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3LDW
Asym. Unit
Info
Asym.Unit (260 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (128 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOSPHATE SYNTHASE PVX_092040 WITH ZOLEDRONATE AND IPP BOUND
Authors
:
A. K. Wernimont, J. Lew, Y. Zhao, I. Kozieradzki, D. Cossar, M. Schapira A. Bochkarev, C. H. Arrowsmith, C. Bountra, J. Weigelt, A. M. Edwards, J. D. Artz, Structural Genomics Consortium (Sgc)
Date
:
13 Jan 10 (Deposition) - 17 Nov 10 (Release) - 06 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.47
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Malaria, Farnesyl Pyrophosphate Synthase Diphosphate, Lyase, Structural Genomics, Isoprene Biosynthesis, Transferase, Structural Genomics Consortium, Sgc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. D. Artz, A. K. Wernimont, J. E. Dunford, M. Schapira, A. Dong, Y. Zhao J. Lew, R. G. Russell, F. H. Ebetino, U. Oppermann, R. Hui
Molecular Characterization Of A Novel Geranylgeranyl Pyrophosphate Synthase From Plasmodium Parasites.
J. Biol. Chem. V. 286 3315 2011
[
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Hetero Components
(5, 25)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEa)
3b: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEb)
3c: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEc)
3d: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
5a: ZOLEDRONIC ACID (ZOLa)
5b: ZOLEDRONIC ACID (ZOLb)
5c: ZOLEDRONIC ACID (ZOLc)
5d: ZOLEDRONIC ACID (ZOLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
3
Ligand/Ion
GLYCEROL
3
IPE
4
Ligand/Ion
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
4
MG
12
Ligand/Ion
MAGNESIUM ION
5
ZOL
4
Ligand/Ion
ZOLEDRONIC ACID
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:126 , ASP A:130 , ARG A:135 , GLN A:195 , LYS A:243 , THR A:244 , GLN A:284 , ASP A:287 , LYS A:301 , IPE A:1101 , MG A:1102 , MG A:1103 , MG A:1104 , HOH A:1116 , HOH A:1117 , HOH A:1130 , HOH A:1142 , HOH A:1144 , HOH A:1155 , HOH A:1162 , HOH A:1164 , HOH A:1251
BINDING SITE FOR RESIDUE ZOL A 397
02
AC2
SOFTWARE
GLY A:80 , LYS A:81 , ARG A:84 , GLN A:119 , ARG A:136 , TYR A:247 , PHE A:283 , GLN A:284 , ZOL A:397 , HOH A:1118 , HOH A:1119 , HOH A:1167 , HOH A:1190 , HOH A:1206 , HOH A:1250
BINDING SITE FOR RESIDUE IPE A 1101
03
AC3
SOFTWARE
ASP A:126 , ASP A:130 , ZOL A:397 , MG A:1103 , HOH A:1142 , HOH A:1164
BINDING SITE FOR RESIDUE MG A 1102
04
AC4
SOFTWARE
ASP A:126 , ASP A:130 , ZOL A:397 , MG A:1102 , HOH A:1130 , HOH A:1143 , HOH A:1161 , HOH A:1162
BINDING SITE FOR RESIDUE MG A 1103
05
AC5
SOFTWARE
ASP A:287 , ZOL A:397 , HOH A:1116 , HOH A:1144 , HOH A:1251
BINDING SITE FOR RESIDUE MG A 1104
06
AC6
SOFTWARE
GLU A:58 , GLU A:60 , HOH A:1152 , ASN B:232 , VAL B:235
BINDING SITE FOR RESIDUE EDO A 1105
07
AC7
SOFTWARE
GLY A:132 , GLU A:133 , LEU A:143 , ILE B:218
BINDING SITE FOR RESIDUE GOL A 1106
08
AC8
SOFTWARE
ASP B:126 , ASP B:130 , ARG B:135 , GLN B:195 , LYS B:243 , THR B:244 , GLN B:284 , ASP B:287 , LYS B:301 , IPE B:1101 , MG B:1102 , MG B:1103 , MG B:1104 , EDO B:1106 , HOH B:1135 , HOH B:1144 , HOH B:1149 , HOH B:1164 , HOH B:1186 , HOH B:1187 , HOH B:1261
BINDING SITE FOR RESIDUE ZOL B 397
09
AC9
SOFTWARE
LYS B:81 , ARG B:84 , GLN B:119 , ARG B:136 , TYR B:247 , PHE B:283 , GLN B:284 , ZOL B:397 , HOH B:1136 , HOH B:1137 , HOH B:1193 , HOH B:1263 , HOH B:1268
