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SMTL ID : 4s1b.3
(2 other biounits)
Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with Cyclic-di-AMP
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.10 Å
Oligo State
homo-dimer
Ligands
4 x
FE
:
FE (III) ION
(Non-covalent)
FE.1:
6 residues within 4Å:
Chain A:
D.51
,
H.87
,
H.111
,
H.112
Ligands:
FE.2
,
2BA.3
6
PLIP interactions
:
4 interactions with chain A
,
1 Ligand-Water interactions
,
1 Ligand-Ligand interactions
Metal complexes:
A:D.51
,
A:H.87
,
A:H.111
,
A:H.112
,
H
2
O.3
,
2BA.3
FE.2:
6 residues within 4Å:
Chain A:
H.21
,
H.50
,
D.51
,
D.155
Ligands:
FE.1
,
2BA.3
6
PLIP interactions
:
4 interactions with chain A
,
1 Ligand-Water interactions
,
1 Ligand-Ligand interactions
Metal complexes:
A:H.21
,
A:H.50
,
A:D.51
,
A:D.155
,
H
2
O.3
,
2BA.3
FE.4:
6 residues within 4Å:
Chain B:
D.51
,
H.87
,
H.111
,
H.112
Ligands:
FE.5
,
2BA.6
6
PLIP interactions
:
4 interactions with chain B
,
1 Ligand-Ligand interactions
,
1 Ligand-Water interactions
Metal complexes:
B:D.51
,
B:H.87
,
B:H.111
,
B:H.112
,
2BA.6
,
H
2
O.7
FE.5:
6 residues within 4Å:
Chain B:
H.21
,
H.50
,
D.51
,
D.155
Ligands:
FE.4
,
2BA.6
6
PLIP interactions
:
4 interactions with chain B
,
1 Ligand-Ligand interactions
,
1 Ligand-Water interactions
Metal complexes:
B:H.21
,
B:H.50
,
B:D.51
,
B:D.155
,
2BA.6
,
H
2
O.7
2 x
2BA
:
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
(Non-covalent)
2BA.3:
25 residues within 4Å:
Chain A:
H.21
,
D.51
,
K.54
,
Y.60
,
F.61
,
V.62
,
E.63
,
Q.65
,
H.72
,
I.84
,
H.87
,
H.112
,
L.117
,
Y.119
,
F.120
,
Y.138
,
D.155
,
S.156
,
A.159
,
A.160
,
S.163
,
I.179
,
R.183
Ligands:
FE.1
,
FE.2
20
PLIP interactions
:
20 interactions with chain A
Hydrogen bonds:
A:K.54
,
A:V.62
,
A:E.63
,
A:Y.138
,
A:S.163
,
A:S.163
,
A:R.183
Water bridges:
A:N.70
,
A:H.112
,
A:L.116
,
A:L.116
,
A:L.116
,
A:K.118
,
A:K.118
,
A:Y.119
Salt bridges:
A:H.21
,
A:K.54
,
A:H.87
,
A:H.112
,
A:H.112
2BA.6:
23 residues within 4Å:
Chain B:
H.21
,
D.51
,
K.54
,
Y.60
,
F.61
,
V.62
,
E.63
,
N.70
,
H.72
,
I.84
,
H.87
,
H.112
,
L.117
,
F.120
,
Y.138
,
D.155
,
S.156
,
A.159
,
A.160
,
I.179
,
R.183
Ligands:
FE.4
,
FE.5
16
PLIP interactions
:
16 interactions with chain B
Hydrogen bonds:
B:K.54
,
B:V.62
,
B:E.63
,
B:N.70
,
B:Y.138
,
B:R.183
Water bridges:
B:H.112
,
B:T.115
,
B:T.115
,
B:T.115
,
B:L.116
Salt bridges:
B:H.21
,
B:K.54
,
B:H.87
,
B:H.112
,
B:H.112
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Huynh, T.N. et al., An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence. Proc.Natl.Acad.Sci.USA (2015)
Release Date
2015-02-11
Peptides
Lmo1466 protein:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
D
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Lmo1466 protein
Related Entries With Identical Sequence
4s1b.1
|
4s1b.2
|
4s1c.1
|
4s1c.2
|
4s1c.3
Cartoon
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Tube
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