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SMTL ID : 3ajr.1
Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.77 Å
Oligo State
homo-dimer
Ligands
2 x
VAH
:
(3R)-3-hydroxy-L-norvaline
(Non-covalent)
VAH.1:
12 residues within 4Å:
Chain A:
L.73
,
S.74
,
T.112
,
I.113
,
F.137
,
Y.164
,
P.165
,
G.177
,
T.178
,
T.179
,
W.273
Ligands:
NAD.2
11
PLIP interactions
:
11 interactions with chain A
Hydrophobic interactions:
A:I.113
,
A:T.179
,
A:W.273
Hydrogen bonds:
A:S.74
,
A:T.112
,
A:T.178
,
A:T.179
,
A:T.179
Water bridges:
A:Q.10
,
A:T.179
,
A:D.180
VAH.4:
11 residues within 4Å:
Chain B:
L.73
,
S.74
,
T.112
,
I.113
,
F.137
,
Y.164
,
P.165
,
G.177
,
T.178
,
T.179
Ligands:
NAD.5
8
PLIP interactions
:
8 interactions with chain B
Hydrophobic interactions:
B:I.113
,
B:T.179
Hydrogen bonds:
B:S.74
,
B:T.178
,
B:T.179
,
B:T.179
Water bridges:
B:A.75
,
B:I.167
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.2:
26 residues within 4Å:
Chain A:
G.6
,
S.8
,
G.9
,
Q.10
,
I.11
,
D.32
,
I.33
,
V.34
,
L.46
,
D.47
,
V.48
,
L.69
,
A.70
,
G.71
,
L.73
,
V.87
,
P.110
,
S.111
,
T.112
,
F.137
,
K.141
,
Y.164
,
P.165
,
G.166
,
I.167
Ligands:
VAH.1
20
PLIP interactions
:
20 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:D.47
,
A:V.48
,
A:S.49
,
A:L.69
,
A:K.141
,
A:I.167
Water bridges:
A:G.12
,
A:I.72
,
A:K.141
,
A:T.179
pi-Stacking:
A:Y.164
NAD.5:
25 residues within 4Å:
Chain B:
S.8
,
G.9
,
Q.10
,
I.11
,
D.32
,
I.33
,
V.34
,
L.46
,
D.47
,
V.48
,
L.69
,
A.70
,
G.71
,
L.73
,
V.87
,
P.110
,
S.111
,
T.112
,
F.137
,
K.141
,
Y.164
,
P.165
,
G.166
,
I.167
Ligands:
VAH.4
19
PLIP interactions
:
19 interactions with chain B
Hydrophobic interactions:
B:Y.164
Hydrogen bonds:
B:S.8
,
B:S.8
,
B:Q.10
,
B:Q.10
,
B:I.11
,
B:G.12
,
B:I.33
,
B:D.47
,
B:V.48
,
B:S.49
,
B:L.69
,
B:K.141
,
B:I.167
Water bridges:
B:G.6
,
B:G.9
,
B:I.72
,
B:K.141
pi-Stacking:
B:Y.164
2 x
MPD
:
(4S)-2-METHYL-2,4-PENTANEDIOL
(Non-functional Binders)
MPD.3:
2 residues within 4Å:
Chain A:
E.173
,
Y.187
4
PLIP interactions
:
4 interactions with chain A
Hydrophobic interactions:
A:E.173
,
A:Y.187
,
A:Y.187
,
A:Y.187
MPD.6:
7 residues within 4Å:
Chain A:
Y.150
,
E.153
,
K.154
Chain B:
R.134
,
K.268
,
I.269
,
T.272
7
PLIP interactions
:
3 interactions with chain A
,
4 interactions with chain B
Hydrophobic interactions:
A:Y.150
,
A:K.154
,
B:R.134
,
B:K.268
,
B:I.269
,
B:T.272
Hydrogen bonds:
A:E.153
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
2011-06-15
Peptides
NDP-sugar epimerase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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