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SMTL ID : 5xb2.1
ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.16 Å
Oligo State
homo-dimer
Ligands
2 x
ADP
:
ADENOSINE-5'-DIPHOSPHATE
(Non-covalent)
ADP.1:
15 residues within 4Å:
Chain A:
I.8
,
D.9
,
G.10
,
S.11
,
G.12
,
K.13
,
T.14
,
T.15
,
R.139
,
G.176
,
E.177
,
E.178
Ligands:
MG.3
,
F.4
,
F.5
17
PLIP interactions
:
17 interactions with chain A
Hydrogen bonds:
A:G.10
,
A:S.11
,
A:G.12
,
A:K.13
,
A:T.14
,
A:T.14
,
A:T.14
,
A:T.15
,
A:T.15
,
A:G.176
Water bridges:
A:K.13
,
A:K.13
,
A:R.139
,
A:E.178
,
A:E.178
Salt bridges:
A:K.13
pi-Cation interactions:
A:R.139
ADP.7:
14 residues within 4Å:
Chain B:
I.8
,
D.9
,
G.10
,
S.11
,
G.12
,
K.13
,
T.14
,
T.15
,
R.139
,
K.143
,
R.145
,
G.176
,
E.177
,
E.178
18
PLIP interactions
:
18 interactions with chain B
Hydrogen bonds:
B:G.10
,
B:S.11
,
B:G.12
,
B:K.13
,
B:T.14
,
B:T.14
,
B:T.14
,
B:T.15
,
B:T.15
,
B:R.139
,
B:R.145
,
B:G.176
Water bridges:
B:D.9
,
B:K.13
,
B:R.139
,
B:R.139
Salt bridges:
B:K.13
pi-Cation interactions:
B:R.139
2 x
TMP
:
THYMIDINE-5'-PHOSPHATE
(Non-covalent)
TMP.2:
16 residues within 4Å:
Chain A:
D.9
,
E.36
,
P.37
,
R.47
,
L.51
,
F.64
,
R.68
,
R.90
,
T.95
,
Y.98
,
Q.99
,
R.145
Ligands:
MG.3
,
F.4
,
F.5
,
F.6
14
PLIP interactions
:
14 interactions with chain A
Hydrophobic interactions:
A:E.36
,
A:F.64
,
A:Y.98
Hydrogen bonds:
A:D.9
,
A:R.68
,
A:Q.99
,
A:Q.99
,
A:R.145
Water bridges:
A:K.13
,
A:R.90
Salt bridges:
A:R.47
,
A:R.90
,
A:R.145
pi-Stacking:
A:F.64
TMP.8:
12 residues within 4Å:
Chain B:
D.9
,
E.36
,
P.37
,
R.47
,
L.51
,
F.64
,
R.68
,
R.90
,
T.95
,
Y.98
,
Q.99
,
R.145
14
PLIP interactions
:
14 interactions with chain B
Hydrophobic interactions:
B:E.36
,
B:Y.98
Hydrogen bonds:
B:D.9
,
B:R.68
,
B:Q.99
Water bridges:
B:T.14
,
B:R.47
,
B:R.47
,
B:R.90
,
B:R.90
Salt bridges:
B:R.47
,
B:R.90
,
B:R.145
pi-Stacking:
B:F.64
1 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.3:
7 residues within 4Å:
Chain A:
T.14
,
D.89
Ligands:
ADP.1
,
TMP.2
,
F.4
,
F.5
,
F.6
3
PLIP interactions
:
1 interactions with chain A
,
2 Ligand-Ligand interactions
Metal complexes:
A:T.14
,
TMP.2
,
TMP.2
3 x
F
:
FLUORIDE ION
(Non-covalent)
F.4:
8 residues within 4Å:
Chain A:
K.13
,
T.14
,
D.89
Ligands:
ADP.1
,
TMP.2
,
MG.3
,
F.5
,
F.6
No protein-ligand interaction detected (PLIP)
F.5:
7 residues within 4Å:
Chain A:
T.14
,
R.145
Ligands:
ADP.1
,
TMP.2
,
MG.3
,
F.4
,
F.6
No protein-ligand interaction detected (PLIP)
F.6:
7 residues within 4Å:
Chain A:
T.14
,
R.47
,
D.89
Ligands:
TMP.2
,
MG.3
,
F.4
,
F.5
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Biswas, A. et al., Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. FEBS J. (2017)
Release Date
2017-06-28
Peptides
Thymidylate kinase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
B
A
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Thymidylate kinase
Toggle Identical (AB)
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|
2pbr.2
|
4s2e.1
|
4s35.1
|
5h56.1
|
5h5b.1
|
5h5k.1
|
5xai.1
|
5xb3.1
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