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SMTL ID : 1k08.1
Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.26 Å
Oligo State
homo-dimer
Ligands
4 x
BZD
:
N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
(Non-covalent)
BZD.1:
16 residues within 4Å:
Chain A:
E.88
,
N.133
,
G.135
,
L.136
,
L.139
,
N.282
,
D.283
,
H.341
,
H.377
,
V.455
,
N.484
,
Y.573
,
E.672
,
A.673
,
S.674
,
G.675
17
PLIP interactions
:
17 interactions with chain A
Hydrogen bonds:
A:L.136
,
A:Y.573
,
A:E.672
,
A:E.672
,
A:S.674
,
A:S.674
,
A:G.675
Water bridges:
A:G.134
,
A:G.134
,
A:G.135
,
A:G.135
,
A:G.135
,
A:D.339
,
A:H.377
,
A:A.673
,
A:T.676
pi-Cation interactions:
A:H.341
BZD.2:
14 residues within 4Å:
Chain A:
R.60
,
V.64
,
W.67
,
P.188
,
W.189
,
E.190
,
K.191
,
P.229
Chain B:
F.37
,
T.38
,
L.39
,
V.40
,
H.57
Ligands:
BZD.5
11
PLIP interactions
:
4 interactions with chain B
,
7 interactions with chain A
Hydrophobic interactions:
B:V.40
,
A:R.60
,
A:V.64
,
A:W.67
,
A:P.229
Hydrogen bonds:
B:T.38
,
B:H.57
,
B:R.60
,
A:R.60
,
A:E.190
,
A:K.191
BZD.4:
16 residues within 4Å:
Chain B:
E.88
,
N.133
,
G.135
,
L.136
,
L.139
,
N.282
,
D.283
,
H.341
,
H.377
,
V.455
,
N.484
,
Y.573
,
E.672
,
A.673
,
S.674
,
G.675
18
PLIP interactions
:
18 interactions with chain B
Hydrogen bonds:
B:L.136
,
B:H.377
,
B:E.672
,
B:S.674
,
B:S.674
,
B:G.675
Water bridges:
B:G.134
,
B:G.134
,
B:G.135
,
B:G.135
,
B:G.135
,
B:D.339
,
B:H.377
,
B:Y.573
,
B:Y.573
,
B:A.673
,
B:T.676
pi-Cation interactions:
B:H.341
BZD.5:
14 residues within 4Å:
Chain A:
F.37
,
T.38
,
L.39
,
V.40
,
H.57
Chain B:
R.60
,
V.64
,
W.67
,
P.188
,
W.189
,
E.190
,
K.191
,
P.229
Ligands:
BZD.2
11
PLIP interactions
:
7 interactions with chain B
,
4 interactions with chain A
Hydrophobic interactions:
B:R.60
,
B:V.64
,
B:W.67
,
B:P.229
,
A:V.40
Hydrogen bonds:
B:R.60
,
B:E.190
,
B:K.191
,
A:T.38
,
A:H.57
,
A:R.60
2 x
PLP
:
PYRIDOXAL-5'-PHOSPHATE
(Covalent)
PLP.3:
14 residues within 4Å:
Chain A:
Y.90
,
G.134
,
G.135
,
W.491
,
K.568
,
K.574
,
Y.648
,
R.649
,
V.650
,
A.653
,
G.675
,
T.676
,
G.677
,
K.680
13
PLIP interactions
:
13 interactions with chain A
Hydrophobic interactions:
A:Y.90
,
A:Y.648
,
A:K.680
Hydrogen bonds:
A:T.676
,
A:T.676
,
A:G.677
Water bridges:
A:K.568
,
A:K.568
,
A:K.574
,
A:K.574
,
A:N.678
Salt bridges:
A:K.568
,
A:K.574
PLP.6:
14 residues within 4Å:
Chain B:
Y.90
,
G.134
,
G.135
,
W.491
,
K.568
,
K.574
,
Y.648
,
R.649
,
V.650
,
A.653
,
G.675
,
T.676
,
G.677
,
K.680
14
PLIP interactions
:
14 interactions with chain B
Hydrophobic interactions:
B:Y.90
,
B:Y.648
,
B:K.680
Hydrogen bonds:
B:Y.648
,
B:T.676
,
B:T.676
,
B:G.677
Water bridges:
B:K.568
,
B:K.568
,
B:K.574
,
B:K.574
,
B:N.678
Salt bridges:
B:K.568
,
B:K.574
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Oikonomakos, N.G. et al., Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies. Eur.J.Biochem. (2002)
Release Date
2001-10-03
Peptides
Glycogen Phosphorylase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Glycogen Phosphorylase
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