PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3EZ3
Asym. Unit
Info
Asym.Unit (258 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (125 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
:
22 Oct 08 (Deposition) - 02 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
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
:
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, R. Hui, J. D. Artz
Crystal Structure Of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Pvx_092040 With Zoledronate And Ipp Bound
To Be Published
[
close entry info
]
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 A1101
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 A1102
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 A1103
05
AC5
SOFTWARE
ASP A:287 , ZOL A:397 , HOH A:1116 , HOH A:1144 , HOH A:1251
BINDING SITE FOR RESIDUE MG A1104
06
AC6
SOFTWARE
GLU A:58 , GLU A:60 , ILE A:61 , HOH A:1152 , MET B:230 , ASN B:232 , VAL B:235
BINDING SITE FOR RESIDUE EDO A1105
07
AC7
SOFTWARE
GLU A:133 , TYR A:139 , LEU A:143 , ILE B:218
BINDING SITE FOR RESIDUE GOL A1106
08
AC8
SOFTWARE
ASP B:126 , ASP B:130 , ARG B:135 , 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:1187 , HOH B:1261
BINDING SITE FOR RESIDUE ZOL B 397
09
AC9
SOFTWARE
GLY B:80 , LYS B:81 , ARG B:84 , GLN B:119 , ARG B:136 , TYR B:247 , PHE B:283 , ZOL B:397 , HOH B:1136 , HOH B:1137 , HOH B:1193 , HOH B:1263 , HOH B:1268
BINDING SITE FOR RESIDUE IPE B1101
10
BC1
SOFTWARE
ASP B:126 , ASP B:130 , ZOL B:397 , MG B:1104 , HOH B:1144 , HOH B:1145 , HOH B:1186
BINDING SITE FOR RESIDUE MG B1102
11
BC2
SOFTWARE
ASP B:287 , ZOL B:397 , HOH B:1135 , HOH B:1149 , HOH B:1164
BINDING SITE FOR RESIDUE MG B1103
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 B1104
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 B1105
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
BINDING SITE FOR RESIDUE EDO B1106
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:1122 , HOH C:1167 , HOH C:1176 , HOH C:1191 , HOH C:1192 , HOH C:1212
BINDING SITE FOR RESIDUE ZOL C 397
16
BC7
SOFTWARE
GLY C:80 , 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:1155 , HOH C:1162 , HOH C:1205 , HOH C:1211 , HOH C:1245
BINDING SITE FOR RESIDUE IPE C1101
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 C1102
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 C1103
19
CC1
SOFTWARE
ASP C:287 , ZOL C:397 , HOH C:1110 , HOH C:1167 , HOH C:1191
BINDING SITE FOR RESIDUE MG C1104
20
CC2
SOFTWARE
ASP D:126 , ASP D:130 , ARG D:135 , 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:1150 , 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
GLY D:80 , 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 D1101
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 D1102
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 D1103
24
CC6
SOFTWARE
ASP D:287 , ZOL D:397 , HOH D:1163 , HOH D:1173 , HOH D:1245
BINDING SITE FOR RESIDUE MG D1104
25
CC7
SOFTWARE
LYS B:343 , ASP D:291 , ILE D:292 , GLY D:303 , ASP D:305 , ILE D:306 , ASP D:346 , HOH D:1164
BINDING SITE FOR RESIDUE GOL D1105
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (258 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (125 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3EZ3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help