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SMTL ID : 5k4y.4
(5 other biounits)
Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei refined to 1.77 angstroms
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.77 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
25 residues within 4Å:
Chain A:
G.8
,
L.10
,
G.11
,
Q.12
,
I.13
,
D.34
,
V.35
,
L.53
,
D.54
,
C.55
,
L.76
,
P.77
,
A.78
,
M.80
,
I.94
,
P.116
,
S.117
,
T.118
,
Y.143
,
K.147
,
L.170
,
P.171
,
G.172
,
I.173
Ligands:
ACT.2
17
PLIP interactions
:
17 interactions with chain A
Hydrophobic interactions:
A:L.170
Hydrogen bonds:
A:G.8
,
A:L.10
,
A:Q.12
,
A:Q.12
,
A:Q.12
,
A:I.13
,
A:V.35
,
A:D.54
,
A:D.54
,
A:C.55
,
A:L.76
,
A:Y.143
,
A:K.147
,
A:I.173
Water bridges:
A:G.11
,
A:G.14
NAD.5:
25 residues within 4Å:
Chain B:
G.8
,
L.10
,
G.11
,
Q.12
,
I.13
,
D.34
,
V.35
,
L.53
,
D.54
,
C.55
,
L.76
,
P.77
,
A.78
,
M.80
,
I.94
,
P.116
,
S.117
,
T.118
,
Y.143
,
K.147
,
L.170
,
P.171
,
G.172
,
I.173
Ligands:
ACT.6
18
PLIP interactions
:
18 interactions with chain B
Hydrophobic interactions:
B:L.170
Hydrogen bonds:
B:G.8
,
B:L.10
,
B:Q.12
,
B:Q.12
,
B:Q.12
,
B:I.13
,
B:V.35
,
B:D.54
,
B:D.54
,
B:C.55
,
B:L.76
,
B:Y.143
,
B:K.147
,
B:I.173
Water bridges:
B:G.11
,
B:G.14
,
B:T.185
2 x
ACT
:
ACETATE ION
(Non-functional Binders)
ACT.2:
6 residues within 4Å:
Chain A:
M.80
,
T.118
,
I.119
,
Y.143
,
W.279
Ligands:
NAD.1
3
PLIP interactions
:
3 interactions with chain A
Hydrophobic interactions:
A:I.119
,
A:W.279
Hydrogen bonds:
A:T.118
ACT.6:
7 residues within 4Å:
Chain B:
M.80
,
T.118
,
I.119
,
Y.143
,
P.171
,
W.279
Ligands:
NAD.5
3
PLIP interactions
:
3 interactions with chain B
Hydrophobic interactions:
B:W.279
Hydrogen bonds:
B:T.118
,
B:Y.143
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.3:
5 residues within 4Å:
Chain A:
S.81
,
V.82
,
G.183
,
A.184
Ligands:
NA.4
Ligand excluded by PLIP
CL.7:
6 residues within 4Å:
Chain B:
M.80
,
S.81
,
V.82
,
G.183
,
A.184
Ligands:
NA.8
Ligand excluded by PLIP
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.4:
6 residues within 4Å:
Chain A:
M.80
,
S.81
,
V.82
,
R.83
,
G.183
Ligands:
CL.3
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:M.80
,
A:V.82
,
A:R.83
Water bridges:
A:M.80
NA.8:
4 residues within 4Å:
Chain B:
M.80
,
V.82
,
R.83
Ligands:
CL.7
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:M.80
,
B:V.82
,
B:R.83
Water bridges:
B:M.80
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Adjogatse, E. et al., Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Acta Crystallogr D Struct Biol (2018)
Release Date
2018-01-17
Peptides
L-threonine 3-dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
C
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L-threonine 3-dehydrogenase
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