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SMTL ID : 2bu2.1
crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.40 Å
Oligo State
homo-dimer
Ligands
2 x
ATP
:
ADENOSINE-5'-TRIPHOSPHATE
(Non-covalent)
ATP.1:
19 residues within 4Å:
Chain A:
E.238
,
N.242
,
A.243
,
R.245
,
A.246
,
D.277
,
V.282
,
L.290
,
L.310
,
A.311
,
G.312
,
F.313
,
G.314
,
Y.315
,
G.316
,
L.317
,
P.318
,
T.341
Ligands:
MG.3
19
PLIP interactions
:
19 interactions with chain A
Hydrogen bonds:
A:E.238
,
A:E.238
,
A:E.238
,
A:N.242
,
A:R.245
,
A:D.277
,
A:G.312
,
A:Y.315
,
A:G.316
,
A:L.317
Water bridges:
A:K.241
,
A:K.241
,
A:N.242
,
A:R.245
,
A:D.277
,
A:D.277
,
A:T.341
,
A:T.341
Salt bridges:
A:K.241
ATP.4:
19 residues within 4Å:
Chain B:
E.238
,
N.242
,
A.243
,
R.245
,
A.246
,
D.277
,
V.282
,
L.290
,
L.310
,
A.311
,
G.312
,
F.313
,
G.314
,
Y.315
,
G.316
,
L.317
,
P.318
,
T.341
Ligands:
MG.6
19
PLIP interactions
:
19 interactions with chain B
Hydrogen bonds:
B:E.238
,
B:E.238
,
B:E.238
,
B:N.242
,
B:R.245
,
B:D.277
,
B:G.312
,
B:Y.315
,
B:G.316
,
B:L.317
Water bridges:
B:K.241
,
B:K.241
,
B:N.242
,
B:R.245
,
B:D.277
,
B:D.277
,
B:T.341
,
B:T.341
Salt bridges:
B:K.241
2 x
TF1
:
4-({(2R,5S)-2,5-DIMETHYL-4-[(2R)-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANOYL]PIPERAZIN-1-YL}CARBONYL)BENZONITRILE
(Non-covalent)
TF1.2:
10 residues within 4Å:
Chain A:
L.18
,
Q.22
,
F.23
,
F.26
,
T.35
,
S.36
,
F.39
,
L.40
,
L.155
,
Q.158
10
PLIP interactions
:
10 interactions with chain A
Hydrophobic interactions:
A:L.18
,
A:L.18
,
A:Q.22
,
A:F.23
,
A:F.26
,
A:F.39
,
A:F.39
,
A:F.39
,
A:Q.158
Hydrogen bonds:
A:Q.22
TF1.5:
10 residues within 4Å:
Chain B:
L.18
,
Q.22
,
F.23
,
F.26
,
T.35
,
S.36
,
F.39
,
L.40
,
L.155
,
Q.158
10
PLIP interactions
:
10 interactions with chain B
Hydrophobic interactions:
B:L.18
,
B:L.18
,
B:Q.22
,
B:F.23
,
B:F.26
,
B:F.39
,
B:F.39
,
B:F.39
,
B:Q.158
Hydrogen bonds:
B:Q.22
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.3:
3 residues within 4Å:
Chain A:
E.238
,
N.242
Ligands:
ATP.1
No protein-ligand interaction detected (PLIP)
MG.6:
3 residues within 4Å:
Chain B:
E.238
,
N.242
Ligands:
ATP.4
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Knoechel, T.R. et al., Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands. Biochemistry (2006)
Release Date
2006-02-02
Peptides
PYRUVATE DEHYDROGENSAE KINASE ISOENZYME 2:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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PYRUVATE DEHYDROGENSAE KINASE ISOENZYME 2
Toggle Identical (AB)
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