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SMTL ID : 4zur.1
Crystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with a hydroxamate inhibitor
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.13 Å
Oligo State
homo-dimer
Ligands
2 x
ZN
:
ZINC ION
(Non-covalent)
ZN.1:
8 residues within 4Å:
Chain A:
H.158
,
D.195
,
F.196
,
H.197
,
D.284
,
G.321
,
Y.323
Ligands:
7XA.4
5
PLIP interactions
:
3 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:D.195
,
A:H.197
,
A:D.284
,
H
2
O.1
,
H
2
O.1
ZN.6:
8 residues within 4Å:
Chain B:
H.158
,
D.195
,
F.196
,
H.197
,
D.284
,
G.321
,
Y.323
Ligands:
7XA.9
5
PLIP interactions
:
3 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:D.195
,
B:H.197
,
B:D.284
,
H
2
O.22
,
H
2
O.22
2 x
K
:
POTASSIUM ION
(Non-covalent)
K.2:
8 residues within 4Å:
Chain A:
D.193
,
D.195
,
H.197
,
H.198
,
G.199
,
S.216
,
L.217
,
H.218
5
PLIP interactions
:
5 interactions with chain A
Metal complexes:
A:D.193
,
A:D.195
,
A:H.197
,
A:S.216
,
A:L.217
K.7:
8 residues within 4Å:
Chain B:
D.193
,
D.195
,
H.197
,
H.198
,
G.199
,
S.216
,
L.217
,
H.218
5
PLIP interactions
:
5 interactions with chain B
Metal complexes:
B:D.193
,
B:D.195
,
B:H.197
,
B:S.216
,
B:L.217
2 x
NH4
:
AMMONIUM ION
(Non-functional Binders)
NH4.3:
6 residues within 4Å:
Chain A:
F.206
,
R.209
,
V.212
,
F.213
,
F.214
,
T.243
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:T.244
NH4.8:
7 residues within 4Å:
Chain B:
F.206
,
Y.207
,
R.209
,
V.212
,
F.213
,
F.214
,
T.243
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:T.243
2 x
7XA
:
7-amino-N-hydroxyheptanamide
(Non-covalent)
7XA.4:
18 residues within 4Å:
Chain A:
E.17
,
L.18
,
Y.19
,
E.117
,
H.158
,
H.159
,
G.167
,
Y.168
,
D.195
,
H.197
,
F.225
,
H.227
,
D.284
,
I.291
,
G.321
,
Y.323
Chain B:
T.90
Ligands:
ZN.1
14
PLIP interactions
:
12 interactions with chain A
,
2 interactions with chain B
Hydrophobic interactions:
A:E.117
,
A:Y.168
,
A:F.225
,
A:F.225
,
A:F.225
,
A:I.291
Hydrogen bonds:
A:H.158
,
A:H.159
,
A:Y.323
,
B:T.90
Water bridges:
A:G.20
,
A:E.117
,
A:H.227
,
B:T.90
7XA.9:
18 residues within 4Å:
Chain A:
T.90
Chain B:
E.17
,
L.18
,
Y.19
,
E.117
,
H.158
,
H.159
,
G.167
,
Y.168
,
D.195
,
H.197
,
F.225
,
H.227
,
D.284
,
I.291
,
G.321
,
Y.323
Ligands:
ZN.6
14
PLIP interactions
:
12 interactions with chain B
,
2 interactions with chain A
Hydrophobic interactions:
B:E.117
,
B:Y.168
,
B:F.225
,
B:F.225
,
B:F.225
,
B:I.291
Hydrogen bonds:
B:H.158
,
B:H.159
,
B:Y.323
,
A:T.90
,
A:T.90
Water bridges:
B:G.20
,
B:E.117
,
B:H.227
3 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.5:
6 residues within 4Å:
Chain A:
K.15
,
W.75
,
K.84
,
G.85
,
E.86
,
P.122
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:K.15
,
A:K.84
Water bridges:
A:E.86
GOL.10:
6 residues within 4Å:
Chain B:
K.15
,
W.75
,
K.84
,
G.85
,
E.86
,
P.122
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:G.85
Water bridges:
B:E.86
GOL.11:
9 residues within 4Å:
Chain A:
Y.207
,
L.229
,
E.233
,
E.234
,
K.237
Chain B:
R.96
,
T.97
,
S.98
,
P.99
4
PLIP interactions
:
3 interactions with chain A
,
1 interactions with chain B
Water bridges:
A:Y.207
,
A:E.233
,
A:E.233
Hydrogen bonds:
B:R.96
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Decroos, C. et al., Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry (2015)
Release Date
2015-07-29
Peptides
Acetylpolyamine aminohydrolase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Acetylpolyamine aminohydrolase
Toggle Identical (AB)
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3q9b.1
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3q9f.1
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3q9f.2
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3q9f.3
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3q9f.4
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|
3q9f.6
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4zum.1
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4zun.1
|
4zuo.1
|
4zup.1
|
4zuq.1
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