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SMTL ID : 8e0v.1
DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.30 Å
Oligo State
homo-tetramer
Ligands
4 x
MN
:
MANGANESE (II) ION
(Non-covalent)
MN.1:
5 residues within 4Å:
Chain A:
C.62
,
R.93
,
H.269
,
E.303
,
D.327
4
PLIP interactions
:
4 interactions with chain A
Metal complexes:
A:C.62
,
A:H.269
,
A:E.303
,
A:D.327
MN.4:
5 residues within 4Å:
Chain B:
C.62
,
H.269
,
E.303
,
D.327
Ligands:
PEP.5
4
PLIP interactions
:
4 interactions with chain B
Metal complexes:
B:C.62
,
B:H.269
,
B:E.303
,
B:D.327
MN.7:
4 residues within 4Å:
Chain C:
C.62
,
H.269
,
E.303
,
D.327
5
PLIP interactions
:
4 interactions with chain C
,
1 Ligand-Water interactions
Metal complexes:
C:C.62
,
C:H.269
,
C:E.303
,
C:D.327
,
H
2
O.17
MN.11:
5 residues within 4Å:
Chain D:
C.62
,
R.93
,
H.269
,
E.303
,
D.327
4
PLIP interactions
:
4 interactions with chain D
Metal complexes:
D:C.62
,
D:H.269
,
D:E.303
,
D:D.327
3 x
GAL
:
beta-D-galactopyranose
(Non-covalent)
GAL.2:
10 residues within 4Å:
Chain A:
E.97
,
I.109
,
N.110
,
D.147
,
T.150
Chain B:
Q.171
,
V.172
,
E.175
,
F.210
,
L.211
8
PLIP interactions
:
6 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:N.110
,
A:T.150
,
A:T.150
,
B:E.175
,
B:L.211
Water bridges:
A:E.97
,
A:N.110
,
A:D.147
GAL.3:
6 residues within 4Å:
Chain A:
E.72
,
R.76
,
L.306
,
V.307
,
Y.321
,
W.332
7
PLIP interactions
:
7 interactions with chain A
Hydrogen bonds:
A:R.76
,
A:L.306
Water bridges:
A:E.333
,
A:E.333
,
A:E.333
,
A:E.333
Salt bridges:
A:R.76
GAL.10:
10 residues within 4Å:
Chain C:
Q.171
,
V.172
,
E.175
,
F.210
,
L.211
Chain D:
E.97
,
I.109
,
N.110
,
D.147
,
T.150
8
PLIP interactions
:
6 interactions with chain C
,
2 interactions with chain D
Hydrogen bonds:
C:Q.171
,
C:E.175
,
C:L.211
,
D:N.110
Water bridges:
C:E.175
,
C:E.175
,
C:L.211
,
D:E.97
2 x
PEP
:
PHOSPHOENOLPYRUVATE
(Non-functional Binders)
PEP.5:
12 residues within 4Å:
Chain B:
R.93
,
Y.95
,
K.98
,
E.144
,
G.164
,
A.165
,
R.166
,
K.187
,
R.235
,
H.269
,
M.301
Ligands:
MN.4
14
PLIP interactions
:
14 interactions with chain B
Hydrogen bonds:
B:A.165
Water bridges:
B:Y.95
,
B:K.98
,
B:R.166
,
B:R.166
,
B:R.166
Salt bridges:
B:R.93
,
B:K.98
,
B:R.166
,
B:K.187
,
B:K.187
,
B:R.235
,
B:H.269
,
B:H.269
PEP.8:
12 residues within 4Å:
Chain C:
R.93
,
Y.95
,
K.98
,
P.99
,
E.144
,
G.164
,
A.165
,
R.166
,
K.187
,
R.235
,
H.269
,
M.301
21
PLIP interactions
:
21 interactions with chain C
Hydrophobic interactions:
C:P.99
Hydrogen bonds:
C:A.165
Water bridges:
C:R.93
,
C:K.98
,
C:K.98
,
C:K.98
,
C:E.144
,
C:E.144
,
C:R.166
,
C:R.166
,
C:K.187
,
C:R.235
,
C:R.235
Salt bridges:
C:R.93
,
C:K.98
,
C:R.166
,
C:K.187
,
C:K.187
,
C:R.235
,
C:H.269
,
C:H.269
2 x
PO4
:
PHOSPHATE ION
(Non-functional Binders)
PO4.6:
2 residues within 4Å:
Chain B:
R.100
,
T.101
6
PLIP interactions
:
6 interactions with chain B
Hydrogen bonds:
B:T.101
,
B:T.101
,
B:T.101
Water bridges:
B:R.100
,
B:T.102
Salt bridges:
B:R.100
PO4.9:
2 residues within 4Å:
Chain C:
R.100
,
T.101
4
PLIP interactions
:
4 interactions with chain C
Hydrogen bonds:
C:T.101
,
C:T.101
Water bridges:
C:T.102
Salt bridges:
C:R.100
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Balachandran, N. et al., Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation. Biochemistry (2022)
Release Date
2022-10-12
Peptides
Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive:
A
B
C
D
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
C
C
D
D
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Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Toggle Identical (AC)
Related Entries With Identical Sequence
5cks.1
|
7rud.1
|
7rue.1
|
8e0s.1
|
8e0t.1
|
8e0u.1
|
8e0x.1
|
8e0y.1
|
8e0z.1
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