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SMTL ID : 6r33.1
Aspergillus niger ferulic acid decarboxylase (Fdc)in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid, following decarboxylation (Int3')
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.01 Å
Oligo State
homo-dimer
Ligands
2 x
MN
:
MANGANESE (II) ION
(Non-covalent)
MN.1:
5 residues within 4Å:
Chain A:
N.168
,
H.191
,
E.233
Ligands:
K.2
,
JQH.4
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:H.191
,
A:E.233
,
H
2
O.3
,
H
2
O.7
MN.5:
5 residues within 4Å:
Chain B:
N.168
,
H.191
,
E.233
Ligands:
K.6
,
JQH.8
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:H.191
,
B:E.233
,
H
2
O.33
,
H
2
O.37
4 x
K
:
POTASSIUM ION
(Non-covalent)
K.2:
7 residues within 4Å:
Chain A:
W.169
,
A.222
,
S.223
,
M.225
,
E.233
Ligands:
MN.1
,
JQH.4
3
PLIP interactions
:
3 interactions with chain A
Metal complexes:
A:A.222
,
A:M.225
,
A:E.233
K.3:
4 residues within 4Å:
Chain A:
R.421
,
D.427
,
D.459
,
L.461
5
PLIP interactions
:
4 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:R.421
,
A:D.427
,
A:D.459
,
A:L.461
,
H
2
O.50
K.6:
7 residues within 4Å:
Chain B:
W.169
,
A.222
,
S.223
,
M.225
,
E.233
Ligands:
MN.5
,
JQH.8
3
PLIP interactions
:
3 interactions with chain B
Metal complexes:
B:A.222
,
B:M.225
,
B:E.233
K.7:
4 residues within 4Å:
Chain B:
R.421
,
D.427
,
D.459
,
L.461
5
PLIP interactions
:
4 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:R.421
,
B:D.427
,
B:D.459
,
B:L.461
,
H
2
O.19
2 x
JQH
:
prFMN cofactor and phenylpropiolic acid adduct
(Non-covalent)
JQH.4:
29 residues within 4Å:
Chain A:
T.153
,
N.168
,
W.169
,
S.170
,
I.171
,
A.172
,
R.173
,
L.185
,
Q.190
,
H.191
,
S.223
,
S.224
,
M.225
,
P.226
,
E.233
,
E.282
,
M.283
,
S.314
,
C.316
,
E.322
,
T.323
,
I.327
,
K.391
,
Y.394
,
T.395
,
F.437
,
L.439
Ligands:
MN.1
,
K.2
24
PLIP interactions
:
24 interactions with chain A
Hydrophobic interactions:
A:I.171
,
A:I.171
,
A:R.173
,
A:I.327
,
A:I.327
,
A:Y.394
,
A:T.395
,
A:F.437
,
A:F.437
,
A:L.439
Hydrogen bonds:
A:N.168
,
A:I.171
,
A:I.171
,
A:R.173
,
A:Q.190
,
A:H.191
,
A:S.224
Water bridges:
A:S.170
,
A:L.185
,
A:I.192
,
A:K.391
,
A:K.391
Salt bridges:
A:H.191
,
A:K.391
JQH.8:
29 residues within 4Å:
Chain B:
T.153
,
N.168
,
W.169
,
S.170
,
I.171
,
A.172
,
R.173
,
L.185
,
Q.190
,
H.191
,
S.223
,
S.224
,
M.225
,
P.226
,
E.233
,
E.282
,
M.283
,
S.314
,
C.316
,
E.322
,
T.323
,
I.327
,
K.391
,
Y.394
,
T.395
,
F.437
,
L.439
Ligands:
MN.5
,
K.6
24
PLIP interactions
:
24 interactions with chain B
Hydrophobic interactions:
B:I.171
,
B:I.171
,
B:R.173
,
B:I.327
,
B:I.327
,
B:Y.394
,
B:T.395
,
B:F.437
,
B:F.437
,
B:L.439
Hydrogen bonds:
B:N.168
,
B:I.171
,
B:I.171
,
B:R.173
,
B:Q.190
,
B:H.191
,
B:S.224
Water bridges:
B:S.170
,
B:L.185
,
B:I.192
,
B:K.391
,
B:K.391
Salt bridges:
B:H.191
,
B:K.391
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Bailey, S.S. et al., Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition. To be published
Release Date
2019-08-28
Peptides
Ferulic acid decarboxylase 1:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
Export Alignment
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Secondary Structure
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Ferulic acid decarboxylase 1
Toggle Identical (AB)
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Cartoon
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Lines
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Surface
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