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SMTL ID : 6s6g.1
Crystal Structure of the Homospermidine Synthase (HSS) variant E117Q from Blastochloris viridis in Complex with NAD
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
NAD
:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(Non-covalent)
NAD.1:
33 residues within 4Å:
Chain A:
I.20
,
G.21
,
F.22
,
G.23
,
S.24
,
I.25
,
G.26
,
R.27
,
I.47
,
D.48
,
P.49
,
S.50
,
A.53
,
A.68
,
V.69
,
T.70
,
L.94
,
S.95
,
V.96
,
D.97
,
T.98
,
T.117
,
V.118
,
Q.120
,
G.163
,
A.164
,
N.165
,
P.166
,
W.232
,
S.233
,
G.236
,
I.353
,
V.403
21
PLIP interactions
:
21 interactions with chain A
Hydrophobic interactions:
A:I.25
,
A:W.232
,
A:V.403
Hydrogen bonds:
A:F.22
,
A:S.24
,
A:S.24
,
A:I.25
,
A:D.48
,
A:V.69
,
A:V.69
,
A:V.96
,
A:G.163
,
A:A.164
,
A:N.165
,
A:P.166
,
A:S.233
,
A:S.233
Water bridges:
A:G.23
,
A:G.26
,
A:S.50
,
A:A.53
NAD.3:
33 residues within 4Å:
Chain B:
I.20
,
G.21
,
F.22
,
G.23
,
S.24
,
I.25
,
G.26
,
R.27
,
I.47
,
D.48
,
P.49
,
S.50
,
A.53
,
A.68
,
V.69
,
T.70
,
L.94
,
S.95
,
V.96
,
D.97
,
T.98
,
T.117
,
V.118
,
Q.120
,
G.163
,
A.164
,
N.165
,
P.166
,
W.232
,
S.233
,
G.236
,
I.353
,
V.403
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:W.232
,
B:V.403
Hydrogen bonds:
B:S.24
,
B:S.24
,
B:I.25
,
B:S.50
,
B:V.69
,
B:V.69
,
B:V.96
,
B:G.163
,
B:A.164
,
B:N.165
,
B:P.166
,
B:S.233
,
B:S.233
Water bridges:
B:F.22
,
B:G.23
,
B:G.26
,
B:Q.120
,
B:G.236
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
6 residues within 4Å:
Chain A:
C.267
,
G.268
,
R.312
,
Q.317
,
A.318
,
R.321
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:A.318
Salt bridges:
A:R.312
,
A:R.321
SO4.4:
6 residues within 4Å:
Chain B:
C.267
,
G.268
,
R.312
,
Q.317
,
A.318
,
R.321
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:A.318
Water bridges:
B:G.268
Salt bridges:
B:R.312
,
B:R.321
1 x
1PS
:
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
(Non-covalent)
1PS.5:
6 residues within 4Å:
Chain B:
S.50
,
D.51
,
E.52
,
D.350
,
W.351
,
R.352
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:S.50
,
B:D.51
,
B:E.52
pi-Stacking:
B:W.351
,
B:W.351
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Helfrich, F. et al., Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction. Acta Crystallogr D Struct Biol (2021)
Release Date
2020-07-15
Peptides
Homospermidine synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Homospermidine synthase
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