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SMTL ID : 6i5y.1
Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-adenosine
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
YSA
:
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
(Non-covalent)
YSA.1:
23 residues within 4Å:
Chain A:
Y.37
,
G.39
,
F.40
,
D.41
,
G.50
,
H.51
,
V.53
,
P.54
,
L.71
,
T.76
,
D.81
,
N.126
,
Y.175
,
Q.179
,
D.182
,
Q.195
,
G.197
,
G.198
,
D.200
,
Q.201
,
P.226
,
L.227
,
I.228
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:Y.37
,
A:L.71
,
A:Q.179
Hydrogen bonds:
A:Y.37
,
A:D.41
,
A:D.41
,
A:Y.175
,
A:Q.179
,
A:G.198
,
A:D.200
,
A:Q.201
,
A:N.204
,
A:I.228
,
A:I.228
Water bridges:
A:G.39
Salt bridges:
A:H.51
YSA.3:
23 residues within 4Å:
Chain B:
Y.37
,
G.39
,
F.40
,
D.41
,
G.50
,
H.51
,
V.53
,
P.54
,
L.71
,
T.76
,
D.81
,
N.126
,
Y.175
,
Q.179
,
D.182
,
Q.195
,
G.197
,
G.198
,
D.200
,
Q.201
,
P.226
,
L.227
,
I.228
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:Y.37
,
B:L.71
,
B:Q.179
Hydrogen bonds:
B:Y.37
,
B:D.41
,
B:D.81
,
B:Q.179
,
B:D.182
,
B:D.182
,
B:G.198
,
B:D.200
,
B:Q.201
,
B:I.228
,
B:I.228
Water bridges:
B:G.39
,
B:D.81
,
B:K.85
,
B:K.85
,
B:K.85
Salt bridges:
B:H.51
3 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.2:
4 residues within 4Å:
Chain A:
P.110
,
F.111
,
L.310
,
V.311
1
PLIP interactions
:
1 interactions with chain A
Water bridges:
A:V.311
EDO.4:
4 residues within 4Å:
Chain B:
P.33
,
I.34
,
K.67
,
E.118
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:P.33
,
B:E.118
EDO.5:
6 residues within 4Å:
Chain B:
I.386
,
E.389
,
K.390
,
Q.391
,
Y.396
,
E.402
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:Q.391
Water bridges:
B:E.402
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Nautiyal, M. et al., Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Eur.J.Med.Chem. (2019)
Release Date
2019-04-17
Peptides
Tyrosine--tRNA ligase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
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Secondary Structure
None
DSSP
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Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
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Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
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Tyrosine--tRNA ligase
Related Entries With Identical Sequence
6hb5.1
|
6hb6.1
|
6hb7.1
|
7ap3.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
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