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SMTL ID : 3ryw.1
(2 other biounits)
Crystal structure of P. vivax geranylgeranyl diphosphate synthase complexed with BPH-811
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.90 Å
Oligo State
homo-dimer
Ligands
2 x
K9H
:
{2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)
(Non-covalent)
K9H.1:
21 residues within 4Å:
Chain A:
F.122
,
A.125
,
D.126
,
D.130
,
R.135
,
V.156
,
L.157
,
T.191
,
Q.195
,
K.243
,
T.244
,
Q.284
,
D.287
,
K.301
Chain B:
V.153
,
N.154
,
L.157
Ligands:
MG.2
,
MG.3
,
MG.4
,
K9H.6
15
PLIP interactions
:
12 interactions with chain A
,
3 interactions with chain B
Hydrophobic interactions:
A:F.122
,
A:A.125
,
A:D.126
,
A:V.156
,
A:L.157
,
A:T.191
,
A:Q.195
,
B:V.153
,
B:L.157
,
B:L.157
Hydrogen bonds:
A:R.135
,
A:R.135
,
A:K.243
,
A:Q.284
,
A:K.301
K9H.6:
21 residues within 4Å:
Chain A:
V.153
,
N.154
,
L.157
Chain B:
F.122
,
A.125
,
D.126
,
D.130
,
R.135
,
V.156
,
T.191
,
Q.195
,
K.243
,
T.244
,
Y.247
,
Q.284
,
D.287
,
K.301
Ligands:
K9H.1
,
MG.7
,
MG.8
,
MG.9
15
PLIP interactions
:
11 interactions with chain B
,
4 interactions with chain A
Hydrophobic interactions:
B:F.122
,
B:A.125
,
B:V.156
,
B:T.191
,
B:Q.195
,
A:V.153
,
A:L.157
,
A:L.157
,
A:L.157
Hydrogen bonds:
B:R.135
,
B:R.135
,
B:K.243
,
B:Q.284
,
B:K.301
pi-Cation interactions:
B:K.243
6 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
4 residues within 4Å:
Chain A:
D.287
,
D.291
,
D.305
Ligands:
K9H.1
1
PLIP interactions
:
1 interactions with chain A
Metal complexes:
A:D.287
MG.3:
4 residues within 4Å:
Chain A:
D.126
,
D.130
Ligands:
K9H.1
,
MG.4
3
PLIP interactions
:
2 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:D.126
,
A:D.130
,
H
2
O.1
MG.4:
6 residues within 4Å:
Chain A:
D.126
,
D.130
,
Q.195
,
D.198
Ligands:
K9H.1
,
MG.3
3
PLIP interactions
:
3 interactions with chain A
Metal complexes:
A:D.126
,
A:D.130
,
A:D.130
MG.7:
4 residues within 4Å:
Chain B:
D.287
,
D.291
,
D.305
Ligands:
K9H.6
1
PLIP interactions
:
1 interactions with chain B
Metal complexes:
B:D.287
MG.8:
3 residues within 4Å:
Chain B:
D.126
,
D.130
Ligands:
K9H.6
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:D.126
,
B:D.130
MG.9:
5 residues within 4Å:
Chain B:
D.126
,
D.130
,
Q.195
,
D.198
Ligands:
K9H.6
4
PLIP interactions
:
4 interactions with chain B
Metal complexes:
B:D.126
,
B:D.130
,
B:D.130
,
B:D.198
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.5:
5 residues within 4Å:
Chain A:
G.80
,
K.81
,
R.84
,
Q.119
,
R.136
5
PLIP interactions
:
5 interactions with chain A
Hydrogen bonds:
A:K.81
,
A:R.84
,
A:Q.119
Salt bridges:
A:K.81
,
A:R.136
SO4.10:
5 residues within 4Å:
Chain B:
G.80
,
K.81
,
R.84
,
Q.119
,
R.136
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:K.81
,
B:R.84
,
B:Q.119
Salt bridges:
B:K.81
,
B:R.136
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
No, J.H. et al., Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity. Proc.Natl.Acad.Sci.USA (2012)
Release Date
2012-05-23
Peptides
Farnesyl pyrophosphate synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
D
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Farnesyl pyrophosphate synthase
Toggle Identical (AB)
Related Entries With Identical Sequence
3cc9.1
|
3cc9.2
|
3ez3.1
|
3ez3.2
|
3ldw.1
|
3ldw.2
|
3ph7.1
|
3ph7.2
|
3rbm.1
|
3rbm.2
|
3ryw.2
|
3ryw.3
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