0.012553
0.000000
0.000000
0.000000
0.012553
0.000000
0.000000
0.000000
0.012553
0.00000
0.00000
0.00000
Wernimont, A.K.
Lew, J.
Kozieradzki, I.
Lin, Y.H.
Sun, X.
Khuu, C.
Zhao, Y.
Schapira, M.
Arrowsmith, C.H.
Edwards, A.M.
Weigelt, J.
Bochkarev, A.
Hui, R.
Artz, J.D.
Xiao, T.
Structural Genomics Consortium (SGC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
79.661
79.661
79.661
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
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
Zn 2
65.409
ZINC ION
non-polymer
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
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
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
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
O
N
296
N
O
N
297
N
H
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
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
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
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
N
332
N
O
N
333
N
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
N
N
346
S
C
N
347
N
C
N
348
N
O
N
349
N
C
N
350
N
C
N
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
ZN
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
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
doub
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
doub
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
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
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
doub
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
sing
N
347
N
sing
To be Published
0353
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax.
10.2210/pdb3b6n/pdb
pdb_00003b6n
100
1
IMAGE PLATE
2007-05-30
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU FR-E+ DW
20215.066
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
4.6.1.12
Residues 102-287
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
18.015
water
40
nat
water
no
no
GYDGVRIGQGYDIHQIRVGPPEDIVADTTADTAANTADPNKQSFKRLTIGGVPVETISVLSHSDGDVIFHALVDALLGGM
SCSDLGTLFPDGSPKYKNKNSLSFLRYARLLLYKRNYAIANVDIIVIAEVPKISPIREEIVRNISSALGISESQVSLKGK
THEQLGPVGQKKAIECFANALLIRKQS
GYDGVRIGQGYDIHQIRVGPPEDIVADTTADTAANTADPNKQSFKRLTIGGVPVETISVLSHSDGDVIFHALVDALLGGM
SCSDLGTLFPDGSPKYKNKNSLSFLRYARLLLYKRNYAIANVDIIVIAEVPKISPIREEIVRNISSALGISESQVSLKGK
THEQLGPVGQKKAIECFANALLIRKQS
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Plasmodium
Plasmodium vivax
Salvador I
Escherichia
sample
PV003920, PVX_003920
126793
Plasmodium vivax SaI-1
562
Escherichia coli
DH5a
