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SYL_ECOLI_226_413

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

Composition of the binding site

Protein chains monomer
A1 (SYL_ECOLI):227, 246:249, 252, 292, 295, 325:327, 330, 331, 333:338, 341, 342, 344, 345, 414, 416, 418227, 246:249, 252, 292, 295, 325:327, 330, 331, 333:338, 341, 342, 344, 345, 414, 416, 418

Full PDB list

2ajg, 2ajh, 2aji, 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
S
2
2
7
Y
2
4
6
T
2
4
7
T
2
4
8
R
2
4
9
T
2
5
2
F
3
2
5
V
3
2
6
L
3
2
7
Y
3
3
0
G
3
3
3
V
3
3
5
M
3
3
6
A
3
3
7
V
3
3
8
H
3
4
1
D
3
4
2
R
3
4
4
D
3
4
5
R
4
1
6
R
4
1
8
[1]2ajh.a M9 - . . . . . . . . . . . . . . . . . . - -
[1]2aji.a I9 - . . . . . . . . . . . . . . . . . . - -
[1]3zgz.d none . . . . . . . . . . . . . . . . . . . . .
[1]3zjt.a C57453 . . . . . . . . . . . . . . . . . . . . .
[1]3zju.a Cdjf56 . . . . . . . . . . . . . . . . . . . . .
[1]3zjv.a C36558 . . . . . . . . . . . . . . . . . . . . .
[1]4arc.a CA42 . . . . . . . . . . . . . . . . . . . . .
[1]4ari.a Cn7951 . . . . . . . . . . . . . . . . . . . . .
[1]4cqn.d ila31 . . . . . . . . . . . . . . . . . . . . .
[1]5omw.d none . . . . . A . . . . . . . . . . . . . . .
[1]5on2.d vrt26 . . . . . A . . . . . . . . . . . . . . .
[1]5on3.a 9yn27 . . . . . A . . . . . . . . . . . . . . .
[1]5onh.a vrt26 . . . . . . . . . . . . . . . . . . . . .

