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SMTL ID : 7t6c.1
E. coli dihydroorotate dehydrogenase bound to the ubiquinone surrogate DCIP
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.53 Å
Oligo State
homo-dimer
Ligands
1 x
PE4
:
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
(Non-functional Binders)
PE4.1:
6 residues within 4Å:
Chain A:
V.38
,
F.53
,
Q.57
,
R.60
,
I.61
,
F.66
No protein-ligand interaction detected (PLIP)
2 x
ORO
:
OROTIC ACID
(Non-covalent)
ORO.2:
12 residues within 4Å:
Chain A:
K.98
,
N.143
,
M.145
,
G.146
,
F.147
,
N.204
,
S.207
,
P.208
,
N.209
,
N.278
,
T.279
Ligands:
FMN.4
9
PLIP interactions
:
9 interactions with chain A
Hydrogen bonds:
A:N.143
,
A:G.146
,
A:F.147
,
A:N.204
,
A:S.207
,
A:N.209
,
A:N.278
,
A:N.278
Salt bridges:
A:K.98
ORO.6:
12 residues within 4Å:
Chain B:
K.98
,
N.143
,
M.145
,
G.146
,
F.147
,
N.204
,
S.207
,
P.208
,
N.209
,
N.278
,
T.279
Ligands:
FMN.8
10
PLIP interactions
:
10 interactions with chain B
Hydrogen bonds:
B:N.143
,
B:M.145
,
B:G.146
,
B:F.147
,
B:N.204
,
B:S.207
,
B:N.209
,
B:N.278
,
B:N.278
Salt bridges:
B:K.98
2 x
RLM
:
2,6-bis(chloranyl)-4-[(4-hydroxyphenyl)amino]phenol
(Non-covalent)
RLM.3:
13 residues within 4Å:
Chain A:
L.42
,
F.43
,
P.47
,
A.50
,
H.51
,
T.54
,
F.55
,
L.58
,
M.109
,
L.132
,
R.134
,
F.353
,
I.354
8
PLIP interactions
:
8 interactions with chain A
Hydrophobic interactions:
A:H.51
,
A:T.54
,
A:T.54
,
A:F.55
,
A:L.58
,
A:F.353
Hydrogen bonds:
A:H.51
,
A:R.134
RLM.7:
11 residues within 4Å:
Chain B:
L.42
,
F.43
,
P.47
,
A.50
,
H.51
,
T.54
,
L.132
,
R.134
,
L.141
,
F.353
,
I.354
5
PLIP interactions
:
5 interactions with chain B
Hydrophobic interactions:
B:A.50
,
B:F.353
Hydrogen bonds:
B:T.54
,
B:R.134
,
B:R.134
2 x
FMN
:
FLAVIN MONONUCLEOTIDE
(Non-covalent)
FMN.4:
24 residues within 4Å:
Chain A:
A.93
,
A.94
,
G.95
,
K.98
,
G.117
,
T.118
,
L.132
,
N.143
,
N.171
,
N.204
,
K.249
,
T.277
,
N.278
,
T.279
,
S.299
,
G.300
,
L.303
,
V.327
,
G.328
,
G.329
,
I.349
,
Y.350
,
S.351
Ligands:
ORO.2
20
PLIP interactions
:
20 interactions with chain A
Hydrophobic interactions:
A:L.132
,
A:N.143
,
A:Y.350
Hydrogen bonds:
A:A.94
,
A:K.98
,
A:T.118
,
A:T.118
,
A:N.171
,
A:N.204
,
A:K.249
,
A:K.249
,
A:N.278
,
A:S.299
,
A:G.300
,
A:G.329
,
A:Y.350
,
A:S.351
Water bridges:
A:G.352
,
A:G.352
pi-Stacking:
A:Y.350
FMN.8:
23 residues within 4Å:
Chain B:
A.93
,
A.94
,
G.95
,
K.98
,
G.117
,
T.118
,
L.132
,
N.143
,
N.171
,
N.204
,
K.249
,
T.277
,
N.278
,
T.279
,
S.299
,
G.300
,
L.303
,
V.327
,
G.328
,
G.329
,
Y.350
,
S.351
Ligands:
ORO.6
18
PLIP interactions
:
18 interactions with chain B
Hydrophobic interactions:
B:L.132
,
B:N.143
,
B:Y.350
Hydrogen bonds:
B:A.94
,
B:T.118
,
B:T.118
,
B:N.171
,
B:N.204
,
B:K.249
,
B:K.249
,
B:N.278
,
B:S.299
,
B:G.300
,
B:G.329
,
B:I.330
,
B:Y.350
,
B:S.351
Water bridges:
B:G.328
1 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.5:
3 residues within 4Å:
Chain B:
V.267
,
N.270
,
R.321
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:N.270
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Horwitz, S.M. et al., Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines. Rsc Chem Biol (2022)
Release Date
2022-03-02
Peptides
Dihydroorotate dehydrogenase (quinone):
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Dihydroorotate dehydrogenase (quinone)
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7t5k.1
|
7t5y.1
|
7t6h.1
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