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SMTL ID : 8ppa.3
(2 other biounits)
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.73 Å
Oligo State
homo-dimer
Ligands
2 x
ANP
:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
(Non-covalent)
ANP.1:
16 residues within 4Å:
Chain A:
H.3
,
S.15
,
F.16
,
K.27
,
P.50
,
Q.67
,
D.68
,
L.69
,
D.80
,
K.154
,
L.219
,
I.233
,
D.234
Ligands:
06G.2
,
MN.6
,
MN.7
13
PLIP interactions
:
13 interactions with chain A
Hydrogen bonds:
A:S.15
,
A:S.15
,
A:K.27
,
A:Q.67
,
A:D.68
,
A:L.69
,
A:D.80
,
A:D.80
,
A:K.154
,
A:K.154
Water bridges:
A:K.82
,
A:D.234
Salt bridges:
A:K.27
ANP.8:
14 residues within 4Å:
Chain B:
H.3
,
S.15
,
F.16
,
K.27
,
P.50
,
Q.67
,
D.68
,
L.69
,
D.80
,
K.154
,
L.219
,
I.233
,
D.234
Ligands:
06G.9
14
PLIP interactions
:
14 interactions with chain B
Hydrogen bonds:
B:S.15
,
B:K.27
,
B:Q.67
,
B:L.69
,
B:D.80
,
B:K.154
,
B:K.154
,
B:D.234
Water bridges:
B:S.15
,
B:K.82
,
B:K.82
,
B:D.234
,
B:D.234
Salt bridges:
B:K.27
2 x
06G
:
D-myo-inositol 1,4,6-trisphosphate
(Non-covalent)
06G.2:
10 residues within 4Å:
Chain A:
K.82
,
R.103
,
M.106
,
K.109
,
K.130
,
Y.133
,
R.137
,
K.165
,
K.237
Ligands:
ANP.1
24
PLIP interactions
:
22 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:K.109
,
A:K.109
,
A:Y.133
,
A:R.137
Water bridges:
A:K.82
,
A:K.82
,
A:R.103
,
A:K.130
,
A:K.130
,
A:K.130
,
A:K.130
,
A:Y.133
,
A:K.237
,
A:K.237
,
B:D.157
,
B:D.157
Salt bridges:
A:K.82
,
A:R.103
,
A:K.109
,
A:K.130
,
A:K.130
,
A:R.137
,
A:K.165
,
A:K.237
06G.9:
9 residues within 4Å:
Chain B:
K.82
,
R.103
,
M.106
,
K.109
,
K.130
,
Y.133
,
R.137
,
K.237
Ligands:
ANP.8
14
PLIP interactions
:
14 interactions with chain B
Hydrogen bonds:
B:K.109
,
B:K.109
,
B:R.137
Water bridges:
B:K.82
,
B:K.82
,
B:K.82
,
B:K.130
Salt bridges:
B:K.82
,
B:R.103
,
B:K.109
,
B:K.130
,
B:K.130
,
B:R.137
,
B:K.237
6 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.3:
3 residues within 4Å:
Chain A:
R.170
,
S.275
,
R.279
5
PLIP interactions
:
5 interactions with chain A
Hydrogen bonds:
A:S.275
Water bridges:
A:S.275
,
A:R.279
Salt bridges:
A:R.170
,
A:R.279
SO4.4:
2 residues within 4Å:
Chain A:
Q.172
,
R.175
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:Q.172
Salt bridges:
A:R.175
SO4.5:
4 residues within 4Å:
Chain A:
S.169
,
E.171
,
Q.172
,
R.175
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:S.169
Water bridges:
A:E.171
Salt bridges:
A:R.175
SO4.10:
3 residues within 4Å:
Chain B:
R.170
,
S.275
,
R.279
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:R.170
,
B:S.275
Water bridges:
B:S.275
Salt bridges:
B:R.279
SO4.11:
2 residues within 4Å:
Chain B:
S.169
,
R.170
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:R.170
,
B:E.171
SO4.12:
2 residues within 4Å:
Chain B:
Q.172
,
R.175
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:Q.172
Water bridges:
B:R.175
Salt bridges:
B:R.175
2 x
MN
:
MANGANESE (II) ION
(Non-covalent)
MN.6:
3 residues within 4Å:
Chain A:
D.234
Ligands:
ANP.1
,
MN.7
4
PLIP interactions
:
1 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:D.234
,
H
2
O.1
,
H
2
O.1
,
H
2
O.2
MN.7:
4 residues within 4Å:
Chain A:
G.215
,
D.234
Ligands:
ANP.1
,
MN.6
2
PLIP interactions
:
1 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:D.234
,
H
2
O.2
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Marquez-Monino, M.A. et al., Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Nat Commun (2024)
Release Date
2024-02-28
Peptides
Inositol-trisphosphate 3-kinase A:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Inositol-trisphosphate 3-kinase A
Related Entries With Identical Sequence
8pp8.1
|
8pp8.2
|
8pp9.1
|
8pp9.2
|
8ppa.1
|
8ppa.2
|
8ppb.1
|
8ppb.2
|
8ppc.1
|
8ppc.2
|
8ppd.1
|
8ppd.2
|
8ppe.1
|
8ppe.2
|
8ppf.1
|
8ppf.2
|
8ppg.1
|
8ppg.2
|
8pph.1
|
8pph.2
|
8ppi.1
|
8ppi.2
|
8ppj.1
|
8ppj.2
Cartoon
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Tube
Trace
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Outline
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