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SMTL ID : 4nb4.3
(3 other biounits)
Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.25 Å
Oligo State
homo-dimer
Ligands
2 x
ADP
:
ADENOSINE-5'-DIPHOSPHATE
(Non-covalent)
ADP.1:
17 residues within 4Å:
Chain A:
G.26
,
G.27
,
T.28
,
L.29
,
K.31
,
L.46
,
G.116
,
T.117
,
G.139
,
G.140
,
Q.143
,
Y.155
,
G.242
,
S.243
,
S.244
Ligands:
MG.2
,
SH3.4
20
PLIP interactions
:
20 interactions with chain A
Hydrogen bonds:
A:G.27
,
A:T.28
,
A:T.28
,
A:T.28
,
A:L.29
,
A:L.29
,
A:T.117
,
A:T.117
,
A:G.139
,
A:Q.143
,
A:S.243
,
A:S.243
,
A:S.244
Water bridges:
A:K.31
,
A:K.31
,
A:S.243
Salt bridges:
A:K.31
,
A:K.31
pi-Stacking:
A:Y.155
,
A:Y.155
ADP.3:
18 residues within 4Å:
Chain B:
G.26
,
G.27
,
T.28
,
L.29
,
K.31
,
V.115
,
G.116
,
T.117
,
G.139
,
G.140
,
Q.143
,
Y.155
,
G.242
,
S.243
,
S.244
,
H.246
Ligands:
SH3.5
,
MG.6
17
PLIP interactions
:
17 interactions with chain B
Hydrogen bonds:
B:G.27
,
B:T.28
,
B:T.28
,
B:L.29
,
B:L.29
,
B:T.117
,
B:G.139
,
B:Q.143
,
B:S.243
,
B:S.243
,
B:S.244
Water bridges:
B:Y.155
,
B:S.243
Salt bridges:
B:K.31
,
B:K.31
pi-Stacking:
B:Y.155
,
B:Y.155
2 x
MG
:
MAGNESIUM ION
(Non-functional Binders)
(Non-covalent)
MG.2:
2 residues within 4Å:
Ligands:
ADP.1
,
SH3.4
No protein-ligand interaction detected (PLIP)
MG.6:
5 residues within 4Å:
Chain B:
D.24
,
G.26
,
E.88
Ligands:
ADP.3
,
SH3.5
2
PLIP interactions
:
1 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:E.88
,
H
2
O.3
2 x
SH3
:
N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
(Non-covalent)
SH3.4:
21 residues within 4Å:
Chain A:
G.27
,
E.88
,
F.89
,
G.116
,
T.117
,
G.118
,
T.119
,
S.120
,
R.131
,
G.134
,
I.135
Chain B:
V.174
,
I.177
,
L.189
,
T.190
,
A.191
,
E.220
,
T.224
,
Y.258
Ligands:
ADP.1
,
MG.2
16
PLIP interactions
:
7 interactions with chain A
,
9 interactions with chain B
Hydrophobic interactions:
A:F.89
,
B:V.174
,
B:E.220
,
B:E.220
Hydrogen bonds:
A:G.27
,
A:T.117
,
A:G.118
,
A:R.131
,
A:R.131
,
B:T.190
,
B:T.190
,
B:T.190
,
B:A.191
,
B:E.220
Water bridges:
A:G.116
pi-Stacking:
B:Y.258
SH3.5:
22 residues within 4Å:
Chain A:
V.174
,
I.185
,
L.189
,
T.190
,
A.191
,
E.220
,
T.224
,
Y.258
Chain B:
G.26
,
G.27
,
E.88
,
F.89
,
G.116
,
T.117
,
G.118
,
T.119
,
S.120
,
R.131
,
G.134
,
I.135
Ligands:
ADP.3
,
MG.6
18
PLIP interactions
:
9 interactions with chain B
,
9 interactions with chain A
Hydrophobic interactions:
B:F.89
,
A:V.174
,
A:I.185
,
A:E.220
,
A:E.220
Hydrogen bonds:
B:G.27
,
B:T.117
,
B:G.118
,
B:R.131
,
B:R.131
,
A:T.190
,
A:T.190
,
A:T.190
,
A:A.191
Water bridges:
B:E.88
,
B:N.114
,
B:G.116
pi-Stacking:
A:Y.258
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Hughes, S.J. et al., Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus. Proteins (2014)
Release Date
2014-03-05
Peptides
Type II pantothenate kinase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
E
B
F
Export Alignment
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Clustal Format
PNG Image
Secondary Structure
None
DSSP
PSIPRED
SSpro
Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
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Size
Charged
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Proline
Ser/Thr
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NGL
PV
2D
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ClustalW
PNG
Type II pantothenate kinase
Related Entries With Identical Sequence
4nb4.1
|
4nb4.2
|
4nb4.4
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
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