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
S
2
2
7
Y
2
4
6
T
2
4
7
T
2
4
8
R
2
4
9
T
2
5
2
E
2
9
2
M
2
9
5
F
3
2
5
V
3
2
6
L
3
2
7
Y
3
3
0
G
3
3
1
G
3
3
3
A
3
3
4
V
3
3
5
M
3
3
6
A
3
3
7
V
3
3
8
H
3
4
1
D
3
4
2
R
3
4
4
D
3
4
5
N
4
1
4
R
4
1
6
R
4
1
8
[1]2ajh.a - . . . . . . . . . . . . . . . . . . . . * . - - -
[1]2aji.a - . . . . . . . . . . . . . . . . . . . . * . - - -
[1]3zgz.d . . . . . . . . . . . . . . . . . . . . . * . . . *
[1]3zjt.a . . . . . . - - * . . . . . . . . . . . . . . . . .
[1]3zju.a . . . . . . - - * . . . . . . . . . . . . . . . . .
[1]3zjv.a . . . . . . - - * . . . . . . . . . . . . . . . . .
[1]4arc.a . . . . . . - - * . . . . . . . . . . . . . . . . .
[1]4ari.a . . . . . . - - * . . . . . . . . . . . . . . . . .
[1]4cqn.d . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]5omw.d . . . . . A . . . . . . . . . . . . . . . * . . . .
[1]5on2.d . . . . . A . . . . . . . . . . . . . . . * . . . .
[1]5on3.a . . . . . A . . . . . . . . . . . . . . . . . . . .
[1]5onh.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
2ajh.a:M
2aji.a:I
3zgz.d is apo
3zjt.a:C574
3zju.a:Cdjf
3zjv.a:C365
4arc.a:CA
4ari.a:Cn79
4cqn.d:ila
5omw.d is apo
5on2.d:vrt
5on3.a:9yn
5onh.a:vrt
[1] 2ajh.a
0
0 - 0.2 0.3 0.2 0.2 0.4 2.6 - 0.2 0.3 0.2
[1] 2aji.a 0
0
- 0.3 0.3 0.3 0.2 0.4 2.6 - 0.2 0.3 0.2
[1] 3zgz.d 0.7 0.7
-
1.8 1.6 1.8 1.4 1.4 3.1 - 0.5 1.0 0.6
[1] 3zjt.a 0.1 0.1 -
0
0.3 0.1 0.1 0.3 2.0 - 0.2 0.4 0.3
[1] 3zju.a 0.3 0 - 0.3
0
0.2 0.2 0.1 2.1 - 0.2 0.6 0.3
[1] 3zjv.a 0.1 0.1 - 0.2 0.1
0
0 0 1.7 - 0.5 0.9 0.4
[1] 4arc.a 0.5 0.1 - 0.5 0.4 0.4
0.1
0.3 1.9 - 0.4 0.6 0.4
[1] 4ari.a 0.2 0 - 0.3 0.3 0.3 0.1
0
2.0 - 0.4 0.5 0.3
[1] 4cqn.d 0.2 0.1 - 2.3 2.7 2.4 1.9 2.3
0.1
- 1.0 0.9 1.2
[1] 5omw.d 0.3 0.2 - 0.8 0.3 0.8 0.3 0.7 2.7
-
0.3 0.6 0.4
[1] 5on2.d 0.2 0.1 - 1.0 1.1 0.6 0.8 0.6 2.5 -
0
0.1 0.2
[1] 5on3.a 0.2 0.1 - 2.8 2.5 2.6 2.3 2.7 1.0 - 0.1
0
0
[1] 5onh.a 0.2 0.1 - 2.0 2.9 2.4 2.7 2.6 3.4 - 0.1 0.2
0
[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
2ajh.a
2aji.a
3zgz.d
3zjt.a
3zju.a
3zjv.a
4arc.a
4ari.a
4cqn.d
5omw.d
5on2.d
5on3.a
5onh.a
[1] 2ajh.a
0
0 .13 .17 .17 .18 .17 .18 .19 .06 .11 .18 .13
[1] 2aji.a 0
0
.12 .17 .18 .19 .18 .18 .20 .07 .11 .18 .12
[1] 3zgz.d .13 .12
0
.23 .24 .25 .22 .23 .22 .08 .15 .19 .15
[1] 3zjt.a .17 .17 .23
0
.04 .02 .04 .04 .15 .18 .13 .17 .24
[1] 3zju.a .17 .18 .24 .04
0
.03 .03 .02 .16 .18 .14 .17 .25
[1] 3zjv.a .18 .19 .25 .02 .03
