A
SER
72
A
THR
75
A
THR
75
A
CYS
78
A
CYS
78
CALCIUM BINDING RESIDUES.
Unknown
6
BINDING SITE FOR RESIDUE NA A 200
A
NA
200
Software
6
A
TYR
27
A
TYR
27
6
1_555
A
CYS
28
A
CYS
28
6
1_555
A
GLY
29
A
GLY
29
6
1_555
A
ARG
30
A
ARG
30
6
1_555
A
GLY
31
A
GLY
31
6
1_555
A
ASP
48
A
ASP
48
6
1_555
A
ASP
39
A
ASP
39
6
10_646
A
ASP
39
A
ASP
39
6
1_555
A
ASP
39
A
ASP
39
6
7_665
A
HOH
292
C
HOH
6
7_665
A
HOH
292
C
HOH
6
10_646
A
HOH
292
C
HOH
6
1_555
198
P 21 3