Plasmid
p15-mhl-LIC
1
2.08
40.98
VAPOR DIFFUSION, HANGING DROP
3.5
25% PEG 3350, 0.1 M Citric acid pH 3.5, 2 mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
Structural Genomics Consortium
SGC
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2007-11-20
1
1
2011-07-13
1
2
2017-10-25
1
3
2023-08-30
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2007-10-29
REL
REL
ZN
ZINC ION
HOH
water
1VH8
PDB entry 1VH8
PDB
experimental model
ZN
1157
2
ZN
ZN
1157
A
HOH
1158
3
HOH
HOH
1158
A
HOH
1159
3
HOH
HOH
1159
A
HOH
1160
3
HOH
HOH
1160
A
HOH
1161
3
HOH
HOH
1161
A
HOH
1162
3
HOH
HOH
1162
A
HOH
1163
3
HOH
HOH
1163
A
HOH
1164
3
HOH
HOH
1164
A
HOH
1165
3
HOH
HOH
1165
A
HOH
1166
3
HOH
HOH
1166
A
HOH
1167
3
HOH
HOH
1167
A
HOH
1168
3
HOH
HOH
1168
A
HOH
1169
3
HOH
HOH
1169
A
HOH
1170
3
HOH
HOH
1170
A
HOH
1171
3
HOH
HOH
1171
A
HOH
1172
3
HOH
HOH
1172
A
HOH
1173
3
HOH
HOH
1173
A
HOH
1174
3
HOH
HOH
1174
A
HOH
1175
3
HOH
HOH
1175
A
HOH
1176
3
HOH
HOH
1176
A
HOH
1177
3
HOH
HOH
1177
A
HOH
1178
3
HOH
HOH
1178
A
HOH
1179
3
HOH
HOH
1179
A
HOH
1180
3
HOH
HOH
1180
A
HOH
1181
3
HOH
HOH
1181
A
HOH
1182
3
HOH
HOH
1182
A
HOH
1183
3
HOH
HOH
1183
A
HOH
1184
3
HOH
HOH
1184
A
HOH
1185
3
HOH
HOH
1185
A
HOH
1187
3
HOH
HOH
1186
A
HOH
1188
3
HOH
HOH
1187
A
HOH
1190
3
HOH
HOH
1188
A
HOH
1191
3
HOH
HOH
1189
A
HOH
1192
3
HOH
HOH
1190
A
HOH
1194
3
HOH
HOH
1191
A
HOH
1195
3
HOH
HOH
1192
A
HOH
1
3
HOH
HOH
1193
A
HOH
2
3
HOH
HOH
1194
A
HOH
3
3
HOH
HOH
1195
A
HOH
1
3
HOH
HOH
1196
A
HOH
2
3
HOH
HOH
1197
A
2.500
2.500
39.830
39.830
Phaser MODE: MR_AUTO
n
1
1
A
n
2
2
A
n
3
3
A
GLY
4
n
4
GLY
4
A
VAL
5
n
5
VAL
5
A
ARG
6
n
6
ARG
6
A
ILE
7
n
7
ILE
7
A
GLY
8
n
8
GLY
8
A
GLN
9
n
9
GLN
9
A
GLY
10
n
10
GLY
10
A
TYR
11
n
11
TYR
11
A
ASP
12
n
12
ASP
12
A
ILE
13
n
13
ILE
13
A
HIS
14
n
14
HIS
14
A
GLN
15
n
15
GLN
15
A
ILE
16
n
16
ILE
16
A
ARG
17
n
17
ARG
17
A
VAL
18
n
18
VAL
18
A
GLY
19
n
19
GLY
19
A
PRO
20
n
20
PRO
20
A
PRO
21
n
21
PRO
21
A
GLU
22
n
22
GLU
22
A
n
23
23
A
n
24
24
A
n
25
25
A
n
26
26
A
n
27
27
A
n
28
28
A
n
29
29
A
n
30
30
A
n
31
31
A
n
32
32
A
n
33
33
A
n
34
34
A
n
35
35
A
n
36
36
A
n
37
37
A
n
38
38
A
n
39
39
A
n
40
40
A
LYS
41
n
41
LYS
41
A
GLN
42
n
42
GLN
42
A
SER
43
n
43
SER
43
A
PHE
44
n
44
PHE
44
A
LYS
45
n
45
LYS
45
A
ARG
46
n
46
ARG
46
A
LEU
47
n
47
LEU
47
A
THR
48
n
48
THR
48
A
ILE
49
n
49
ILE
49
A
GLY
50
n
50
GLY
50
A
GLY
51
n
51
GLY
51
A
VAL
52
n
52
VAL
52
A
PRO
53
n
53
PRO
53
A
VAL
54
n
54
VAL
54
A
GLU
55
n
55
GLU
55
A
THR
56
n
56
THR
56
A
ILE
57
n
57
ILE
57
A
SER
58
n
58
SER
58
A
VAL
59
n
59
VAL
59
A
