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SMTL ID : 2zce.1
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with pyrrolysine and an ATP analogue
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.80 Å
Oligo State
homo-dimer
Ligands
4 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
3 residues within 4Å:
Chain A:
E.120
,
R.167
Ligands:
ANP.4
No protein-ligand interaction detected (PLIP)
MG.2:
3 residues within 4Å:
Chain A:
E.233
,
S.236
Ligands:
ANP.4
2
PLIP interactions
:
2 interactions with chain A
Metal complexes:
A:E.233
,
A:S.236
MG.5:
3 residues within 4Å:
Chain B:
E.120
,
R.167
Ligands:
ANP.8
No protein-ligand interaction detected (PLIP)
MG.6:
3 residues within 4Å:
Chain B:
E.233
,
S.236
Ligands:
ANP.8
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:E.233
,
B:S.236
2 x
PYL
:
PYRROLYSINE
(Non-covalent)
PYL.3:
16 residues within 4Å:
Chain A:
M.137
,
A.139
,
L.142
,
Y.143
,
R.167
,
M.181
,
N.183
,
F.184
,
C.185
,
S.236
,
V.238
,
W.254
,
G.256
,
A.257
,
G.258
Ligands:
ANP.4
8
PLIP interactions
:
8 interactions with chain A
Hydrophobic interactions:
A:L.142
,
A:Y.143
,
A:V.238
,
A:W.254
,
A:W.254
Hydrogen bonds:
A:N.183
Water bridges:
A:L.138
Salt bridges:
A:R.167
PYL.7:
16 residues within 4Å:
Chain B:
M.137
,
A.139
,
L.142
,
Y.143
,
R.167
,
M.181
,
N.183
,
F.184
,
C.185
,
S.236
,
V.238
,
W.254
,
G.256
,
A.257
,
G.258
Ligands:
ANP.8
8
PLIP interactions
:
8 interactions with chain B
Hydrophobic interactions:
B:L.142
,
B:Y.143
,
B:V.238
,
B:W.254
,
B:W.254
Hydrogen bonds:
B:N.183
Water bridges:
B:L.138
Salt bridges:
B:R.167
2 x
ANP
:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
(Non-covalent)
ANP.4:
17 residues within 4Å:
Chain A:
R.167
,
E.169
,
H.175
,
L.176
,
F.179
,
M.181
,
E.233
,
L.234
,
S.235
,
S.236
,
G.258
,
F.259
,
G.260
,
R.263
Ligands:
MG.1
,
MG.2
,
PYL.3
16
PLIP interactions
:
16 interactions with chain A
Hydrogen bonds:
A:R.167
,
A:E.169
,
A:H.175
,
A:L.176
,
A:E.233
,
A:E.233
,
A:E.233
,
A:G.260
,
A:R.263
,
A:R.263
Water bridges:
A:H.175
Salt bridges:
A:R.167
pi-Stacking:
A:F.179
,
A:F.179
pi-Cation interactions:
A:R.263
,
A:R.263
ANP.8:
17 residues within 4Å:
Chain B:
R.167
,
E.169
,
H.175
,
L.176
,
F.179
,
M.181
,
E.233
,
L.234
,
S.235
,
S.236
,
G.258
,
F.259
,
G.260
,
R.263
Ligands:
MG.5
,
MG.6
,
PYL.7
16
PLIP interactions
:
16 interactions with chain B
Hydrogen bonds:
B:R.167
,
B:E.169
,
B:H.175
,
B:L.176
,
B:E.233
,
B:E.233
,
B:E.233
,
B:G.260
,
B:R.263
,
B:R.263
Water bridges:
B:H.175
Salt bridges:
B:R.167
pi-Stacking:
B:F.179
,
B:F.179
pi-Cation interactions:
B:R.263
,
B:R.263
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Yanagisawa, T. et al., Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase. J.Mol.Biol. (2008)
Release Date
2008-04-22
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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