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SMTL ID : 4fwn.1
Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with Adenosine Tetraphosphate (AP4)
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 3.00 Å
Oligo State
homo-dimer
Ligands
4 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.1:
6 residues within 4Å:
Chain A:
D.156
,
H.188
,
M.236
,
P.240
,
R.249
Ligands:
AQP.3
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:D.156
,
A:R.249
,
A:R.249
EDO.2:
2 residues within 4Å:
Chain A:
T.265
Chain B:
S.179
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:S.179
,
B:S.179
EDO.4:
6 residues within 4Å:
Chain B:
D.156
,
H.188
,
M.236
,
P.240
,
R.249
Ligands:
AQP.6
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:R.249
,
B:R.249
EDO.5:
2 residues within 4Å:
Chain A:
S.179
Chain B:
T.265
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:S.179
,
A:S.179
2 x
AQP
:
ADENOSINE-5'-TETRAPHOSPHATE
(Non-covalent)
AQP.3:
14 residues within 4Å:
Chain A:
H.188
,
H.216
,
G.218
,
N.219
,
G.220
,
D.291
,
L.292
,
R.293
,
E.296
,
G.339
,
I.340
,
N.343
,
S.344
Ligands:
EDO.1
17
PLIP interactions
:
17 interactions with chain A
Hydrogen bonds:
A:N.219
,
A:N.219
,
A:N.219
,
A:G.220
,
A:G.220
,
A:L.292
,
A:R.293
,
A:R.293
,
A:G.339
,
A:N.343
,
A:N.343
Water bridges:
A:E.394
Salt bridges:
A:K.31
,
A:H.188
,
A:H.188
,
A:H.216
pi-Cation interactions:
A:R.293
AQP.6:
14 residues within 4Å:
Chain B:
H.188
,
H.216
,
G.218
,
N.219
,
G.220
,
D.291
,
L.292
,
R.293
,
E.296
,
G.339
,
I.340
,
N.343
,
S.344
Ligands:
EDO.4
18
PLIP interactions
:
18 interactions with chain B
Hydrogen bonds:
B:N.219
,
B:N.219
,
B:N.219
,
B:G.220
,
B:G.220
,
B:L.292
,
B:R.293
,
B:R.293
,
B:E.296
,
B:G.339
,
B:N.343
,
B:N.343
Water bridges:
B:E.394
Salt bridges:
B:K.31
,
B:H.188
,
B:H.188
,
B:H.216
pi-Cation interactions:
B:R.293
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Chittori, S. et al., Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies. Biochim.Biophys.Acta (2013)
Release Date
2013-06-19
Peptides
Propionate kinase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Propionate kinase
Toggle Identical (AB)
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|
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|
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|
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|
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|
4fws.1
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