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SMTL ID : 5lc1.1
(5 other biounits)
L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.10 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
26 residues within 4Å:
Chain A:
G.9
,
L.11
,
G.12
,
Q.13
,
I.14
,
D.35
,
V.36
,
L.54
,
D.55
,
C.56
,
L.77
,
P.78
,
A.79
,
M.81
,
I.95
,
P.117
,
S.118
,
T.119
,
Y.144
,
K.148
,
L.171
,
P.172
,
G.173
,
I.174
,
G.182
Ligands:
PYR.2
19
PLIP interactions
:
19 interactions with chain A
Hydrophobic interactions:
A:L.171
Hydrogen bonds:
A:G.9
,
A:L.11
,
A:Q.13
,
A:Q.13
,
A:Q.13
,
A:I.14
,
A:G.15
,
A:V.36
,
A:D.55
,
A:C.56
,
A:L.77
,
A:K.148
,
A:I.174
Water bridges:
A:G.12
,
A:P.181
,
A:G.182
,
A:G.182
,
A:G.182
NAD.4:
26 residues within 4Å:
Chain B:
G.9
,
L.11
,
G.12
,
Q.13
,
I.14
,
D.35
,
V.36
,
L.54
,
D.55
,
C.56
,
L.77
,
P.78
,
A.79
,
M.81
,
I.95
,
P.117
,
S.118
,
T.119
,
Y.144
,
K.148
,
L.171
,
P.172
,
G.173
,
I.174
,
G.182
Ligands:
PYR.5
22
PLIP interactions
:
22 interactions with chain B
Hydrophobic interactions:
B:L.171
Hydrogen bonds:
B:G.9
,
B:L.11
,
B:Q.13
,
B:Q.13
,
B:Q.13
,
B:I.14
,
B:V.36
,
B:D.55
,
B:C.56
,
B:L.77
,
B:K.148
,
B:I.174
Water bridges:
B:G.12
,
B:G.15
,
B:R.84
,
B:P.181
,
B:G.182
,
B:G.182
,
B:T.186
,
B:T.186
,
B:T.186
2 x
PYR
:
PYRUVIC ACID
(Non-covalent)
PYR.2:
10 residues within 4Å:
Chain A:
M.81
,
S.82
,
T.119
,
Y.144
,
G.173
,
G.184
,
A.185
,
T.186
,
W.280
Ligands:
NAD.1
7
PLIP interactions
:
7 interactions with chain A
Hydrophobic interactions:
A:W.280
Hydrogen bonds:
A:S.82
,
A:S.82
,
A:S.82
,
A:Y.144
,
A:A.185
,
A:T.186
PYR.5:
11 residues within 4Å:
Chain B:
M.81
,
S.82
,
T.119
,
I.120
,
Y.144
,
G.173
,
G.184
,
A.185
,
T.186
,
W.280
Ligands:
NAD.4
8
PLIP interactions
:
8 interactions with chain B
Hydrophobic interactions:
B:I.120
,
B:W.280
Hydrogen bonds:
B:S.82
,
B:S.82
,
B:S.82
,
B:Y.144
,
B:A.185
,
B:T.186
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.3:
3 residues within 4Å:
Chain A:
E.210
,
S.211
,
D.282
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:S.211
,
A:S.211
,
A:D.282
Water bridges:
A:K.129
NA.8:
4 residues within 4Å:
Chain B:
K.129
,
E.210
,
S.211
,
D.282
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:K.129
,
B:E.210
,
B:E.210
,
B:S.211
,
B:D.282
1 x
BME
:
BETA-MERCAPTOETHANOL
(Non-functional Binders)
BME.6:
7 residues within 4Å:
Chain B:
Y.188
,
H.191
,
M.192
,
S.195
,
C.202
,
V.203
,
P.205
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:H.191
1 x
ACT
:
ACETATE ION
(Non-functional Binders)
ACT.7:
5 residues within 4Å:
Chain B:
D.17
,
S.176
,
A.177
,
A.178
,
Y.216
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:A.177
,
B:A.178
,
B:Y.216
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
2016-07-27
Peptides
L-threonine 3-dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
A
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L-threonine 3-dehydrogenase
Toggle Identical (AB)
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5k4t.1
|
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|
5l9a.1
|
5l9a.2
|
5lc1.2
|
5lc1.3
|
5lc1.4
|
5lc1.5
|
5lc1.6
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