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SMTL ID : 2y6p.2
(1 other biounit)
Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.10 Å
Oligo State
homo-dimer
Ligands
2 x
CTP
:
CYTIDINE-5'-TRIPHOSPHATE
(Non-covalent)
CTP.1:
18 residues within 4Å:
Chain A:
P.8
,
A.9
,
R.10
,
S.13
,
T.14
,
R.15
,
K.19
,
L.70
,
P.71
,
S.72
,
G.73
,
R.76
,
Q.93
,
G.94
,
D.95
,
D.219
Ligands:
MG.2
,
MG.3
22
PLIP interactions
:
22 interactions with chain A
Hydrogen bonds:
A:R.10
,
A:R.10
,
A:T.14
,
A:T.14
,
A:R.15
,
A:R.15
,
A:L.70
,
A:R.76
,
A:G.94
,
A:D.95
Water bridges:
A:R.10
,
A:R.10
,
A:L.16
,
A:G.73
,
A:G.73
,
A:D.219
Salt bridges:
A:R.10
,
A:R.10
,
A:R.15
,
A:K.19
,
A:K.19
,
A:K.19
CTP.5:
18 residues within 4Å:
Chain B:
P.8
,
A.9
,
R.10
,
S.13
,
T.14
,
R.15
,
K.19
,
L.70
,
P.71
,
S.72
,
G.73
,
R.76
,
Q.93
,
G.94
,
D.95
,
D.219
Ligands:
MG.6
,
MG.7
21
PLIP interactions
:
21 interactions with chain B
Hydrogen bonds:
B:R.10
,
B:R.10
,
B:T.14
,
B:R.15
,
B:R.15
,
B:L.70
,
B:R.76
,
B:G.94
,
B:D.95
Water bridges:
B:R.10
,
B:R.10
,
B:L.16
,
B:G.73
,
B:G.73
,
B:D.219
Salt bridges:
B:R.10
,
B:R.10
,
B:R.15
,
B:K.19
,
B:K.19
,
B:K.19
4 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
3 residues within 4Å:
Chain A:
D.95
,
D.219
Ligands:
CTP.1
3
PLIP interactions
:
2 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:D.95
,
A:D.219
,
H
2
O.1
MG.3:
2 residues within 4Å:
Chain A:
R.15
Ligands:
CTP.1
No protein-ligand interaction detected (PLIP)
MG.6:
3 residues within 4Å:
Chain B:
D.95
,
D.219
Ligands:
CTP.5
3
PLIP interactions
:
2 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:D.95
,
B:D.219
,
H
2
O.2
MG.7:
2 residues within 4Å:
Chain B:
R.15
Ligands:
CTP.5
No protein-ligand interaction detected (PLIP)
2 x
IPA
:
ISOPROPYL ALCOHOL
(Non-functional Binders)
IPA.4:
6 residues within 4Å:
Chain A:
S.74
,
N.91
,
Y.170
,
F.172
,
F.180
,
E.195
3
PLIP interactions
:
3 interactions with chain A
Hydrophobic interactions:
A:F.172
,
A:F.180
,
A:E.195
IPA.8:
6 residues within 4Å:
Chain B:
S.74
,
N.91
,
Y.170
,
F.172
,
F.180
,
E.195
4
PLIP interactions
:
4 interactions with chain B
Hydrophobic interactions:
B:F.172
,
B:F.180
,
B:E.195
Hydrogen bonds:
B:E.195
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Schmidt, H. et al., Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, an Enzyme Involved in Lipopolysaccharide Biosynthesis. Plos One (2011)
Release Date
2011-08-24
Peptides
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
C
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3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
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