If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

SYL_ECOLI_413_860

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

Composition of the binding site

Protein chains monomer
A1 (SYL_ECOLI):40:43, 49, 51, 52, 55, 56, 80, 493, 496, 499, 527, 529, 530, 532, 533, 537, 566:569, 619, 620, 62240:43, 49, 51, 52, 55, 56, 80, 493, 496, 499, 527, 529, 530, 532, 533, 537, 566:569, 619, 620, 622

Full PDB list

3zgz, 3zjt, 3zju, 3zjv, 4aq7, 4arc, 4ari, 4as1, 4cqn, 5omw, 5on2, 5on3, 5onh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
4
0
L
4
1
P
4
2
Y
4
3
H
4
9
G
5
1
H
5
2
N
5
5
Y
5
6
D
8
0
S
4
9
6
Y
5
2
7
G
5
2
9
G
5
3
0
E
5
3
2
H
5
3
3
H
5
3
7
Q
5
6
6
G
5
6
7
M
5
6
8
V
5
6
9
K
6
1
9
M
6
2
0
K
6
2
2
[1]3zgz.d 84t31 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4aq7.a lmsL31 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4arc.a L9 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4as1.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]4cqn.a ila31 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5omw.a lss31 . . . . . . . . . . . . . . . . . . . . . . . .

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
M
4
0
L
4
1
P
4
2
Y
4
3
H
4
9
G
5
1
H
5
2
N
5
5
Y
5
6
D
8
0
F
4
9
3
S
4
9
6
Y
4
9
9
Y
5
2
7
G
5
2
9
G
5
3
0
E
5
3
2
H
5
3
3
H
5
3
7
Q
5
6
6
G
5
6
7
M
5
6
8
V
5
6
9
K
6
1
9
M
6
2
0
K
6
2
2
[1]3zgz.d . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4aq7.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4arc.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4as1.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4cqn.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5omw.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3zgz.d:84t
4aq7.a:lmsL
4arc.a:L
4as1.a is apo
4cqn.a:ila
5omw.a:lss
[1] 3zgz.d
0.1
0.2 0.1 - 0.2 0.3
[1] 4aq7.a 0.4
0.1
0.1 - 0.3 0.2
[1] 4arc.a 0.3 0.3
0
- 0.3 0.3
[1] 4as1.a 0.2 0 0
-
0.2 0.2
[1] 4cqn.a 0.5 0.3 0.1 -
0.1
0.3
[1] 5omw.a 0.1 0.1 0.1 - 0.2
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3zgz.d
4aq7.a
4arc.a
4as1.a
4cqn.a
5omw.a
[1] 3zgz.d
0
.02 .03 .02 .03 .02
[1] 4aq7.a .02
0
.02 .02 .02 .02
[1] 4arc.a .03 .02
0
0 .02 .01
[1] 4as1.a .02 .02 0
0
.02 0
[1] 4cqn.a .03 .02 .02 .02
0
.02
[1] 5omw.a .02 .02 .01 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
3zgz.d
4aq7.a
4arc.a
4as1.a
4cqn.a
5omw.a
[1] 3zgz.d
0
0.5 2.6 2.5 0.4 0.4
[1] 4aq7.a 0.5
0
2.4 2.3 0.3 0.2
[1] 4arc.a 2.6 2.4
0
0.2 2.5 2.4
[1] 4as1.a 2.5 2.3 0.2
0
2.4 2.3
[1] 4cqn.a 0.4 0.3 2.5 2.4
0
0.3
[1] 5omw.a 0.4 0.2 2.4 2.3 0.3
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

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
3zgz.d
4aq7.a
4arc.a
4as1.a
4cqn.a
5omw.a
[1] 3zgz.d
0
1.4 3.0 2.9 1.4 1.4
[1] 4aq7.a 1.4
0
2.5 2.5 0.4 0.2
[1] 4arc.a 3.0 2.5
0
1.4 2.6 2.5
[1] 4as1.a 2.9 2.5 1.4
0
2.6 2.5
[1] 4cqn.a 1.4 0.4 2.6 2.6
0
0.4
[1] 5omw.a 1.4 0.2 2.5 2.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...