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SMTL ID : 3n7u.4
(5 other biounits)
NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.00 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
27 residues within 4Å:
Chain A:
F.71
,
I.95
,
N.119
,
V.120
,
V.123
,
A.172
,
G.173
,
R.174
,
I.175
,
H.193
,
D.194
,
R.195
,
L.196
,
M.228
,
P.229
,
T.234
,
N.255
,
A.256
,
R.257
,
D.281
,
V.282
,
H.305
,
S.307
,
G.308
,
Q.349
,
Y.350
Ligands:
AZI.2
18
PLIP interactions
:
18 interactions with chain A
Hydrophobic interactions:
A:I.95
,
A:V.123
,
A:I.175
Hydrogen bonds:
A:D.98
,
A:R.174
,
A:I.175
,
A:R.195
,
A:D.281
,
A:G.308
Water bridges:
A:G.173
,
A:R.174
,
A:G.176
,
A:L.230
,
A:L.230
,
A:Q.349
,
A:R.351
,
A:R.351
Salt bridges:
A:R.174
NAD.5:
27 residues within 4Å:
Chain B:
F.71
,
I.95
,
G.96
,
N.119
,
V.120
,
V.123
,
A.172
,
G.173
,
R.174
,
I.175
,
H.193
,
D.194
,
R.195
,
M.228
,
P.229
,
T.234
,
N.255
,
A.256
,
R.257
,
D.281
,
V.282
,
H.305
,
S.307
,
G.308
,
Q.349
,
Y.350
Ligands:
AZI.6
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:I.95
,
B:V.123
,
B:I.175
Hydrogen bonds:
B:A.172
,
B:R.174
,
B:I.175
,
B:R.195
,
B:N.255
,
B:G.308
Water bridges:
B:G.96
,
B:G.173
,
B:R.174
,
B:R.174
,
B:G.176
,
B:R.195
,
B:R.195
,
B:L.230
,
B:Q.349
,
B:Y.350
Salt bridges:
B:R.174
2 x
AZI
:
AZIDE ION
(Non-covalent)
AZI.2:
8 residues within 4Å:
Chain A:
P.70
,
F.71
,
G.94
,
I.95
,
N.119
,
R.257
,
H.305
Ligands:
NAD.1
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:I.95
,
A:N.119
,
A:R.257
,
A:R.257
AZI.6:
8 residues within 4Å:
Chain B:
P.70
,
F.71
,
G.94
,
I.95
,
N.119
,
R.257
,
H.305
Ligands:
NAD.5
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:I.95
,
B:N.119
,
B:R.257
,
B:R.257
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.3:
3 residues within 4Å:
Chain A:
T.111
,
K.342
,
D.343
4
PLIP interactions
:
4 interactions with chain A
Water bridges:
A:Y.339
,
A:K.342
,
A:D.343
Salt bridges:
A:K.342
SO4.7:
4 residues within 4Å:
Chain B:
K.88
,
T.111
,
K.342
Ligands:
GOL.8
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:T.111
Water bridges:
B:K.88
,
B:K.88
Salt bridges:
B:K.88
,
B:K.342
3 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.4:
3 residues within 4Å:
Chain A:
G.31
,
R.33
,
D.34
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:G.31
,
A:R.33
,
A:D.34
Water bridges:
A:R.33
GOL.8:
8 residues within 4Å:
Chain B:
R.327
,
Y.328
,
G.331
,
E.332
,
F.334
,
Y.339
,
K.342
Ligands:
SO4.7
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:R.327
,
B:Y.339
Water bridges:
B:G.331
GOL.9:
5 residues within 4Å:
Chain B:
Y.75
,
V.76
,
T.77
,
H.99
,
D.101
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:H.99
Water bridges:
B:I.100
,
B:D.101
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Shabalin, I.G. et al., Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana. To be Published
Release Date
2010-06-09
Peptides
Formate dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
G
B
H
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Formate dehydrogenase
Toggle Identical (AB)
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|
3jtm.2
|
3n7u.1
|
3n7u.2
|
3n7u.3
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|
3n7u.6
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