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SMTL ID : 1rya.1
Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.30 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
5 residues within 4Å:
Chain A:
G.50
,
G.51
,
E.70
,
Q.123
Ligands:
GDP.2
3
PLIP interactions
:
2 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:G.50
,
A:E.70
,
H
2
O.1
MG.4:
5 residues within 4Å:
Chain B:
G.50
,
G.51
,
E.70
,
Q.123
Ligands:
GDP.6
3
PLIP interactions
:
2 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:G.50
,
B:E.70
,
H
2
O.15
2 x
GDP
:
GUANOSINE-5'-DIPHOSPHATE
(Non-covalent)
GDP.2:
14 residues within 4Å:
Chain A:
F.3
,
L.4
,
F.9
,
R.37
,
N.39
,
G.50
,
G.51
,
R.52
,
E.70
,
F.94
,
Y.103
,
Q.123
Ligands:
MG.1
,
TRS.3
16
PLIP interactions
:
16 interactions with chain A
Hydrogen bonds:
A:L.4
,
A:L.4
,
A:N.39
,
A:R.52
,
A:R.52
,
A:Q.123
Water bridges:
A:R.37
,
A:R.37
,
A:R.37
,
A:N.39
,
A:Y.103
,
A:Y.103
Salt bridges:
A:R.37
pi-Stacking:
A:F.3
,
A:F.9
,
A:F.9
GDP.6:
15 residues within 4Å:
Chain B:
F.3
,
L.4
,
Q.6
,
F.9
,
R.37
,
N.39
,
G.50
,
G.51
,
R.52
,
E.70
,
F.94
,
Y.103
,
Q.123
Ligands:
MG.4
,
TRS.7
22
PLIP interactions
:
22 interactions with chain B
Hydrogen bonds:
B:L.4
,
B:L.4
,
B:G.50
,
B:R.52
,
B:R.52
,
B:Y.103
,
B:Q.123
Water bridges:
B:Q.6
,
B:Q.6
,
B:Q.6
,
B:R.37
,
B:R.37
,
B:R.37
,
B:N.39
,
B:N.39
,
B:N.39
,
B:N.39
,
B:E.70
Salt bridges:
B:R.37
pi-Stacking:
B:F.3
,
B:F.9
,
B:F.9
2 x
TRS
:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
(Non-functional Binders)
TRS.3:
8 residues within 4Å:
Chain A:
S.20
,
D.22
,
R.37
,
F.47
,
H.88
,
Y.90
,
Y.103
Ligands:
GDP.2
7
PLIP interactions
:
7 interactions with chain A
Hydrogen bonds:
A:S.20
,
A:L.21
,
A:D.22
,
A:H.88
,
A:Y.90
Water bridges:
A:R.37
,
A:P.41
TRS.7:
8 residues within 4Å:
Chain B:
S.20
,
D.22
,
R.37
,
F.47
,
H.88
,
Y.90
,
Y.103
Ligands:
GDP.6
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:S.20
,
B:S.20
,
B:D.22
,
B:H.88
1 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.5:
4 residues within 4Å:
Chain B:
N.27
,
S.28
,
S.113
,
E.114
Ligand excluded by PLIP
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Gabelli, S.B. et al., Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure (2004)
Release Date
2004-06-22
Peptides
GDP-mannose mannosyl hydrolase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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GDP-mannose mannosyl hydrolase
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