0
.04 .03 .17 .19 .15 .19 .26
[1] 4arc.a .17 .18 .22 .04 .03 .04
0
.03 .14 .17 .13 .17 .24
[1] 4ari.a .18 .18 .23 .04 .02 .03 .03
0
.15 .18 .13 .17 .23
[1] 4cqn.d .19 .20 .22 .15 .16 .17 .14 .15
0
.16 .13 .12 .17
[1] 5omw.d .06 .07 .08 .18 .18 .19 .17 .18 .16
0
.13 .18 .13
[1] 5on2.d .11 .11 .15 .13 .14 .15 .13 .13 .13 .13
0
.10 .11
[1] 5on3.a .18 .18 .19 .17 .17 .19 .17 .17 .12 .18 .10
0
.09
[1] 5onh.a .13 .12 .15 .24 .25 .26 .24 .23 .17 .13 .11 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
2ajh.a
2aji.a
3zgz.d
3zjt.a
3zju.a
3zjv.a
4arc.a
4ari.a
4cqn.d
5omw.d
5on2.d
5on3.a
5onh.a
[1] 2ajh.a
0
0.2 1.1 1.1 1.2 1.2 1.1 1.2 1.3 1.2 1.4 1.6 1.7
[1] 2aji.a 0.2
0
1.1 1.1 1.1 1.1 1.1 1.1 1.3 1.2 1.4 1.6 1.6
[1] 3zgz.d 1.1 1.1
0
1.4 1.4 1.4 1.3 1.4 0.7 0.6 1.2 1.6 1.5
[1] 3zjt.a 1.1 1.1 1.4
0
0.3 0.4 0.3 0.4 1.5 1.4 0.7 1.1 1.0
[1] 3zju.a 1.2 1.1 1.4 0.3
0
0.5 0.3 0.2 1.4 1.4 0.7 1.0 0.9
[1] 3zjv.a 1.2 1.1 1.4 0.4 0.5
0
0.4 0.5 1.4 1.4 0.7 0.9 0.8
[1] 4arc.a 1.1 1.1 1.3 0.3 0.3 0.4
0
0.3 1.4 1.3 0.7 1.0 0.9
[1] 4ari.a 1.2 1.1 1.4 0.4 0.2 0.5 0.3
0
1.4 1.4 0.7 1.1 1.0
[1] 4cqn.d 1.3 1.3 0.7 1.5 1.4 1.4 1.4 1.4
0
0.8 1.1 1.4 1.4
[1] 5omw.d 1.2 1.2 0.6 1.4 1.4 1.4 1.3 1.4 0.8
0
1.0 1.4 1.3
[1] 5on2.d 1.4 1.4 1.2 0.7 0.7 0.7 0.7 0.7 1.1 1.0
0
1.0 0.9
[1] 5on3.a 1.6 1.6 1.6 1.1 1.0 0.9 1.0 1.1 1.4 1.4 1.0
0
0.3
[1] 5onh.a 1.7 1.6 1.5 1.0 0.9 0.8 0.9 1.0 1.4 1.3 0.9 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
2ajh.a
2aji.a
3zgz.d
3zjt.a
3zju.a
3zjv.a
4arc.a
4ari.a
4cqn.d
5omw.d
5on2.d
5on3.a
5onh.a
[1] 2ajh.a
0
0.2 1.8 2.2 2.2 2.1 2.2 2.2 2.2 2.0 2.4 2.5 2.4
[1] 2aji.a 0.2
0
1.8 2.1 2.2 2.1 2.1 2.2 2.2 1.9 2.3 2.4 2.4
[1] 3zgz.d 1.8 1.8
0
2.6 2.5 2.5 2.4 2.5 1.4 0.9 2.1 2.5 2.4
[1] 3zjt.a 2.2 2.1 2.6
0
0.8 0.7 0.9 0.9 2.4 2.6 1.4 1.7 1.5
[1] 3zju.a 2.2 2.2 2.5 0.8
0
0.7 0.4 0.4 2.3 2.5 1.1 1.4 1.3
[1] 3zjv.a 2.1 2.1 2.5 0.7 0.7
0
0.8 0.8 2.3 2.4 1.1 1.4 1.2
[1] 4arc.a 2.2 2.1 2.4 0.9 0.4 0.8
0
0.4 2.2 2.4 1.1 1.4 1.3
[1] 4ari.a 2.2 2.2 2.5 0.9 0.4 0.8 0.4
0
2.3 2.4 1.1 1.4 1.3
[1] 4cqn.d 2.2 2.2 1.4 2.4 2.3 2.3 2.2 2.3
0
1.2 2.0 2.4 2.3
[1] 5omw.d 2.0 1.9 0.9 2.6 2.5 2.4 2.4 2.4 1.2
0
1.9 2.4 2.3
[1] 5on2.d 2.4 2.3 2.1 1.4 1.1 1.1 1.1 1.1 2.0 1.9
0
1.3 1.2
[1] 5on3.a 2.5 2.4 2.5 1.7 1.4 1.4 1.4 1.4 2.4 2.4 1.3
0
0.8
[1] 5onh.a 2.4 2.4 2.4 1.5 1.3 1.2 1.3 1.3 2.3 2.3 1.2 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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