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SMTL ID : 3e4v.1
Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.40 Å
Oligo State
homo-dimer
Ligands
2 x
FMN
:
FLAVIN MONONUCLEOTIDE
(Non-covalent)
FMN.1:
28 residues within 4Å:
Chain A:
I.20
,
N.33
,
L.34
,
M.35
,
T.36
,
M.37
,
G.38
,
F.39
,
I.53
,
I.54
,
G.55
,
W.57
,
D.58
,
Y.59
,
S.60
,
V.84
,
I.86
,
G.87
,
N.88
,
C.89
,
S.90
,
G.91
,
K.96
,
H.159
Chain B:
M.178
,
K.180
,
W.181
Ligands:
GOL.9
20
PLIP interactions
:
18 interactions with chain A
,
2 interactions with chain B
Hydrophobic interactions:
A:T.36
Hydrogen bonds:
A:N.33
,
A:T.36
,
A:T.36
,
A:G.38
,
A:F.39
,
A:I.53
,
A:G.55
,
A:D.58
,
A:D.58
,
A:Y.59
,
A:S.60
,
A:S.60
,
A:G.87
,
A:C.89
,
A:S.90
,
A:G.91
,
B:K.180
Salt bridges:
A:K.96
,
B:K.180
FMN.7:
29 residues within 4Å:
Chain A:
M.178
,
K.180
,
W.181
Chain B:
I.20
,
N.33
,
L.34
,
M.35
,
T.36
,
M.37
,
G.38
,
F.39
,
I.53
,
I.54
,
G.55
,
W.57
,
D.58
,
Y.59
,
S.60
,
V.84
,
I.86
,
G.87
,
N.88
,
C.89
,
S.90
,
G.91
,
K.96
,
H.159
,
F.165
Ligands:
GOL.4
20
PLIP interactions
:
18 interactions with chain B
,
2 interactions with chain A
Hydrophobic interactions:
B:T.36
,
B:F.165
Hydrogen bonds:
B:N.33
,
B:T.36
,
B:T.36
,
B:G.38
,
B:F.39
,
B:I.53
,
B:G.55
,
B:D.58
,
B:Y.59
,
B:S.60
,
B:S.60
,
B:G.87
,
B:C.89
,
B:S.90
,
B:G.91
,
A:K.180
Salt bridges:
B:K.96
,
A:K.180
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.2:
2 residues within 4Å:
Chain A:
H.40
Chain B:
H.40
4
PLIP interactions
:
1 interactions with chain A
,
3 interactions with chain B
Water bridges:
A:H.40
,
B:H.40
,
B:H.40
Hydrogen bonds:
B:H.40
NA.8:
1 residues within 4Å:
Chain B:
D.111
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:D.111
1 x
ACT
:
ACETATE ION
(Non-functional Binders)
ACT.3:
5 residues within 4Å:
Chain A:
G.175
,
M.178
,
W.181
,
R.182
Chain B:
D.162
2
PLIP interactions
:
1 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:D.162
Salt bridges:
A:R.182
4 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.4:
5 residues within 4Å:
Chain A:
H.45
,
M.178
,
W.181
Chain B:
W.57
Ligands:
FMN.7
5
PLIP interactions
:
2 interactions with chain A
,
3 interactions with chain B
Hydrogen bonds:
A:W.181
,
B:W.57
Water bridges:
A:H.45
,
B:H.159
,
B:H.159
GOL.5:
3 residues within 4Å:
Chain A:
L.94
,
H.99
Ligands:
PEG.6
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:H.99
GOL.9:
6 residues within 4Å:
Chain A:
W.57
Chain B:
H.45
,
M.178
,
W.181
Ligands:
FMN.1
,
GOL.10
3
PLIP interactions
:
1 interactions with chain A
,
2 interactions with chain B
Water bridges:
A:H.159
,
B:H.45
Hydrogen bonds:
B:W.181
GOL.10:
7 residues within 4Å:
Chain A:
F.39
,
I.53
,
W.57
Chain B:
M.43
,
Q.44
,
H.45
Ligands:
GOL.9
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:H.45
,
B:H.45
Water bridges:
B:E.46
1 x
PEG
:
DI(HYDROXYETHYL)ETHER
(Non-functional Binders)
PEG.6:
2 residues within 4Å:
Chain A:
A.93
Ligands:
GOL.5
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Joint Center for Structural Genomics (JCSG), Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution. To be published
Release Date
2008-09-02
Peptides
NADH:FMN oxidoreductase like protein:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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NADH:FMN oxidoreductase like protein
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