BINDING SITE FOR RESIDUE IPE B 1101
10
BC1
SOFTWARE
ASP B:126 , ASP B:130 , ASP B:198 , ZOL B:397 , MG B:1104 , HOH B:1144 , HOH B:1145 , HOH B:1186
BINDING SITE FOR RESIDUE MG B 1102
11
BC2
SOFTWARE
ASP B:287 , ZOL B:397 , HOH B:1135 , HOH B:1149 , HOH B:1164
BINDING SITE FOR RESIDUE MG B 1103
12
BC3
SOFTWARE
ASP B:126 , ASP B:130 , ZOL B:397 , MG B:1102 , HOH B:1162 , HOH B:1187
BINDING SITE FOR RESIDUE MG B 1104
13
BC4
SOFTWARE
LEU B:290 , ASP B:291 , GLY B:294 , SER B:296 , THR B:299 , LYS B:301 , GLY B:303 , EDO B:1106
BINDING SITE FOR RESIDUE GOL B 1105
14
BC5
SOFTWARE
ASP B:291 , LYS B:301 , VAL B:302 , GLY B:303 , ZOL B:397 , GOL B:1105 , HOH B:1149 , HOH B:1164 , HOH B:1188
BINDING SITE FOR RESIDUE EDO B 1106
15
BC6
SOFTWARE
ASP C:126 , ASP C:130 , ARG C:135 , GLN C:195 , LYS C:243 , THR C:244 , GLN C:284 , ASP C:287 , LYS C:301 , IPE C:1101 , MG C:1102 , MG C:1103 , MG C:1104 , HOH C:1110 , HOH C:1120 , HOH C:1122 , HOH C:1167 , HOH C:1176 , HOH C:1191 , HOH C:1192
BINDING SITE FOR RESIDUE ZOL C 397
16
BC7
SOFTWARE
LYS C:81 , ARG C:84 , GLN C:119 , ARG C:136 , TYR C:247 , PHE C:283 , GLN C:284 , ZOL C:397 , HOH C:1121 , HOH C:1155 , HOH C:1162 , HOH C:1205 , HOH C:1211 , HOH C:1245
BINDING SITE FOR RESIDUE IPE C 1101
17
BC8
SOFTWARE
ASP C:126 , ASP C:130 , ZOL C:397 , MG C:1103 , HOH C:1118 , HOH C:1192
BINDING SITE FOR RESIDUE MG C 1102
18
BC9
SOFTWARE
ASP C:126 , ASP C:130 , ZOL C:397 , MG C:1102 , HOH C:1120 , HOH C:1122 , HOH C:1175
BINDING SITE FOR RESIDUE MG C 1103
19
CC1
SOFTWARE
ASP C:287 , ZOL C:397 , HOH C:1110 , HOH C:1167 , HOH C:1191
BINDING SITE FOR RESIDUE MG C 1104
20
CC2
SOFTWARE
ASP D:126 , ASP D:130 , ARG D:135 , GLN D:195 , LYS D:243 , THR D:244 , GLN D:284 , ASP D:287 , LYS D:301 , IPE D:1101 , MG D:1102 , MG D:1103 , MG D:1104 , HOH D:1157 , HOH D:1158 , HOH D:1159 , HOH D:1163 , HOH D:1200 , HOH D:1245 , HOH D:1264
BINDING SITE FOR RESIDUE ZOL D 397
21
CC3
SOFTWARE
LYS D:81 , ARG D:84 , GLN D:119 , ARG D:136 , TYR D:247 , PHE D:283 , GLN D:284 , ZOL D:397 , HOH D:1165 , HOH D:1218 , HOH D:1230 , HOH D:1251 , HOH D:1255
BINDING SITE FOR RESIDUE IPE D 1101
22
CC4
SOFTWARE
ASP D:126 , ASP D:130 , ZOL D:397 , MG D:1103 , HOH D:1157 , HOH D:1160 , HOH D:1200
BINDING SITE FOR RESIDUE MG D 1102
23
CC5
SOFTWARE
ASP D:126 , ASP D:130 , ZOL D:397 , MG D:1102 , HOH D:1150 , HOH D:1158
BINDING SITE FOR RESIDUE MG D 1103
24
CC6
SOFTWARE
ASP D:287 , ZOL D:397 , HOH D:1163 , HOH D:1196 , HOH D:1245
BINDING SITE FOR RESIDUE MG D 1104
25
CC7
SOFTWARE
LEU B:339 , LYS B:343 , ASP D:291 , ILE D:292 , ASP D:305 , ILE D:306 , ASP D:346 , HOH D:1164
BINDING SITE FOR RESIDUE GOL D 1105
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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View:
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Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_polyprenyl_synt_3ldwD01 (D:69-359)
1b: PFAM_polyprenyl_synt_3ldwD02 (D:69-359)
1c: PFAM_polyprenyl_synt_3ldwD03 (D:69-359)
1d: PFAM_polyprenyl_synt_3ldwD04 (D:69-359)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: polyprenyl_synt]
(86)
Family
:
polyprenyl_synt
(86)
Plasmodium vivax (strain Salvador I)
(3)
1a
polyprenyl_synt-3ldwD01
D:69-359
1b
polyprenyl_synt-3ldwD02
D:69-359
1c
polyprenyl_synt-3ldwD03
D:69-359
1d
polyprenyl_synt-3ldwD04
D:69-359
[
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