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SMTL ID : 1umd.1
branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as an intermediate
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
hetero-oligomer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
4 residues within 4Å:
Chain A:
D.175
,
N.204
,
Y.206
Ligands:
TDP.3
3
PLIP interactions
:
2 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:D.175
,
A:Y.206
,
H
2
O.32
MG.2:
4 residues within 4Å:
Chain C:
D.175
,
N.204
,
Y.206
Ligands:
TDP.5
3
PLIP interactions
:
2 interactions with chain C
,
1 Ligand-Water interactions
Metal complexes:
C:D.175
,
C:Y.206
,
H
2
O.666
2 x
TDP
:
THIAMIN DIPHOSPHATE
(Non-covalent)
TDP.3:
24 residues within 4Å:
Chain A:
Y.94
,
Y.95
,
R.96
,
S.144
,
P.145
,
I.146
,
G.174
,
D.175
,
G.176
,
A.177
,
E.180
,
N.204
,
Y.206
,
A.207
,
I.208
,
H.273
Chain D:
E.29
,
L.58
,
E.60
,
Q.82
,
Y.86
,
P.89
Ligands:
MG.1
,
COI.4
19
PLIP interactions
:
16 interactions with chain A
,
3 interactions with chain D
Hydrophobic interactions:
A:I.208
,
A:I.208
,
D:Y.86
,
D:P.89
Hydrogen bonds:
A:Y.95
,
A:Y.95
,
A:S.144
,
A:I.146
,
A:G.174
,
A:D.175
,
A:G.176
,
A:A.177
,
A:N.204
Water bridges:
A:N.204
,
A:I.208
,
A:I.208
Salt bridges:
A:R.96
,
A:H.273
pi-Stacking:
D:Y.86
TDP.5:
24 residues within 4Å:
Chain B:
E.29
,
L.58
,
E.60
,
Q.82
,
Y.86
,
P.89
Chain C:
Y.94
,
Y.95
,
R.96
,
S.144
,
P.145
,
I.146
,
G.174
,
D.175
,
G.176
,
A.177
,
E.180
,
N.204
,
Y.206
,
A.207
,
I.208
,
H.273
Ligands:
MG.2
,
COI.6
19
PLIP interactions
:
16 interactions with chain C
,
3 interactions with chain B
Hydrophobic interactions:
C:I.208
,
C:I.208
,
B:Y.86
,
B:P.89
Hydrogen bonds:
C:Y.95
,
C:Y.95
,
C:S.144
,
C:I.146
,
C:G.174
,
C:D.175
,
C:G.176
,
C:A.177
,
C:N.204
,
C:N.204
Water bridges:
C:I.208
,
C:I.208
Salt bridges:
C:R.96
,
C:H.273
pi-Stacking:
B:Y.86
2 x
COI
:
2-OXO-4-METHYLPENTANOIC ACID
(Non-covalent)
COI.4:
7 residues within 4Å:
Chain A:
F.66
,
Y.95
,
H.131
,
S.144
Chain D:
Y.86
,
H.129
Ligands:
TDP.3
5
PLIP interactions
:
2 interactions with chain D
,
3 interactions with chain A
Hydrogen bonds:
D:Y.86
,
D:H.129
Hydrophobic interactions:
A:F.66
,
A:Y.95
,
A:Y.95
COI.6:
6 residues within 4Å:
Chain B:
Y.86
,
H.129
Chain C:
F.66
,
Y.95
,
S.144
Ligands:
TDP.5
3
PLIP interactions
:
1 interactions with chain B
,
2 interactions with chain C
Hydrogen bonds:
B:H.129
Hydrophobic interactions:
C:F.66
,
C:Y.95
Links
RCSB
PDBe
PDBj
PDBsum
CATH
PLIP
Citation
Nakai, T. et al., Ligand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography. J.Mol.Biol. (2004)
Release Date
2004-03-30
Peptides
2-oxo acid dehydrogenase alpha subunit:
A
C
2-oxo acid dehydrogenase beta subunit:
B
D
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
C
C
B
B
D
D
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2-oxo acid dehydrogenase alpha subunit
2-oxo acid dehydrogenase beta subunit
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