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SMTL ID : 4cqk.1
(6 other biounits)
Crystal structure of ligand-bound NaD1
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
PIO
:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
(Non-covalent)
PIO.1:
11 residues within 4Å:
Chain A:
K.4
,
H.33
,
S.35
,
K.36
,
I.37
,
L.38
,
R.40
,
L.42
Chain B:
I.37
,
R.40
Ligands:
PIO.5
16
PLIP interactions
:
11 interactions with chain A
,
5 interactions with chain B
Hydrogen bonds:
A:K.36
,
A:I.37
,
A:L.38
,
A:R.40
Water bridges:
A:K.36
,
A:K.36
,
B:R.40
,
B:R.40
,
B:R.40
Salt bridges:
A:K.4
,
A:K.4
,
A:H.33
,
A:K.36
,
A:R.40
,
B:R.40
Hydrophobic interactions:
B:I.37
PIO.5:
11 residues within 4Å:
Chain A:
I.37
,
R.40
Chain B:
K.4
,
H.33
,
S.35
,
K.36
,
I.37
,
L.38
,
R.40
,
L.42
Ligands:
PIO.1
14
PLIP interactions
:
12 interactions with chain B
,
2 interactions with chain A
Hydrophobic interactions:
B:L.38
,
A:I.37
Hydrogen bonds:
B:K.36
,
B:I.37
,
B:L.38
,
B:R.40
Water bridges:
B:K.36
,
B:K.36
Salt bridges:
B:K.4
,
B:K.4
,
B:H.33
,
B:K.36
,
B:R.40
,
A:R.40
4 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
3 residues within 4Å:
Chain A:
R.1
,
C.47
Chain B:
N.8
8
PLIP interactions
:
7 interactions with chain A
,
1 interactions with chain B
Water bridges:
A:R.1
,
A:R.1
,
A:R.1
,
A:C.47
,
A:C.47
,
A:C.47
Salt bridges:
A:R.1
Hydrogen bonds:
B:N.8
SO4.3:
1 residues within 4Å:
Chain A:
R.21
2
PLIP interactions
:
2 interactions with chain A
Water bridges:
A:R.21
Salt bridges:
A:R.21
SO4.6:
3 residues within 4Å:
Chain A:
N.8
Chain B:
R.1
,
C.47
6
PLIP interactions
:
1 interactions with chain A
,
5 interactions with chain B
Hydrogen bonds:
A:N.8
Water bridges:
B:R.1
,
B:R.1
,
B:R.1
,
B:C.47
Salt bridges:
B:R.1
SO4.7:
3 residues within 4Å:
Chain B:
K.36
,
I.37
,
R.39
No protein-ligand interaction detected (PLIP)
1 x
MRD
:
(4R)-2-METHYLPENTANE-2,4-DIOL
(Non-functional Binders)
MRD.4:
3 residues within 4Å:
Chain A:
K.45
,
C.47
Chain B:
K.45
2
PLIP interactions
:
1 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:K.45
Water bridges:
A:K.45
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Poon, I.K.H. et al., Phosphoinositide-Mediated Oligomerization of a Defensin Induces Cell Lysis. Elife (2014)
Release Date
2014-04-16
Peptides
FLOWER-SPECIFIC DEFENSIN:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
C
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FLOWER-SPECIFIC DEFENSIN
Toggle Identical (AB)
Related Entries With Identical Sequence
1mr4.1
|
4aaz.1
|
4aaz.2
|
4ab0.1
|
4cqk.2
|
4cqk.3
|
4cqk.4
|
4cqk.5
|
4cqk.6
|
4cqk.7
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