LEU
60
n
60
LEU
60
A
SER
61
n
61
SER
61
A
HIS
62
n
62
HIS
62
A
SER
63
n
63
SER
63
A
ASP
64
n
64
ASP
64
A
GLY
65
n
65
GLY
65
A
ASP
66
n
66
ASP
66
A
VAL
67
n
67
VAL
67
A
ILE
68
n
68
ILE
68
A
PHE
69
n
69
PHE
69
A
HIS
70
n
70
HIS
70
A
ALA
71
n
71
ALA
71
A
LEU
72
n
72
LEU
72
A
VAL
73
n
73
VAL
73
A
ASP
74
n
74
ASP
74
A
ALA
75
n
75
ALA
75
A
LEU
76
n
76
LEU
76
A
LEU
77
n
77
LEU
77
A
GLY
78
n
78
GLY
78
A
GLY
79
n
79
GLY
79
A
MET
80
n
80
MET
80
A
SER
81
n
81
SER
81
A
CYS
82
n
82
CYS
82
A
SER
83
n
83
SER
83
A
n
84
84
A
n
85
85
A
n
86
86
A
n
87
87
A
n
88
88
A
n
89
89
A
n
90
90
A
n
91
91
A
n
92
92
A
n
93
93
A
n
94
94
A
n
95
95
A
n
96
96
A
n
97
97
A
n
98
98
A
LYS
99
n
99
LYS
99
A
ASN
100
n
100
ASN
100
A
SER
101
n
101
SER
101
A
LEU
102
n
102
LEU
102
A
SER
103
n
103
SER
103
A
PHE
104
n
104
PHE
104
A
LEU
105
n
105
LEU
105
A
ARG
106
n
106
ARG
106
A
TYR
107
n
107
TYR
107
A
ALA
108
n
108
ALA
108
A
ARG
109
n
109
ARG
109
A
LEU
110
n
110
LEU
110
A
LEU
111
n
111
LEU
111
A
LEU
112
n
112
LEU
112
A
TYR
113
n
113
TYR
113
A
LYS
114
n
114
LYS
114
A
ARG
115
n
115
ARG
115
A
ASN
116
n
116
ASN
116
A
TYR
117
n
117
TYR
117
A
ALA
118
n
118
ALA
118
A
ILE
119
n
119
ILE
119
A
ALA
120
n
120
ALA
120
A
ASN
121
n
121
ASN
121
A
VAL
122
n
122
VAL
122
A
ASP
123
n
123
ASP
123
A
ILE
124
n
124
ILE
124
A
ILE
125
n
125
ILE
125
A
VAL
126
n
126
VAL
126
A
ILE
127
n
127
ILE
127
A
ALA
128
n
128
ALA
128
A
GLU
129
n
129
GLU
129
A
VAL
130
n
130
VAL
130
A
PRO
131
n
131
PRO
131
A
LYS
132
n
132
LYS
132
A
ILE
133
n
133
ILE
133
A
SER
134
n
134
SER
134
A
PRO
135
n
135
PRO
135
A
ILE
136
n
136
ILE
136
A
ARG
137
n
137
ARG
137
A
GLU
138
n
138
GLU
138
A
GLU
139
n
139
GLU
139
A
ILE
140
n
140
ILE
140
A
VAL
141
n
141
VAL
141
A
ARG
142
n
142
ARG
142
A
ASN
143
n
143
ASN
143
A
ILE
144
n
144
ILE
144
A
SER
145
n
145
SER
145
A
SER
146
n
146
SER
146
A
ALA
147
n
147
ALA
147
A
LEU
148
n
148
LEU
148
A
GLY
149
n
149
GLY
149
A
ILE
150
n
150
ILE
150
A
SER
151
n
151
SER
151
A
GLU
152
n
152
GLU
152
A
SER
153
n
153
SER
153
A
GLN
154
n
154
GLN
154
A
VAL
155
n
155
VAL
155
A
SER
156
n
156
SER
156
A
LEU
157
n
157
LEU
157
A
LYS
158
n
158
LYS
158
A
GLY
159
n
159
GLY
159
A
LYS
160
n
160
LYS
160
A
THR
161
n
161
THR
161
A
HIS
162
n
162
HIS
162
A
GLU
163
n
163
GLU
163
A
GLN
164
n
164
GLN
164
A
LEU
165
n
165
LEU
165
A
GLY
166
n
166
GLY
166
A
PRO
167
n
167
PRO
167
A
VAL
168
n
168
VAL
168
A
GLY
169
n
169
GLY
169
A
GLN
170
n
170
GLN
170
A
LYS
171
n
171
LYS
171
A
LYS
172
n
172
LYS
172
A
ALA
173
n
173
ALA
173
A
ILE
174
n
174
ILE
174
A
GLU
175
n
175
GLU
175
A
CYS
176
n
176
CYS
176
A
