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SMTL ID : 8bxx.2
(1 other biounit)
Crystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.97 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
29 residues within 4Å:
Chain A:
F.99
,
I.123
,
G.124
,
N.147
,
S.148
,
V.151
,
V.198
,
A.199
,
G.201
,
R.202
,
I.203
,
F.221
,
D.222
,
Q.223
,
H.224
,
N.255
,
A.256
,
P.257
,
H.259
,
T.262
,
T.283
,
A.284
,
R.285
,
D.309
,
V.310
,
H.333
,
S.335
,
G.336
Ligands:
AZI.2
15
PLIP interactions
:
15 interactions with chain A
Hydrophobic interactions:
A:I.123
,
A:V.151
,
A:I.203
Hydrogen bonds:
A:R.202
,
A:I.203
,
A:Q.223
,
A:D.309
,
A:G.336
Water bridges:
A:D.126
,
A:S.148
,
A:S.148
,
A:G.201
,
A:G.204
,
A:L.258
Salt bridges:
A:R.202
NAD.4:
27 residues within 4Å:
Chain B:
F.99
,
I.123
,
N.147
,
S.148
,
V.151
,
A.199
,
G.201
,
R.202
,
I.203
,
F.221
,
D.222
,
Q.223
,
H.224
,
N.255
,
A.256
,
P.257
,
H.259
,
T.262
,
T.283
,
A.284
,
R.285
,
D.309
,
V.310
,
H.333
,
S.335
,
G.336
Ligands:
AZI.5
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:I.123
,
B:V.151
,
B:I.203
Hydrogen bonds:
B:R.202
,
B:I.203
,
B:Q.223
,
B:Q.223
,
B:H.224
,
B:D.309
,
B:G.336
Water bridges:
B:S.125
,
B:D.126
,
B:S.148
,
B:S.148
,
B:G.201
,
B:R.202
,
B:G.204
,
B:L.258
,
B:G.261
Salt bridges:
B:R.202
2 x
AZI
:
AZIDE ION
(Non-covalent)
AZI.2:
8 residues within 4Å:
Chain A:
P.98
,
F.99
,
G.122
,
I.123
,
N.147
,
R.285
,
H.333
Ligands:
NAD.1
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:I.123
,
A:I.123
,
A:I.123
,
A:N.147
,
A:R.285
,
A:R.285
AZI.5:
8 residues within 4Å:
Chain B:
P.98
,
F.99
,
G.122
,
I.123
,
N.147
,
R.285
,
H.333
Ligands:
NAD.4
6
PLIP interactions
:
6 interactions with chain B
Hydrogen bonds:
B:I.123
,
B:I.123
,
B:N.147
,
B:R.285
,
B:R.285
,
B:H.333
2 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.3:
9 residues within 4Å:
Chain A:
V.94
,
S.96
,
A.102
,
L.104
,
A.118
,
V.119
,
T.120
,
H.127
,
V.128
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:S.96
,
A:A.102
,
A:V.119
EDO.6:
8 residues within 4Å:
Chain B:
V.94
,
S.96
,
A.102
,
L.104
,
V.119
,
T.120
,
H.127
,
V.128
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:S.96
,
B:A.102
,
B:A.102
,
B:V.119
Water bridges:
B:T.120
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Rubini, R. et al., From the amelioration of a NADP+-dependent formate dehydrogenase to the discovery of a new enzyme: round trip from theory to practice. ChemCatChem (2020)
Release Date
2023-01-18
Peptides
Formate dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
BB
B
CC
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Formate dehydrogenase
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6t8c.1
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6t8c.2
|
8bxx.1
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