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SMTL ID : 3b1r.3
(2 other biounits)
Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with AMP-Mg-AMP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.00 Å
Oligo State
homo-dimer
Ligands
4 x
AMP
:
ADENOSINE MONOPHOSPHATE
(Non-covalent)
AMP.1:
19 residues within 4Å:
Chain A:
S.16
,
A.18
,
D.20
,
G.55
,
G.56
,
C.57
,
N.60
,
A.111
,
I.113
,
Q.121
,
T.123
,
F.125
,
M.130
,
P.151
,
Q.177
,
G.258
,
D.261
Chain B:
S.44
Ligands:
MG.3
15
PLIP interactions
:
13 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:S.16
,
A:D.20
,
A:G.56
,
A:N.60
,
A:Q.121
,
A:Q.177
,
A:G.258
,
A:D.261
,
B:S.44
,
B:S.44
Water bridges:
A:N.119
,
A:D.152
,
A:C.259
,
A:G.260
pi-Stacking:
A:F.125
AMP.2:
16 residues within 4Å:
Chain A:
N.119
,
T.228
,
R.229
,
G.230
,
E.231
,
G.233
,
V.248
,
V.253
,
C.259
,
G.260
,
F.263
,
S.285
,
G.288
,
A.289
,
I.292
Chain B:
H.39
12
PLIP interactions
:
11 interactions with chain A
,
1 interactions with chain B
Hydrogen bonds:
A:N.119
,
A:T.228
,
A:T.228
,
A:G.230
,
A:S.285
Water bridges:
A:N.200
,
A:A.250
,
A:G.260
,
A:G.260
,
A:A.289
,
A:A.289
Salt bridges:
B:H.39
AMP.4:
17 residues within 4Å:
Chain A:
S.44
Chain B:
S.16
,
A.18
,
D.20
,
G.55
,
G.56
,
C.57
,
N.60
,
A.111
,
Q.121
,
F.125
,
M.130
,
P.151
,
Q.177
,
G.258
,
D.261
Ligands:
MG.6
17
PLIP interactions
:
15 interactions with chain B
,
2 interactions with chain A
Hydrogen bonds:
B:S.16
,
B:D.20
,
B:G.56
,
B:N.60
,
B:Q.121
,
B:Q.177
,
B:G.258
,
B:D.261
,
A:S.44
,
A:S.44
Water bridges:
B:N.119
,
B:T.123
,
B:D.152
,
B:G.260
,
B:G.260
pi-Stacking:
B:F.125
,
B:F.125
AMP.5:
14 residues within 4Å:
Chain A:
H.39
Chain B:
N.119
,
T.228
,
R.229
,
G.230
,
E.231
,
G.233
,
V.248
,
C.259
,
G.260
,
F.263
,
S.285
,
G.288
,
I.292
11
PLIP interactions
:
10 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:N.119
,
B:T.228
,
B:T.228
,
B:R.229
,
B:G.230
Water bridges:
B:N.200
,
B:A.250
,
B:G.260
,
B:A.289
,
B:A.289
Salt bridges:
A:H.39
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
(Non-functional Binders)
MG.3:
2 residues within 4Å:
Chain A:
Q.177
Ligands:
AMP.1
No protein-ligand interaction detected (PLIP)
MG.6:
1 residues within 4Å:
Ligands:
AMP.4
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Yasutake, Y. et al., Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity. Acta Crystallogr.,Sect.D (2011)
Release Date
2011-11-02
Peptides
Ribokinase, putative:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
F
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Ribokinase, putative
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