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SYL_MYCTU_307_513

Leucine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYL_MYCTU):335:338, 341, 430:432, 435, 440, 441, 443, 446, 447, 449, 450335:338, 341, 430:432, 435, 440, 441, 443, 446, 447, 449, 450

Full PDB list

5agr, 5ags, 5agt

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
3
5
T
3
3
6
T
3
3
7
R
3
3
8
T
3
4
1
Y
4
3
0
V
4
3
1
L
4
3
2
Y
4
3
5
I
4
4
0
M
4
4
1
V
4
4
3
H
4
4
6
D
4
4
7
R
4
4
9
D
4
5
0
[1]5agr.a a5237 . . . . . . . . . . . . . . . .
[1]5ags.a 38y38 . . . . . . . . . . . . . . . .
[1]5agt.a a2h38 . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
F
3
3
5
T
3
3
6
T
3
3
7
R
3
3
8
T
3
4
1
Y
4
3
0
V
4
3
1
L
4
3
2
Y
4
3
5
I
4
4
0
M
4
4
1
V
4
4
3
H
4
4
6
D
4
4
7
R
4
4
9
D
4
5
0
[1]5agr.a . . . . . . . . . . . . . . . .
[1]5ags.a . . . . . . . . . . . . . . . .
[1]5agt.a . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
5agr.a:a52
5ags.a:38y
5agt.a:a2h
[1] 5agr.a
0.1
0.1 0.1
[1] 5ags.a 0
0.1
0
[1] 5agt.a 0 0.1
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
5agr.a
5ags.a
5agt.a
[1] 5agr.a
0
0 0
[1] 5ags.a 0
0
0
[1] 5agt.a 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
5agr.a
5ags.a
5agt.a
[1] 5agr.a
0
0.1 0.1
[1] 5ags.a 0.1
0
0.1
[1] 5agt.a 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
5agr.a
5ags.a
5agt.a
[1] 5agr.a
0
0.1 0.1
[1] 5ags.a 0.1
0
0.1
[1] 5agt.a 0.1 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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