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SYL_STRPJ_227_410

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

Composition of the binding site

Protein chains monomer
A1 (SYL_STRPJ):246:249, 327:329, 332, 337, 338, 340, 343, 344, 373246:249, 327:329, 332, 337, 338, 340, 343, 344, 373

Full PDB list

4k47, 4k48

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
4
6
T
2
4
7
T
2
4
8
R
2
4
9
Y
3
2
7
V
3
2
8
L
3
2
9
Y
3
3
2
V
3
3
7
M
3
3
8
V
3
4
0
H
3
4
3
D
3
4
4
T
3
7
3
[1]4k47.a wmp40 . . . . . . . . . . . . . .
[1]4k48.a none . . . . . . . . . . . . . .

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
2
4
6
T
2
4
7
T
2
4
8
R
2
4
9
Y
3
2
7
V
3
2
8
L
3
2
9
Y
3
3
2
V
3
3
7
M
3
3
8
V
3
4
0
H
3
4
3
D
3
4
4
T
3
7
3
[1]4k47.a . . . . . . . . . . . . . .
[1]4k48.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
4k47.a:wmp
4k48.a is apo
[1] 4k47.a
0.1
-
[1] 4k48.a 3.5
-
[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
4k47.a
4k48.a
[1] 4k47.a
0
.24
[1] 4k48.a .24
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4k47.a
4k48.a
[1] 4k47.a
0
0.8
[1] 4k48.a 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
4k47.a
4k48.a
[1] 4k47.a
0
1.4
[1] 4k48.a 1.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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