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SMTL ID : 3a4v.1
Crystal structure of pyruvate bound L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.78 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
25 residues within 4Å:
Chain A:
G.6
,
S.8
,
G.9
,
Q.10
,
I.11
,
D.32
,
I.33
,
L.46
,
D.47
,
V.48
,
L.69
,
A.70
,
G.71
,
L.73
,
V.87
,
P.110
,
S.111
,
T.112
,
Y.137
,
K.141
,
Y.164
,
P.165
,
G.166
,
I.167
Ligands:
PYR.2
19
PLIP interactions
:
19 interactions with chain A
Hydrophobic interactions:
A:Y.164
Hydrogen bonds:
A:G.6
,
A:S.8
,
A:S.8
,
A:Q.10
,
A:Q.10
,
A:I.11
,
A:I.33
,
A:D.47
,
A:V.48
,
A:L.69
,
A:G.71
,
A:Y.137
,
A:K.141
,
A:I.167
,
A:T.179
Water bridges:
A:G.9
,
A:G.12
pi-Stacking:
A:Y.164
NAD.4:
26 residues within 4Å:
Chain B:
G.6
,
S.8
,
G.9
,
Q.10
,
I.11
,
D.32
,
I.33
,
L.46
,
D.47
,
V.48
,
S.49
,
L.69
,
A.70
,
G.71
,
L.73
,
V.87
,
P.110
,
S.111
,
T.112
,
Y.137
,
K.141
,
Y.164
,
P.165
,
G.166
,
I.167
Ligands:
PYR.5
19
PLIP interactions
:
19 interactions with chain B
Hydrophobic interactions:
B:Y.164
Hydrogen bonds:
B:G.6
,
B:Q.10
,
B:Q.10
,
B:I.11
,
B:I.33
,
B:D.47
,
B:D.47
,
B:V.48
,
B:S.49
,
B:L.69
,
B:G.71
,
B:K.141
,
B:I.167
Water bridges:
B:G.9
,
B:G.12
,
B:I.72
,
B:K.141
,
B:T.179
2 x
PYR
:
PYRUVIC ACID
(Non-covalent)
PYR.2:
8 residues within 4Å:
Chain A:
L.73
,
S.74
,
T.112
,
Y.137
,
T.178
,
T.179
,
W.273
Ligands:
NAD.1
8
PLIP interactions
:
8 interactions with chain A
Hydrophobic interactions:
A:T.179
,
A:W.273
Hydrogen bonds:
A:S.74
,
A:S.74
,
A:S.74
,
A:T.178
,
A:T.178
,
A:T.179
PYR.5:
10 residues within 4Å:
Chain B:
L.73
,
S.74
,
T.112
,
Y.137
,
P.165
,
G.166
,
T.178
,
T.179
,
W.273
Ligands:
NAD.4
10
PLIP interactions
:
10 interactions with chain B
Hydrophobic interactions:
B:T.179
,
B:W.273
Hydrogen bonds:
B:S.74
,
B:S.74
,
B:S.74
,
B:T.112
,
B:Y.137
,
B:T.179
Water bridges:
B:A.75
,
B:T.178
2 x
MPD
:
(4S)-2-METHYL-2,4-PENTANEDIOL
(Non-functional Binders)
MPD.3:
4 residues within 4Å:
Chain A:
E.173
,
V.183
,
E.184
,
Y.187
6
PLIP interactions
:
6 interactions with chain A
Hydrophobic interactions:
A:E.173
,
A:E.173
,
A:V.183
,
A:E.184
,
A:Y.187
,
A:Y.187
MPD.6:
5 residues within 4Å:
Chain A:
E.153
,
K.154
Chain B:
R.134
,
T.135
,
K.268
3
PLIP interactions
:
2 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:T.135
,
B:K.268
,
A:K.154
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Yoneda, K. et al., Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium. J.Biol.Chem. (2012)
Release Date
2010-07-28
Peptides
NDP-sugar epimerase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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NDP-sugar epimerase
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3a1n.1
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