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SMTL ID : 2ccj.1
Crystal structure of S. aureus thymidylate kinase complexed with thymidine monophosphate
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.70 Å
Oligo State
homo-dimer
Ligands
5 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.1:
4 residues within 4Å:
Chain A:
N.132
,
S.180
,
V.181
,
N.182
Ligand excluded by PLIP
CL.2:
4 residues within 4Å:
Chain A:
T.35
,
R.36
,
G.39
,
K.77
Ligand excluded by PLIP
CL.3:
2 residues within 4Å:
Chain A:
P.186
,
L.187
Ligand excluded by PLIP
CL.6:
2 residues within 4Å:
Chain B:
P.186
,
L.187
Ligand excluded by PLIP
CL.7:
4 residues within 4Å:
Chain B:
N.132
,
S.180
,
V.181
,
N.182
Ligand excluded by PLIP
3 x
TMP
:
THYMIDINE-5'-PHOSPHATE
(Non-covalent)
TMP.4:
9 residues within 4Å:
Chain A:
K.15
,
E.37
,
F.66
,
R.70
,
R.92
,
S.96
,
S.97
,
Y.100
,
Q.101
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:R.92
Hydrogen bonds:
A:R.70
,
A:R.70
,
A:Q.101
,
A:Q.101
Water bridges:
A:K.15
,
A:K.15
,
A:K.15
,
A:T.16
,
A:R.92
,
A:R.92
,
A:R.92
Salt bridges:
A:K.15
,
A:R.92
pi-Stacking:
A:F.66
,
A:Y.100
TMP.8:
11 residues within 4Å:
Chain B:
E.11
,
K.15
,
R.36
,
E.37
,
R.70
,
R.92
,
S.96
,
S.97
,
Y.100
,
Q.101
Ligands:
TMP.9
17
PLIP interactions
:
17 interactions with chain B
Hydrophobic interactions:
B:R.92
Hydrogen bonds:
B:E.11
,
B:R.70
,
B:D.91
,
B:Q.101
,
B:Q.101
Water bridges:
B:K.15
,
B:K.15
,
B:R.36
,
B:R.70
,
B:R.70
,
B:R.92
,
B:R.92
Salt bridges:
B:K.15
,
B:R.36
,
B:R.92
pi-Stacking:
B:Y.100
TMP.9:
6 residues within 4Å:
Chain B:
R.48
,
A.63
,
F.66
,
Q.101
,
R.105
Ligands:
TMP.8
10
PLIP interactions
:
10 interactions with chain B
Hydrophobic interactions:
B:F.66
,
B:Q.101
Water bridges:
B:R.48
,
B:R.48
,
B:E.62
,
B:R.70
,
B:Q.101
,
B:Q.101
Salt bridges:
B:R.105
pi-Stacking:
B:F.66
3 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.5:
5 residues within 4Å:
Chain A:
R.71
,
L.74
,
I.79
,
I.120
,
N.121
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:R.71
,
A:R.71
,
A:I.120
,
A:N.121
EDO.10:
5 residues within 4Å:
Chain B:
R.71
,
L.74
,
I.79
,
I.120
,
N.121
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:R.71
,
B:R.71
,
B:I.120
,
B:N.121
EDO.11:
6 residues within 4Å:
Chain B:
E.37
,
P.38
,
R.48
,
F.66
,
S.69
,
R.70
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:R.48
,
B:F.66
,
B:S.69
,
B:R.70
Water bridges:
B:R.70
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Kotaka, M. et al., Structures of S. Aureus Thymidylate Kinase Reveal an Atypical Active Site Configuration and an Intermediate Conformational State Upon Substrate Binding. Protein Sci. (2006)
Release Date
2006-03-08
Peptides
THYMIDYLATE KINASE:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Secondary Structure
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THYMIDYLATE KINASE
Related Entries With Identical Sequence
2cck.1
|
4gfd.1
|
4gsy.1
|
4gsy.2
|
4gsy.3
|
4hdc.1
|
4hej.1
|
4hlc.1
|
4hld.1
|
4qg7.1
|
4qga.1
|
4qgf.1
|
4qgg.1
|
4qgh.1
|
4xwa.1
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