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SMTL ID : 1v8r.1
Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose and Zn
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.80 Å
Oligo State
homo-dimer
Ligands
4 x
ZN
:
ZINC ION
(Non-covalent)
ZN.1:
3 residues within 4Å:
Chain A:
E.82
,
E.86
Ligands:
APR.3
5
PLIP interactions
:
2 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:E.82
,
A:E.82
,
H
2
O.2
,
H
2
O.2
,
H
2
O.3
ZN.2:
1 residues within 4Å:
Chain A:
E.70
2
PLIP interactions
:
2 interactions with chain A
Metal complexes:
A:E.70
,
A:E.70
ZN.4:
3 residues within 4Å:
Chain B:
E.82
,
E.86
Ligands:
APR.6
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:E.82
,
B:E.82
,
H
2
O.4
,
H
2
O.5
,
H
2
O.5
ZN.5:
1 residues within 4Å:
Chain B:
E.70
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:E.70
,
B:E.70
2 x
APR
:
ADENOSINE-5-DIPHOSPHORIBOSE
(Non-covalent)
APR.3:
19 residues within 4Å:
Chain A:
R.18
,
I.19
,
H.33
,
A.36
,
Q.52
,
R.54
,
E.63
,
A.66
,
G.67
,
L.68
,
E.82
,
E.108
Chain B:
R.27
,
Y.28
,
E.29
,
S.102
,
P.103
,
G.104
Ligands:
ZN.1
16
PLIP interactions
:
9 interactions with chain A
,
7 interactions with chain B
Hydrogen bonds:
A:R.18
,
A:Q.52
,
A:L.68
,
A:E.108
,
B:E.29
,
B:E.29
,
B:E.29
,
B:S.102
,
B:G.104
Water bridges:
A:L.68
,
A:E.82
Salt bridges:
A:R.54
,
A:R.54
pi-Cation interactions:
A:R.18
pi-Stacking:
B:Y.28
,
B:Y.28
APR.6:
19 residues within 4Å:
Chain A:
R.27
,
Y.28
,
E.29
,
S.102
,
P.103
,
G.104
Chain B:
R.18
,
I.19
,
H.33
,
A.36
,
Q.52
,
R.54
,
E.63
,
A.66
,
G.67
,
L.68
,
E.82
,
E.108
Ligands:
ZN.4
17
PLIP interactions
:
11 interactions with chain B
,
6 interactions with chain A
Hydrogen bonds:
B:R.18
,
B:Q.52
,
B:L.68
,
B:E.108
,
B:E.108
,
A:E.29
,
A:E.29
,
A:S.102
,
A:G.104
Water bridges:
B:E.63
,
B:L.68
,
B:E.82
Salt bridges:
B:R.54
,
B:R.54
pi-Cation interactions:
B:R.18
pi-Stacking:
A:Y.28
,
A:Y.28
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Yoshiba, S. et al., Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal. J.Biol.Chem. (2004)
Release Date
2005-02-22
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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