PHE
177
n
177
PHE
177
A
ALA
178
n
178
ALA
178
A
ASN
179
n
179
ASN
179
A
ALA
180
n
180
ALA
180
A
LEU
181
n
181
LEU
181
A
LEU
182
n
182
LEU
182
A
ILE
183
n
183
ILE
183
A
ARG
184
n
184
ARG
184
A
LYS
185
n
185
LYS
185
A
GLN
186
n
186
GLN
186
A
n
187
187
A
software_defined_assembly
PISA
3
trimeric
5600
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
8_555
-z,x+1/2,-y+1/2
crystal symmetry operation
0.0000000000
39.8305000000
39.8305000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
-1.0000000000
0.0000000000
0.0000000000
11_455
y-1/2,-z+1/2,-x
crystal symmetry operation
-39.8305000000
39.8305000000
0.0000000000
A
N
LEU
47
A
N
LEU
47
A
O
ILE
57
A
O
ILE
57
A
O
LEU
60
A
O
LEU
60
A
N
GLN
15
A
N
GLN
15
A
N
ARG
6
A
N
ARG
6
A
O
LEU
182
A
O
LEU
182
A
O
ILE
183
A
O
ILE
183
A
N
ALA
118
A
N
ALA
118
A
N
ILE
124
A
N
ILE
124
A
O
SER
156
A
O
SER
156
1
A
HOH
1184
C
HOH
1
A
CG
GLU
22
A
CG
GLU
22
1
Y
1
A
CD
GLU
22
A
CD
GLU
22
1
Y
1
A
OE1
GLU
22
A
OE1
GLU
22
1
Y
1
A
OE2
GLU
22
A
OE2
GLU
22
1
Y
1
A
CG
LYS
41
A
CG
LYS
41
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
LYS
99
A
CG
LYS
99
1
Y
1
A
CD
LYS
99
A
CD
LYS
99
1
Y
1
A
CE
LYS
99
A
CE
LYS
99
1
Y
1
A
NZ
LYS
99
A
NZ
LYS
99
1
Y
1
A
CD1
PHE
104
A
CD1
PHE
104
1
Y
1
A
CD2
PHE
104
A
CD2
PHE
104
1
Y
1
A
CE1
PHE
104
A
CE1
PHE
104
1
Y
1
A
CE2
PHE
104
A
CE2
PHE
104
1
Y
1
A
CZ
PHE
104
A
CZ
PHE
104
1
Y
1
A
OE1
GLU
138
A
OE1
GLU
138
1
Y
1
A
OE2
GLU
138
A
OE2
GLU
138
1
Y
1
A
CG1
ILE
183
A
CG1
ILE
183
1
Y
1
A
CG2
ILE
183
A
CG2
ILE
183
1
Y
1
A
CD1
ILE
183
A
CD1
ILE
183
1
Y
1
A
GLY
1
A
GLY
1
1
Y
1
A
TYR
2
A
TYR
2
1
Y
1
A
ASP
3
A
ASP
3
1
Y
1
A
ASP
23
A
ASP
23
1
Y
1
A
ILE
24
A
ILE
24
1
Y
1
A
VAL
25
A
VAL
25
1
Y
1
A
ALA
26
A
ALA
26
1
Y
1
A
ASP
27
A
ASP
27
1
Y
1
A
THR
28
A
THR
28
1
Y
1
A
THR
29
A
THR
29
1
Y
1
A
ALA
30
A
ALA
30
1
Y
1
A
ASP
31
A
ASP
31
1
Y
1
A
THR
32
A
THR
32
1
Y
1
A
ALA
33
A
ALA
33
1
Y
1
A
ALA
34
A
ALA
34
1
Y
1
A
ASN
35
A
ASN
35
1
Y
1
A
THR
36
A
THR
36
1
Y
1
A
ALA
37
A
ALA
37
1
Y
1
A
ASP
38
A
ASP
38
1
Y
1
A
PRO
39
A
PRO
39
1
Y
1
A
ASN
40
A
ASN
40
1
Y
1
A
ASP
84
A
ASP
84
1
Y
1
A
LEU
85
A
LEU
85
1
Y
1
A
GLY
86
A
GLY
86
1
Y
1
A
THR
87
A
THR
87
1
Y
1
A
LEU
88
A
LEU
88
1
Y
1
A
PHE
89
A
PHE
89
1
Y
1
A
PRO
90
A
PRO
90
1
Y
1
A
ASP
91
A
ASP
91
1
Y
1
A
GLY
92
A
GLY
92
1
Y
1
A
SER
93
A
SER
93
1
Y
1
A
PRO
94
A
PRO
94
1
Y
1
A
LYS
95
A
LYS
95
1
Y
1
A
TYR
96
A
TYR
96
1
Y
1
A
LYS
97
A
LYS
97
1
Y
1
A
ASN
98
A
ASN
98
1
Y
1
A
SER
187
A
SER
187
1
Y
1
A
A
GLY
PRO
19
20
144.60
1
A
A
CB
CG1
VAL
VAL
67
67
-0.149
0.021
1.524
1.375
N
1
A
ASN
116
72.42
35.21
45.102
