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SMTL ID : 2a2z.1
(1 other biounit)
Crystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 3.02 Å
Oligo State
homo-dimer
Ligands
1 x
CA
:
CALCIUM ION
(Non-covalent)
CA.1:
1 residues within 4Å:
Chain A:
N.63
No protein-ligand interaction detected (PLIP)
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
4 residues within 4Å:
Chain A:
S.38
,
E.115
,
R.180
Ligands:
UDP.4
5
PLIP interactions
:
2 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:S.38
,
A:E.115
,
H
2
O.1
,
H
2
O.1
,
H
2
O.1
MG.5:
3 residues within 4Å:
Chain B:
S.38
,
E.115
Ligands:
UDP.7
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:S.38
,
B:E.115
,
H
2
O.1
,
H
2
O.1
,
H
2
O.1
2 x
DCZ
:
2'-DEOXYCYTIDINE
(Non-covalent)
DCZ.3:
12 residues within 4Å:
Chain A:
I.33
,
E.56
,
W.61
,
L.70
,
M.73
,
Y.74
,
F.84
,
Q.85
,
R.116
,
D.121
,
F.125
,
E.185
11
PLIP interactions
:
11 interactions with chain A
Hydrophobic interactions:
A:I.33
,
A:F.125
Hydrogen bonds:
A:E.56
,
A:Y.74
,
A:Q.85
,
A:R.116
,
A:R.116
,
A:D.121
,
A:D.121
Water bridges:
A:R.182
pi-Stacking:
A:F.125
DCZ.6:
14 residues within 4Å:
Chain B:
I.33
,
E.56
,
W.61
,
L.70
,
M.73
,
Y.74
,
F.84
,
Q.85
,
R.92
,
R.116
,
D.121
,
F.125
,
R.182
,
E.185
11
PLIP interactions
:
11 interactions with chain B
Hydrophobic interactions:
B:F.125
Hydrogen bonds:
B:E.56
,
B:Y.74
,
B:Y.74
,
B:Q.85
,
B:R.116
,
B:R.116
,
B:D.121
,
B:E.185
Water bridges:
B:K.37
pi-Stacking:
B:F.125
2 x
UDP
:
URIDINE-5'-DIPHOSPHATE
(Non-covalent)
UDP.4:
14 residues within 4Å:
Chain A:
A.34
,
A.35
,
G.36
,
K.37
,
S.38
,
T.39
,
E.115
,
R.176
,
L.179
,
R.180
,
D.229
,
F.230
,
K.231
Ligands:
MG.2
19
PLIP interactions
:
19 interactions with chain A
Hydrophobic interactions:
A:F.230
Hydrogen bonds:
A:A.34
,
A:G.36
,
A:K.37
,
A:S.38
,
A:T.39
,
A:T.39
,
A:T.39
,
A:D.229
,
A:F.230
,
A:K.231
Water bridges:
A:K.37
,
A:S.38
,
A:S.38
,
A:E.56
,
A:R.182
Salt bridges:
A:K.37
,
A:R.180
,
A:R.180
UDP.7:
15 residues within 4Å:
Chain B:
I.33
,
A.34
,
A.35
,
G.36
,
K.37
,
S.38
,
T.39
,
E.115
,
R.176
,
L.179
,
R.180
,
D.229
,
F.230
,
K.231
Ligands:
MG.5
20
PLIP interactions
:
20 interactions with chain B
Hydrogen bonds:
B:A.34
,
B:A.35
,
B:G.36
,
B:K.37
,
B:S.38
,
B:S.38
,
B:T.39
,
B:T.39
,
B:T.39
,
B:R.176
,
B:D.229
,
B:F.230
,
B:K.231
,
B:K.231
Water bridges:
B:R.180
Salt bridges:
B:K.37
,
B:R.180
,
B:R.180
pi-Stacking:
B:F.230
pi-Cation interactions:
B:R.176
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Godsey, M.H. et al., Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization. Biochemistry (2006)
Release Date
2006-01-17
Peptides
Deoxycytidine kinase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Deoxycytidine kinase
Related Entries With Identical Sequence
2a2z.2
|
2a30.1
|
2a30.2
Cartoon
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