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SMTL ID : 5k1x.1
Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant Y306A/N346A/C348A/Y384F in complex with AMPPNP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.95 Å
Oligo State
homo-dimer
Ligands
2 x
ANP
:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
(Non-covalent)
ANP.1:
16 residues within 4Å:
Chain A:
R.144
,
E.146
,
H.152
,
L.153
,
F.156
,
M.158
,
E.210
,
L.211
,
S.212
,
S.213
,
G.235
,
G.237
,
R.240
,
I.251
Ligands:
MG.2
,
MG.3
22
PLIP interactions
:
22 interactions with chain A
Hydrogen bonds:
A:R.144
,
A:E.146
,
A:H.152
,
A:H.152
,
A:L.153
,
A:E.210
,
A:E.210
,
A:E.210
,
A:S.213
,
A:G.237
,
A:R.240
,
A:R.240
Water bridges:
A:H.152
,
A:E.210
,
A:E.210
,
A:E.210
,
A:E.210
Salt bridges:
A:R.144
pi-Stacking:
A:F.156
,
A:F.156
pi-Cation interactions:
A:R.240
,
A:R.240
ANP.7:
16 residues within 4Å:
Chain B:
R.144
,
E.146
,
H.152
,
L.153
,
F.156
,
M.158
,
E.210
,
L.211
,
S.212
,
S.213
,
G.235
,
G.237
,
R.240
,
I.251
Ligands:
MG.8
,
MG.9
22
PLIP interactions
:
22 interactions with chain B
Hydrogen bonds:
B:R.144
,
B:E.146
,
B:E.146
,
B:H.152
,
B:H.152
,
B:L.153
,
B:E.210
,
B:E.210
,
B:E.210
,
B:E.210
,
B:S.213
,
B:G.237
,
B:R.240
,
B:R.240
Water bridges:
B:H.152
,
B:E.210
,
B:E.210
Salt bridges:
B:R.144
pi-Stacking:
B:F.156
,
B:F.156
pi-Cation interactions:
B:R.240
,
B:R.240
4 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
3 residues within 4Å:
Chain A:
E.210
,
S.213
Ligands:
ANP.1
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:E.210
,
A:S.213
,
H
2
O.2
,
H
2
O.2
MG.3:
2 residues within 4Å:
Chain A:
R.144
Ligands:
ANP.1
No protein-ligand interaction detected (PLIP)
MG.8:
3 residues within 4Å:
Chain B:
E.210
,
S.213
Ligands:
ANP.7
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:E.210
,
B:S.213
,
H
2
O.7
,
H
2
O.8
MG.9:
2 residues within 4Å:
Chain B:
R.144
Ligands:
ANP.7
No protein-ligand interaction detected (PLIP)
2 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.4:
7 residues within 4Å:
Chain A:
Y.56
,
K.59
,
L.60
,
E.63
,
L.242
,
K.245
,
H.246
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:E.63
,
A:K.245
,
A:H.246
EDO.10:
7 residues within 4Å:
Chain B:
Y.56
,
K.59
,
L.60
,
E.63
,
L.242
,
K.245
,
H.246
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:E.63
,
B:K.245
,
B:H.246
2 x
PEG
:
DI(HYDROXYETHYL)ETHER
(Non-functional Binders)
PEG.5:
4 residues within 4Å:
Chain A:
A.120
,
L.123
,
I.227
,
W.231
2
PLIP interactions
:
2 interactions with chain A
Water bridges:
A:D.222
,
A:D.222
PEG.11:
4 residues within 4Å:
Chain B:
A.120
,
L.123
,
I.227
,
W.231
1
PLIP interactions
:
1 interactions with chain B
Water bridges:
B:D.222
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.6:
3 residues within 4Å:
Chain A:
M.114
,
L.115
,
A.116
Ligand excluded by PLIP
CL.12:
3 residues within 4Å:
Chain B:
M.114
,
L.115
,
A.116
Ligand excluded by PLIP
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Lee, Y.J. et al., Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader. Chem.Commun.(Camb.) (2016)
Release Date
2016-10-19
Peptides
Pyrrolysine--tRNA ligase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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