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SMTL ID : 2yaz.2
(1 other biounit)
The Crystal Structure of Leishmania major dUTPase in complex dUMP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.40 Å
Oligo State
homo-dimer
Ligands
2 x
UMP
:
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
(Non-covalent)
UMP.1:
17 residues within 4Å:
Chain A:
Q.24
,
L.27
,
N.28
,
I.31
,
W.44
,
D.82
,
H.85
,
F.86
,
K.182
,
N.186
,
R.189
,
Y.194
,
K.201
Chain B:
K.62
,
W.63
,
W.64
Ligands:
MG.2
18
PLIP interactions
:
14 interactions with chain A
,
4 interactions with chain B
Hydrophobic interactions:
A:I.31
,
A:H.85
,
A:F.86
,
B:W.64
Hydrogen bonds:
A:Q.24
,
A:N.28
,
A:H.85
,
A:K.182
,
A:N.186
,
A:Y.194
,
A:Y.194
Water bridges:
A:E.51
,
B:K.62
Salt bridges:
A:K.182
,
A:R.189
,
A:K.201
,
B:K.62
pi-Stacking:
B:W.64
UMP.5:
17 residues within 4Å:
Chain A:
W.63
,
W.64
Chain B:
Q.24
,
L.27
,
N.28
,
I.31
,
W.44
,
E.51
,
D.82
,
H.85
,
F.86
,
K.182
,
N.186
,
R.189
,
Y.194
,
K.201
Ligands:
MG.6
20
PLIP interactions
:
4 interactions with chain A
,
16 interactions with chain B
Hydrophobic interactions:
A:W.64
,
B:I.31
,
B:H.85
,
B:F.86
Salt bridges:
A:K.62
,
A:K.65
,
B:K.182
,
B:R.189
,
B:K.201
pi-Stacking:
A:W.64
Hydrogen bonds:
B:Q.24
,
B:N.28
,
B:D.82
,
B:H.85
,
B:K.182
,
B:N.186
,
B:Y.194
,
B:Y.194
Water bridges:
B:R.189
,
B:R.189
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
6 residues within 4Å:
Chain A:
E.51
,
I.78
,
E.79
,
D.82
,
K.182
Ligands:
UMP.1
1
PLIP interactions
:
1 interactions with chain A
Metal complexes:
A:D.82
MG.6:
4 residues within 4Å:
Chain B:
E.51
,
E.79
,
D.82
Ligands:
UMP.5
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:E.51
,
B:E.79
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.3:
4 residues within 4Å:
Chain A:
D.57
,
K.62
,
K.65
,
N.66
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:N.66
Salt bridges:
A:K.62
,
A:K.65
SO4.4:
3 residues within 4Å:
Chain B:
K.62
,
K.65
,
N.66
4
PLIP interactions
:
3 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:N.66
Salt bridges:
B:K.62
,
B:K.65
,
A:K.201
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Hemsworth, G.R. et al., The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine. J.Biol.Chem. (2011)
Release Date
2011-03-16
Peptides
DUTPASE:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
D
B
E
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2yay.1
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2yaz.1
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2yb0.1
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2yb0.2
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