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SMTL ID : 3x0q.1
ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESMM-state at reaction time of 20 min
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.14 Å
Oligo State
homo-dimer
Ligands
2 x
AR6
:
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
(Non-covalent)
AR6.1:
18 residues within 4Å:
Chain A:
I.19
,
R.54
,
E.63
,
A.66
,
G.67
,
L.68
,
E.82
,
E.86
,
E.108
Chain B:
R.27
,
Y.28
,
E.29
,
S.102
,
P.103
,
G.104
,
F.105
Ligands:
MN.2
,
MN.3
19
PLIP interactions
:
13 interactions with chain A
,
6 interactions with chain B
Hydrogen bonds:
A:L.68
,
B:E.29
,
B:S.102
,
B:G.104
,
B:F.105
Water bridges:
A:Q.52
,
A:R.54
,
A:R.54
,
A:R.54
,
A:R.54
,
A:R.54
,
A:E.63
,
A:A.66
,
A:R.81
,
A:T.110
Salt bridges:
A:R.54
,
A:R.54
pi-Stacking:
B:Y.28
,
B:Y.28
AR6.7:
18 residues within 4Å:
Chain A:
R.27
,
Y.28
,
E.29
,
S.102
,
P.103
,
G.104
,
F.105
Chain B:
I.19
,
R.54
,
E.63
,
A.66
,
G.67
,
L.68
,
E.82
,
E.86
,
E.108
Ligands:
MN.8
,
MN.9
17
PLIP interactions
:
6 interactions with chain A
,
11 interactions with chain B
Hydrogen bonds:
A:E.29
,
A:S.102
,
A:G.104
,
A:F.105
,
B:L.68
pi-Stacking:
A:Y.28
,
A:Y.28
Water bridges:
B:Q.52
,
B:R.54
,
B:R.54
,
B:R.54
,
B:R.54
,
B:R.54
,
B:A.66
,
B:R.81
Salt bridges:
B:R.54
,
B:R.54
6 x
MN
:
MANGANESE (II) ION
(Non-covalent)
MN.2:
4 residues within 4Å:
Chain A:
A.66
,
E.86
Ligands:
AR6.1
,
MN.3
5
PLIP interactions
:
2 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:A.66
,
A:E.86
,
H
2
O.1
,
H
2
O.1
,
H
2
O.4
MN.3:
4 residues within 4Å:
Chain A:
E.82
,
E.86
Ligands:
AR6.1
,
MN.2
3
PLIP interactions
:
2 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:E.82
,
A:E.86
,
H
2
O.1
MN.4:
2 residues within 4Å:
Chain A:
E.129
,
I.131
3
PLIP interactions
:
1 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:I.131
,
H
2
O.2
,
H
2
O.4
MN.8:
4 residues within 4Å:
Chain B:
A.66
,
E.86
Ligands:
AR6.7
,
MN.9
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:A.66
,
B:E.86
,
H
2
O.5
,
H
2
O.5
,
H
2
O.9
MN.9:
4 residues within 4Å:
Chain B:
E.82
,
E.86
Ligands:
AR6.7
,
MN.8
3
PLIP interactions
:
2 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:E.82
,
B:E.86
,
H
2
O.5
MN.10:
2 residues within 4Å:
Chain B:
E.129
,
I.131
3
PLIP interactions
:
1 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:I.131
,
H
2
O.6
,
H
2
O.9
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.5:
8 residues within 4Å:
Chain A:
G.17
,
R.18
,
I.19
,
L.20
,
N.21
,
E.32
,
H.33
,
K.34
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:G.17
Water bridges:
A:H.33
,
A:H.33
GOL.11:
8 residues within 4Å:
Chain B:
G.17
,
R.18
,
I.19
,
L.20
,
N.21
,
E.32
,
H.33
,
K.34
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:G.17
Water bridges:
B:H.33
,
B:H.33
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.6:
3 residues within 4Å:
Chain A:
R.51
,
R.144
,
E.149
6
PLIP interactions
:
6 interactions with chain A
Water bridges:
A:R.51
,
A:R.51
,
A:R.51
,
A:R.51
Salt bridges:
A:R.51
,
A:R.144
SO4.12:
3 residues within 4Å:
Chain B:
R.51
,
R.144
,
E.149
6
PLIP interactions
:
6 interactions with chain B
Water bridges:
B:R.51
,
B:R.51
,
B:R.51
,
B:R.51
Salt bridges:
B:R.51
,
B:R.144
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Furuike, Y. et al., ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors. Biochemistry (2016)
Release Date
2016-04-27
Peptides
ADP-ribose pyrophosphatase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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ADP-ribose pyrophosphatase
Toggle Identical (AB)
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1v8i.1
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1v8l.1
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1v8n.1
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1v8r.1
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1v8s.1
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1v8t.1
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3x0i.1
|
3x0j.1
|
3x0k.1
|
3x0l.1
|
3x0m.1
|
3x0n.1
|
3x0o.1
|
3x0p.1
|
3x0r.1
|
3x0s.1
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