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SMTL ID : 3fv1.3
(2 other biounits)
Crystal Structure of the human glutamate receptor, GluR5, ligand-binding core in complex with dysiherbaine in space group P1
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.50 Å
Oligo State
homo-dimer
Ligands
2 x
DYH
:
(2R,3aR,6S,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-7-(methylamino)hexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid
(Non-covalent)
DYH.1:
15 residues within 4Å:
Chain A:
E.12
,
Y.60
,
P.87
,
L.88
,
T.89
,
R.94
,
V.136
,
G.139
,
S.140
,
T.141
,
S.172
,
M.188
,
E.189
,
S.192
,
Y.215
17
PLIP interactions
:
17 interactions with chain A
Hydrophobic interactions:
A:Y.60
,
A:Y.60
,
A:V.136
Hydrogen bonds:
A:T.89
,
A:S.140
,
A:T.141
,
A:T.141
,
A:E.189
,
A:E.189
,
A:E.189
,
A:E.189
,
A:E.189
,
A:S.192
,
A:S.192
Water bridges:
A:V.136
,
A:M.142
Salt bridges:
A:R.94
DYH.9:
16 residues within 4Å:
Chain B:
E.12
,
Y.15
,
Y.60
,
P.87
,
L.88
,
T.89
,
R.94
,
V.136
,
G.139
,
S.140
,
T.141
,
S.172
,
M.188
,
E.189
,
S.192
,
Y.215
19
PLIP interactions
:
19 interactions with chain B
Hydrophobic interactions:
B:Y.60
,
B:Y.60
,
B:V.136
Hydrogen bonds:
B:T.89
,
B:T.89
,
B:S.140
,
B:T.141
,
B:E.189
,
B:E.189
,
B:E.189
,
B:E.189
,
B:S.192
,
B:S.192
,
B:Y.215
Water bridges:
B:Y.15
,
B:V.136
,
B:M.142
,
B:E.189
Salt bridges:
B:R.94
5 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
4 residues within 4Å:
Chain A:
R.30
,
F.31
,
K.53
,
L.54
7
PLIP interactions
:
7 interactions with chain A
Hydrogen bonds:
A:L.54
Water bridges:
A:Y.18
,
A:R.30
,
A:R.30
,
A:R.30
,
A:L.54
Salt bridges:
A:R.30
SO4.3:
2 residues within 4Å:
Chain A:
R.3
,
Y.225
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:Y.225
Salt bridges:
A:R.3
SO4.4:
1 residues within 4Å:
Chain A:
K.248
5
PLIP interactions
:
5 interactions with chain A
Water bridges:
A:R.19
,
A:K.248
,
A:K.248
Salt bridges:
A:K.40
,
A:K.248
SO4.5:
4 residues within 4Å:
Chain A:
D.123
,
I.150
,
T.152
,
Y.153
2
PLIP interactions
:
2 interactions with chain A
Water bridges:
A:T.152
,
A:T.152
SO4.10:
4 residues within 4Å:
Chain B:
R.30
,
V.52
,
K.53
,
L.54
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:L.54
Water bridges:
B:K.53
Salt bridges:
B:R.30
,
B:K.53
3 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.6:
6 residues within 4Å:
Chain B:
R.137
,
D.138
,
M.142
,
K.146
,
W.157
,
L.168
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:R.137
,
B:D.138
,
B:D.138
Water bridges:
B:K.146
GOL.7:
7 residues within 4Å:
Chain B:
A.126
,
K.127
,
Q.128
,
T.129
,
K.155
,
F.159
,
R.163
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:K.127
,
B:K.155
,
B:R.163
Water bridges:
B:R.163
GOL.8:
4 residues within 4Å:
Chain B:
D.123
,
I.150
,
T.152
,
Y.153
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:T.152
,
B:T.152
Water bridges:
B:D.123
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Unno, M. et al., Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors. J.Mol.Biol. (2011)
Release Date
2010-01-19
Peptides
Glutamate receptor, ionotropic kainate 1:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Glutamate receptor, ionotropic kainate 1
Toggle Identical (AB)
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2zns.1
|
2znt.1
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2znu.1
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3fuz.1
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3fuz.2
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3fv1.1
|
3fv1.2
|
3fv2.1
|
3fv2.2
|
3fv2.3
|
3fvg.1
|
3fvg.2
|
3fvg.3
|
3fvk.1
|
3fvk.2
|
3fvk.3
|
3fvn.1
|
3fvn.2
|
3fvn.3
|
3fvo.1
|
3fvo.2
|
3fvo.3
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