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SMTL ID : 2xy3.2
(1 other biounit)
STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE WITH DUPNHPP
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.55 Å
Oligo State
homo-trimer
Ligands
3 x
DUP
:
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
(Non-covalent)
DUP.1:
8 residues within 4Å:
Chain A:
N.74
,
G.77
,
V.78
,
I.79
,
Y.83
,
F.91
,
P.93
Chain C:
S.62
5
PLIP interactions
:
2 interactions with chain A
,
3 interactions with chain C
Hydrophobic interactions:
A:Y.83
Hydrogen bonds:
A:N.74
,
C:S.62
Water bridges:
C:S.62
,
C:S.62
DUP.2:
14 residues within 4Å:
Chain A:
R.61
,
S.62
,
S.63
,
Q.110
Chain B:
Q.72
,
N.74
,
G.77
,
V.78
,
I.79
,
Y.83
,
W.90
,
F.91
,
P.93
Ligands:
MG.3
14
PLIP interactions
:
7 interactions with chain A
,
7 interactions with chain B
Hydrogen bonds:
A:R.61
,
A:S.62
,
A:S.62
,
A:S.62
,
A:S.63
,
A:S.63
,
A:Q.110
,
B:Q.72
,
B:N.74
,
B:F.91
,
B:F.91
Hydrophobic interactions:
B:I.79
,
B:Y.83
pi-Stacking:
B:F.91
DUP.4:
14 residues within 4Å:
Chain B:
R.61
,
S.62
,
S.63
,
Q.110
Chain C:
Q.72
,
N.74
,
G.77
,
V.78
,
I.79
,
Y.83
,
W.90
,
F.91
,
P.93
Ligands:
MG.5
16
PLIP interactions
:
7 interactions with chain B
,
9 interactions with chain C
Hydrogen bonds:
B:R.61
,
B:S.62
,
B:S.62
,
B:S.62
,
B:S.63
,
B:Q.110
,
C:Q.72
,
C:N.74
,
C:V.78
,
C:D.80
,
C:F.91
,
C:F.91
Salt bridges:
B:R.61
Hydrophobic interactions:
C:I.79
,
C:Y.83
pi-Stacking:
C:F.91
2 x
MG
:
MAGNESIUM ION
(Non-functional Binders)
(Non-covalent)
MG.3:
1 residues within 4Å:
Ligands:
DUP.2
No protein-ligand interaction detected (PLIP)
MG.5:
2 residues within 4Å:
Chain B:
D.25
Ligands:
DUP.4
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Garcia-Nafria, J. et al., The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and its Complexes with Two Nucleotides. Acta Crystallogr.,Sect.D (2011)
Release Date
2011-02-23
Peptides
SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS:
A
B
C
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
D
B
E
C
F
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Secondary Structure
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SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
Related Entries With Identical Sequence
2baz.1
|
2xx6.1
|
2xx6.2
|
2xy3.1
|
2y1t.1
|
2y1t.2
Cartoon
Cartoon
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