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SMTL ID : 3q1o.2
(2 other biounits)
Crystal structure of geranyltransferase from helicobacter pylori complexed with magnesium and isoprenyl diphosphate
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.40 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
4 residues within 4Å:
Chain A:
D.101
,
D.107
,
R.112
Ligands:
DMA.3
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:D.101
,
A:D.107
,
H
2
O.1
,
H
2
O.2
MG.5:
4 residues within 4Å:
Chain B:
D.101
,
D.107
,
R.112
Ligands:
DMA.7
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:D.101
,
B:D.107
,
H
2
O.3
,
H
2
O.4
4 x
DMA
:
DIMETHYLALLYL DIPHOSPHATE
(Non-covalent)
DMA.2:
11 residues within 4Å:
Chain A:
G.55
,
K.56
,
R.59
,
H.94
,
L.98
,
R.113
,
T.196
,
F.233
,
Q.234
,
D.237
Ligands:
DMA.3
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:L.98
,
A:T.196
,
A:F.233
Hydrogen bonds:
A:K.56
Water bridges:
A:K.56
,
A:K.56
,
A:R.57
,
A:R.57
,
A:R.59
,
A:R.112
Salt bridges:
A:K.56
,
A:K.56
,
A:R.59
,
A:H.94
,
A:H.94
,
A:R.113
DMA.3:
13 residues within 4Å:
Chain A:
S.97
,
L.98
,
D.101
,
D.107
,
R.112
,
M.168
,
Q.172
,
K.195
,
D.237
,
K.251
,
H.254
Ligands:
MG.1
,
DMA.2
12
PLIP interactions
:
12 interactions with chain A
Hydrophobic interactions:
A:L.98
,
A:D.101
,
A:Q.172
,
A:K.195
Hydrogen bonds:
A:Q.234
Water bridges:
A:R.112
,
A:Q.172
,
A:Q.172
Salt bridges:
A:R.112
,
A:K.195
,
A:K.251
,
A:H.254
DMA.6:
11 residues within 4Å:
Chain B:
G.55
,
K.56
,
R.59
,
H.94
,
L.98
,
R.113
,
T.196
,
F.233
,
Q.234
,
D.237
Ligands:
DMA.7
16
PLIP interactions
:
16 interactions with chain B
Hydrophobic interactions:
B:L.98
,
B:T.196
,
B:F.233
Hydrogen bonds:
B:K.56
Water bridges:
B:K.56
,
B:K.56
,
B:R.57
,
B:R.57
,
B:R.59
,
B:R.112
Salt bridges:
B:K.56
,
B:K.56
,
B:R.59
,
B:H.94
,
B:H.94
,
B:R.113
DMA.7:
13 residues within 4Å:
Chain B:
S.97
,
L.98
,
D.101
,
D.107
,
R.112
,
M.168
,
Q.172
,
K.195
,
D.237
,
K.251
,
H.254
Ligands:
MG.5
,
DMA.6
12
PLIP interactions
:
12 interactions with chain B
Hydrophobic interactions:
B:L.98
,
B:D.101
,
B:Q.172
,
B:K.195
Hydrogen bonds:
B:Q.234
Water bridges:
B:R.112
,
B:Q.172
,
B:Q.172
Salt bridges:
B:R.112
,
B:K.195
,
B:K.251
,
B:H.254
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.4:
4 residues within 4Å:
Chain A:
Q.276
,
K.279
,
F.308
,
K.309
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:Q.276
,
A:Q.276
Salt bridges:
A:K.279
,
A:K.309
SO4.8:
4 residues within 4Å:
Chain B:
Q.276
,
K.279
,
F.308
,
K.309
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:Q.276
,
B:Q.276
Salt bridges:
B:K.279
,
B:K.309
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Wallrapp, F.H. et al., Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc.Natl.Acad.Sci.USA (2013)
Release Date
2011-01-12
Peptides
Geranyltranstransferase (IspA):
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
B
B
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Geranyltranstransferase (IspA)
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