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SMTL ID : 5gt2.2
(1 other biounit)
Crystal Structure and Biochemical Features of dye-decolorizing peroxidase YfeX from Escherichia coli O157
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.09 Å
Oligo State
homo-dimer
Ligands
2 x
HEM
:
PROTOPORPHYRIN IX CONTAINING FE
(Non-covalent)
HEM.1:
24 residues within 4Å:
Chain A:
D.137
,
F.141
,
V.142
,
D.143
,
G.144
,
T.145
,
E.146
,
Q.174
,
W.176
,
H.178
,
R.197
,
H.215
,
L.216
,
V.219
,
D.220
,
I.230
,
R.232
,
L.246
,
F.248
,
Q.261
,
L.262
,
M.265
,
M.276
,
T.280
28
PLIP interactions
:
27 interactions with chain A
,
1 Ligand-Water interactions
Hydrophobic interactions:
A:F.141
,
A:W.176
,
A:L.216
,
A:V.219
,
A:V.219
,
A:I.230
,
A:L.246
,
A:F.248
,
A:F.248
,
A:F.248
,
A:Q.261
,
A:L.262
,
A:T.280
Hydrogen bonds:
A:D.143
,
A:G.144
,
A:T.145
,
A:E.146
Water bridges:
A:R.197
,
A:V.219
,
A:K.229
,
A:K.229
Salt bridges:
A:K.229
,
A:R.232
pi-Stacking:
A:H.215
,
A:F.248
pi-Cation interactions:
A:R.232
Metal complexes:
A:H.215
,
H
2
O.6
HEM.2:
24 residues within 4Å:
Chain B:
D.137
,
F.141
,
V.142
,
D.143
,
G.144
,
T.145
,
E.146
,
Q.174
,
W.176
,
H.178
,
I.195
,
R.197
,
H.215
,
V.219
,
D.220
,
I.230
,
R.232
,
L.246
,
F.248
,
Q.261
,
L.262
,
M.265
,
M.276
,
T.280
27
PLIP interactions
:
26 interactions with chain B
,
1 Ligand-Water interactions
Hydrophobic interactions:
B:F.141
,
B:W.176
,
B:I.195
,
B:V.219
,
B:V.219
,
B:V.219
,
B:I.230
,
B:L.246
,
B:F.248
,
B:F.248
,
B:F.248
,
B:Q.261
,
B:L.262
,
B:T.280
Hydrogen bonds:
B:D.143
,
B:G.144
,
B:T.145
,
B:E.146
Water bridges:
B:E.146
,
B:E.146
,
B:R.197
Salt bridges:
B:K.229
,
B:R.232
pi-Stacking:
B:F.248
pi-Cation interactions:
B:R.232
Metal complexes:
B:H.215
,
H
2
O.11
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Liu, X. et al., Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp(143) and Arg(232) play divergent roles toward different substrates. Biochem. Biophys. Res. Commun. (2017)
Release Date
2017-02-08
Peptides
Probable deferrochelatase/peroxidase YfeX:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
B
D
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Probable deferrochelatase/peroxidase YfeX
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