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SMTL ID : 1m83.1
Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.20 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
2 residues within 4Å:
Chain A:
Q.9
Ligands:
ATP.2
No protein-ligand interaction detected (PLIP)
MG.6:
2 residues within 4Å:
Chain B:
Q.9
Ligands:
ATP.7
No protein-ligand interaction detected (PLIP)
2 x
ATP
:
ADENOSINE-5'-TRIPHOSPHATE
(Non-covalent)
ATP.2:
23 residues within 4Å:
Chain A:
G.7
,
I.8
,
Q.9
,
S.11
,
G.17
,
N.18
,
G.21
,
A.22
,
K.111
,
V.143
,
G.144
,
D.146
,
Q.147
,
G.180
,
A.181
,
R.182
,
I.183
,
K.192
,
M.193
,
S.194
,
K.195
,
S.196
Ligands:
MG.1
26
PLIP interactions
:
26 interactions with chain A
Hydrogen bonds:
A:Q.9
,
A:Q.9
,
A:Q.9
,
A:S.11
,
A:N.18
,
A:G.21
,
A:P.142
,
A:I.183
,
A:K.192
,
A:M.193
,
A:M.193
,
A:K.195
,
A:S.196
,
A:S.196
,
A:S.196
Water bridges:
A:N.18
,
A:K.111
,
A:K.111
,
A:S.194
,
A:S.194
Salt bridges:
A:K.111
,
A:K.192
,
A:K.192
,
A:K.195
,
A:K.195
,
A:K.195
ATP.7:
23 residues within 4Å:
Chain B:
G.7
,
I.8
,
Q.9
,
S.11
,
G.17
,
N.18
,
G.21
,
A.22
,
K.111
,
V.143
,
G.144
,
D.146
,
Q.147
,
G.180
,
A.181
,
R.182
,
I.183
,
K.192
,
M.193
,
S.194
,
K.195
,
S.196
Ligands:
MG.6
26
PLIP interactions
:
26 interactions with chain B
Hydrogen bonds:
B:Q.9
,
B:Q.9
,
B:Q.9
,
B:S.11
,
B:N.18
,
B:G.21
,
B:P.142
,
B:I.183
,
B:K.192
,
B:M.193
,
B:M.193
,
B:K.195
,
B:S.196
,
B:S.196
,
B:S.196
Water bridges:
B:N.18
,
B:K.111
,
B:K.111
,
B:S.194
,
B:S.194
Salt bridges:
B:K.111
,
B:K.192
,
B:K.192
,
B:K.195
,
B:K.195
,
B:K.195
6 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.3:
6 residues within 4Å:
Chain A:
S.11
,
V.47
,
W.48
,
Q.49
,
D.50
,
S.196
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:W.48
,
A:Q.49
,
A:D.50
Water bridges:
A:N.57
GOL.4:
5 residues within 4Å:
Chain A:
K.218
,
T.222
,
Y.265
,
G.266
,
K.269
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:T.222
Water bridges:
A:K.218
,
A:G.266
GOL.5:
8 residues within 4Å:
Chain A:
N.34
,
C.35
,
Y.36
,
T.73
,
Q.74
,
A.75
,
T.76
,
K.306
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:C.35
,
A:T.73
,
A:Q.74
,
A:K.306
GOL.8:
6 residues within 4Å:
Chain B:
S.11
,
V.47
,
W.48
,
Q.49
,
D.50
,
S.196
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:W.48
,
B:Q.49
,
B:D.50
Water bridges:
B:N.57
GOL.9:
5 residues within 4Å:
Chain B:
K.218
,
T.222
,
Y.265
,
G.266
,
K.269
2
PLIP interactions
:
2 interactions with chain B
Water bridges:
B:K.218
,
B:G.266
GOL.10:
8 residues within 4Å:
Chain B:
N.34
,
C.35
,
Y.36
,
T.73
,
Q.74
,
A.75
,
T.76
,
K.306
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:C.35
,
B:T.73
,
B:Q.74
,
B:T.76
,
B:K.306
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Retailleau, P. et al., Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J.Mol.Biol. (2003)
Release Date
2002-12-18
Peptides
Tryptophan-tRNA ligase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Tryptophan-tRNA ligase
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7cms.1
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