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SMTL ID : 7x32.1
(3 other biounits)
Crystal structure of E. coli NfsB in complex with berberine
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.83 Å
Oligo State
homo-dimer
Ligands
2 x
FMN
:
FLAVIN MONONUCLEOTIDE
(Non-covalent)
FMN.1:
24 residues within 4Å:
Chain A:
R.10
,
H.11
,
S.12
,
K.14
,
F.70
,
N.71
,
K.74
,
Y.144
,
V.162
,
P.163
,
I.164
,
E.165
,
G.166
,
N.200
,
K.205
,
R.207
Chain B:
P.38
,
S.39
,
S.40
,
T.41
,
N.42
,
Q.142
,
L.145
Ligands:
BER.4
22
PLIP interactions
:
4 interactions with chain B
,
18 interactions with chain A
Hydrogen bonds:
B:S.39
,
B:T.41
,
B:N.42
,
A:S.12
,
A:S.12
,
A:S.12
,
A:K.14
,
A:N.71
,
A:N.71
,
A:K.74
,
A:E.165
,
A:G.166
,
A:N.200
Water bridges:
B:R.107
,
A:K.205
,
A:R.207
,
A:R.207
Hydrophobic interactions:
A:Y.144
,
A:P.163
Salt bridges:
A:R.10
,
A:K.205
,
A:R.207
FMN.3:
21 residues within 4Å:
Chain A:
P.38
,
S.39
,
S.40
,
T.41
,
N.42
,
Q.142
,
L.145
Chain B:
R.10
,
H.11
,
S.12
,
K.14
,
F.70
,
N.71
,
K.74
,
P.163
,
I.164
,
E.165
,
G.166
,
N.200
,
K.205
,
R.207
19
PLIP interactions
:
5 interactions with chain A
,
14 interactions with chain B
Hydrogen bonds:
A:S.39
,
A:T.41
,
A:N.42
,
A:Q.142
,
B:S.12
,
B:S.12
,
B:S.12
,
B:S.12
,
B:E.165
,
B:N.200
Water bridges:
A:R.107
,
B:K.14
,
B:K.205
,
B:R.207
,
B:R.207
Hydrophobic interactions:
B:F.70
Salt bridges:
B:R.10
,
B:K.205
,
B:R.207
1 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.2:
5 residues within 4Å:
Chain A:
D.2
,
I.4
,
S.5
Chain B:
E.25
,
Q.29
4
PLIP interactions
:
2 interactions with chain B
,
2 interactions with chain A
Hydrogen bonds:
B:E.25
,
B:Q.29
,
A:D.2
,
A:S.5
1 x
BER
:
BERBERINE
(Non-covalent)
BER.4:
14 residues within 4Å:
Chain A:
K.14
,
F.70
,
F.199
,
L.203
Chain B:
S.40
,
T.41
,
E.102
,
R.107
,
F.108
,
N.117
,
R.121
,
F.124
Ligands:
FMN.1
,
DMS.5
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:T.41
,
B:R.107
,
B:N.117
1 x
DMS
:
DIMETHYL SULFOXIDE
(Non-functional Binders)
DMS.5:
4 residues within 4Å:
Chain B:
N.117
,
G.120
,
R.121
Ligands:
BER.4
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Wen, H.Y. et al., Structural basis for the transformation of the traditional medicine berberine by bacterial nitroreductase. Acta Crystallogr D Struct Biol (2022)
Release Date
2022-10-12
Peptides
Dihydropteridine reductase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
C
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Dihydropteridine reductase
Toggle Identical (AB)
Related Entries With Identical Sequence
1ds7.1
|
1icr.1
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1icu.1
|
1icu.2
|
1icv.1
|
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|
1idt.1
|
1oo5.1
|
1oo6.1
|
1oon.1
|
1ooq.1
|
1yki.1
|
1yki.2
|
1ylr.1
|
1ylu.1
|
7x32.2
|
7x32.3
|
7x32.4
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