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SMTL ID : 3tfj.1
DMSP-dependent demethylase from P. ubique - with cofactor THF
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
THG
:
(6S)-5,6,7,8-TETRAHYDROFOLATE
(Non-covalent)
THG.1:
17 residues within 4Å:
Chain A:
Y.32
,
E.63
,
Y.95
,
D.108
,
V.110
,
S.122
,
I.123
,
A.124
,
F.177
,
F.178
,
G.196
,
W.197
,
K.199
,
E.204
,
Y.206
,
L.244
,
Y.265
21
PLIP interactions
:
21 interactions with chain A
Hydrophobic interactions:
A:Y.95
,
A:V.110
,
A:F.177
,
A:L.244
Hydrogen bonds:
A:D.108
,
A:S.122
,
A:S.122
,
A:S.122
,
A:W.197
,
A:Y.265
,
A:Y.265
Water bridges:
A:E.63
,
A:R.83
,
A:S.195
,
A:G.196
,
A:G.196
,
A:W.197
Salt bridges:
A:E.63
,
A:R.83
,
A:K.199
,
A:E.204
THG.5:
17 residues within 4Å:
Chain B:
Y.32
,
E.63
,
Y.95
,
D.108
,
V.110
,
S.122
,
I.123
,
A.124
,
F.177
,
F.178
,
G.196
,
W.197
,
K.199
,
E.204
,
Y.206
,
L.244
,
Y.265
18
PLIP interactions
:
18 interactions with chain B
Hydrophobic interactions:
B:V.110
,
B:F.177
,
B:L.244
Hydrogen bonds:
B:D.108
,
B:S.122
,
B:S.122
,
B:S.122
,
B:W.197
,
B:Y.206
,
B:Y.265
Water bridges:
B:R.83
,
B:S.195
,
B:G.196
,
B:G.196
,
B:W.197
Salt bridges:
B:E.63
,
B:K.199
,
B:E.204
2 x
ACT
:
ACETATE ION
(Non-functional Binders)
ACT.2:
3 residues within 4Å:
Chain A:
Y.32
,
W.197
,
S.246
8
PLIP interactions
:
7 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:Y.32
,
A:W.197
Hydrogen bonds:
A:S.246
Water bridges:
A:Y.32
,
A:R.239
,
A:S.246
,
A:N.249
Salt bridges:
B:R.11
ACT.6:
3 residues within 4Å:
Chain B:
Y.32
,
W.197
,
S.246
6
PLIP interactions
:
5 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:Y.32
,
B:W.197
Hydrogen bonds:
B:S.246
Water bridges:
B:R.239
,
B:N.249
Salt bridges:
A:R.11
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.3:
9 residues within 4Å:
Chain A:
D.125
,
S.126
,
Y.247
Chain B:
R.13
,
H.34
,
D.127
,
I.129
,
F.130
,
E.147
4
PLIP interactions
:
2 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:D.125
,
A:Y.247
,
B:H.34
Water bridges:
B:R.13
GOL.7:
9 residues within 4Å:
Chain A:
R.13
,
H.34
,
D.127
,
I.129
,
F.130
,
E.147
Chain B:
D.125
,
S.126
,
Y.247
4
PLIP interactions
:
1 interactions with chain B
,
3 interactions with chain A
Hydrogen bonds:
B:D.125
Water bridges:
A:R.13
,
A:R.13
,
A:R.13
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.4:
7 residues within 4Å:
Chain A:
T.15
,
L.36
,
L.37
,
D.59
,
V.60
,
A.61
,
A.62
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:D.59
,
A:A.62
NA.8:
7 residues within 4Å:
Chain B:
T.15
,
L.36
,
L.37
,
D.59
,
V.60
,
A.61
,
A.62
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:D.59
,
B:A.61
,
B:A.62
Water bridges:
B:T.15
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Schuller, D.J. et al., Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Protein Sci. (2012)
Release Date
2011-12-28
Peptides
GcvT-like Aminomethyltransferase protein:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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GcvT-like Aminomethyltransferase protein
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3tfh.1
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3tfi.1
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