0.949
0.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25746
0.20405
0.20664
2.26
39.84
376
8159
8156
4.6
99.96
7.221
0.182
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.291
0.230
0.80
0.80
1.40
PDB entry 1VH8
MAXIMUM LIKELIHOOD
MASK
2.26
39.84
40
1179
1
0
1138
0.021
0.022
1153
1.835
1.978
1555
8.023
5.000
149
36.390
22.955
44
19.282
15.000
209
12.583
15.000
10
0.123
0.200
185
0.007
0.020
835
0.217
0.200
476
0.308
0.200
776
0.162
0.200
51
0.207
0.200
35
0.220
0.200
6
1.121
1.500
773
1.940
2.000
1194
3.047
3.000
428
4.695
4.500
360
0.365
0.276
2.319
29
573
20
99.83
53.20
2.260
50.000
3B6N
8156
8156
0
0
0.105
0.070
1
8.900
18.300
100.000
0.8958
2.26
2.34
1.57
0.7177
6.80
99.90
data reduction
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
DENZO
package
data scaling
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
SCALEPACK
package
phasing
R. J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
other
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
July 2, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.000
N
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax
1
N
N
2
N
N
3
N
N
Authors state that the biological unit of this protein is unknown
A
ASP
66
A
ASP
66
HELX_P
A
MET
80
A
MET
80
1
1
15
A
SER
101
A
SER
101
HELX_P
A
ARG
115
A
ARG
115
1
2
15
A
ILE
133
A
ILE
133
HELX_P
A
GLY
149
A
GLY
149
1
3
17
A
SER
151
A
SER
151
HELX_P
A
SER
153
A
SER
153
5
4
3
A
LEU
165
A
LEU
165
HELX_P
A
GLN
170
A
GLN
170
1
5
6
metalc
2.331
A
ASP
12
A
OD2
ASP
12
1_555
A
ZN
1157
B
ZN
ZN
1_555
LYASE
malaria isoprenoid biosynthesis and prenylation pathways ISPF, Isoprene biosynthesis, Lyase, Structural Genomics, Structural Genomics Consortium, SGC
A
VAL
130
A
VAL
130
1
A
PRO
131
A
PRO
131
1.46
A
LYS
185
A
LYS
185
1
A
GLN
186
A
GLN
186
11.14
A5KBP6_PLAVI
UNP
1
102
A5KBP6
YDGVRIGQGYDIHQIRVGPPEDIVADTTADTAANTADPNKQSFKRLTIGGVPVETISVLSHSDGDVIFHALVDALLGGMS
CSDLGTLFPDGSPKYKNKNSLSFLRYARLLLYKRNYAIANVDIIVIAEVPKISPIREEIVRNISSALGISESQVSLKGKT
HEQLGPVGQKKAIECFANALLIRKQS
102
287
3B6N
2
187
A5KBP6
A
1
2
187
1
expression tag
GLY
1
3B6N
A
A5KBP6
UNP
1
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
A
SER
43
A
SER
43
A
ILE
49
A
ILE
49
A
VAL
52
A
VAL
52
A
SER
61
A
SER
61
A
VAL
5
A
VAL
5
A
ARG
17
A
ARG
17
A
ALA
173
A
ALA
173
A
ARG
184
A
ARG
184
A
TYR
117
A
TYR
117
A
ILE
127
A
ILE
127
A
VAL
155
A
VAL
155
A
LYS
160
A
LYS
160
BINDING SITE FOR RESIDUE ZN A 1157
A
ZN
1157
Software
4
A
ASP
12
A
ASP
12
4
1_555
A
HIS
14
A
HIS
14
4
1_555
A
HIS
62
A
HIS
62
4
1_555
A
HIS
70
A
HIS
70
4
1_555
198
P 21 3