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SMTL ID : 2zio.1
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.06 Å
Oligo State
homo-dimer
Ligands
2 x
2PN
:
IMIDODIPHOSPHORIC ACID
(Non-covalent)
2PN.1:
4 residues within 4Å:
Chain A:
H.175
,
L.232
,
E.233
,
R.263
5
PLIP interactions
:
5 interactions with chain A
Hydrogen bonds:
A:H.175
,
A:E.233
,
A:E.233
,
A:R.263
,
A:R.263
2PN.3:
4 residues within 4Å:
Chain B:
H.175
,
L.232
,
E.233
,
R.263
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:H.175
,
B:E.233
,
B:E.233
,
B:R.263
,
B:R.263
2 x
AYB
:
5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine
(Non-covalent)
AYB.2:
24 residues within 4Å:
Chain A:
A.139
,
Y.143
,
L.146
,
R.167
,
E.169
,
E.174
,
H.175
,
L.176
,
F.179
,
M.181
,
N.183
,
E.233
,
L.234
,
S.235
,
S.236
,
V.238
,
W.254
,
G.256
,
A.257
,
G.258
,
F.259
,
G.260
,
R.263
,
I.274
20
PLIP interactions
:
20 interactions with chain A
Hydrophobic interactions:
A:Y.143
,
A:L.146
,
A:V.238
,
A:W.254
Hydrogen bonds:
A:E.169
,
A:L.176
,
A:N.183
,
A:N.183
,
A:E.233
,
A:E.233
,
A:G.260
Water bridges:
A:L.138
,
A:R.167
,
A:R.167
,
A:R.167
Salt bridges:
A:R.167
,
A:R.167
pi-Stacking:
A:F.179
,
A:F.179
pi-Cation interactions:
A:R.263
AYB.4:
24 residues within 4Å:
Chain B:
A.139
,
Y.143
,
L.146
,
R.167
,
E.169
,
E.174
,
H.175
,
L.176
,
F.179
,
M.181
,
N.183
,
E.233
,
L.234
,
S.235
,
S.236
,
V.238
,
W.254
,
G.256
,
A.257
,
G.258
,
F.259
,
G.260
,
R.263
,
I.274
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:Y.143
,
B:L.146
,
B:V.238
,
B:W.254
Hydrogen bonds:
B:E.169
,
B:L.176
,
B:N.183
,
B:N.183
,
B:E.233
,
B:E.233
,
B:G.260
Water bridges:
B:L.138
,
B:R.167
,
B:R.167
,
B:R.167
Salt bridges:
B:R.167
,
B:R.167
pi-Stacking:
B:F.179
,
B:F.179
pi-Cation interactions:
B:R.263
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Yanagisawa, T. et al., Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification. Chem.Biol. (2008)
Release Date
2008-12-02
Peptides
Pyrrolysyl-tRNA synthetase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Pyrrolysyl-tRNA synthetase
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2e3c.1
|
2zce.1
|
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|
3vqv.1
|
3vqw.1
|
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|
3vqx.2
|
3vqy.1
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