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SYM_BRUSU_1_515

Methionine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. MetG type 2B subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYM_BRUSU):11, 12, 14, 51, 53:56, 132, 210, 213, 227:230, 232:234, 236, 237, 265, 268, 26911, 12, 14, 51, 53:56, 132, 210, 213, 227:230, 232:234, 236, 237, 265, 268, 269

Full PDB list

4dlp, 4py2, 5k0s, 5k0t

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
1
1
I
1
2
Y
1
4
D
5
1
H
5
3
G
5
4
F
2
1
3
M
2
2
7
Y
2
2
8
V
2
2
9
W
2
3
0
D
2
3
2
A
2
3
3
L
2
3
4
Y
2
3
7
I
2
6
5
F
2
6
8
H
2
6
9
[1]4py2.a 43e22 . . . . . . . . . . . . . . . . . .
[1]5k0s.a 0ou25 . . . . . . . . . . . . . . . . . .
[1]5k0t.a 41524 . . . . . . . . . . . . . . . . . .
[2]4dlp.a mse9 . . . . . . - . . . . . . . . . . .

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
A
1
1
I
1
2
Y
1
4
D
5
1
H
5
3
G
5
4
I
5
5
K
5
6
E
1
3
2
R
2
1
0
F
2
1
3
M
2
2
7
Y
2
2
8
V
2
2
9
W
2
3
0
D
2
3
2
A
2
3
3
L
2
3
4
N
2
3
6
Y
2
3
7
I
2
6
5
F
2
6
8
H
2
6
9
[1]4py2.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5k0s.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5k0t.a . . . . . . . . . . . . . . . . . . . . . . .
[2]4dlp.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
4py2.a:43e
5k0s.a:0ou
5k0t.a:415
4dlp.a:mse
[1] 4py2.a
0
0.2 0 0
[1] 5k0s.a 0
0
0 0.1
[1] 5k0t.a 0 0.1
0
0
[2] 4dlp.a 8.3 9.1 8.5
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4py2.a
5k0s.a
5k0t.a
4dlp.a
[1] 4py2.a
0
.01 0 .38
[1] 5k0s.a .01
0
.01 .40
[1] 5k0t.a 0 .01
0
.39
[2] 4dlp.a .38 .40 .39
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
4py2.a
5k0s.a
5k0t.a
4dlp.a
[1] 4py2.a
0
0.2 0.2 2.5
[1] 5k0s.a 0.2
0
0.2 2.5
[1] 5k0t.a 0.2 0.2
0
2.5
[2] 4dlp.a 2.5 2.5 2.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
4py2.a
5k0s.a
5k0t.a
4dlp.a
[1] 4py2.a
0
0.3 0.4 3.3
[1] 5k0s.a 0.3
0
0.4 2.8
[1] 5k0t.a 0.4 0.4
0
3.4
[2] 4dlp.a 3.3 2.8 3.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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