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SYV_THETH_192_338

Valine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYV_THETH):R: Interaction with the Thr-AMP intermediate (261, 264, 265, 267, 269, 270, 272, 276, 278, 279)
213:216, 219, 259, 260, 337
213:216, 219, 259:261, 264, 265, 267, 269, 270, 272, 276, 278, 279, 337

Full PDB list

1gax, 1ivs, 1wk9, 1wka (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
2
1
3
T
2
1
4
V
2
1
5
R
2
1
6
T
2
1
9
V
2
6
0
E
2
6
1
F
2
6
4
L
2
6
9
K
2
7
0
T
2
7
2
D
2
7
6
L
2
7
8
D
2
7
9
Y
3
3
7
[1]1gax.b A22 . . . . . . . . . . . . . . .
[1]1wk9.a tsb30 . . . . . . . . . . . . . . .
[1]1wka.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
A
2
1
3
T
2
1
4
V
2
1
5
R
2
1
6
T
2
1
9
A
2
5
9
V
2
6
0
E
2
6
1
F
2
6
4
G
2
6
5
G
2
6
7
L
2
6
9
K
2
7
0
T
2
7
2
D
2
7
6
L
2
7
8
D
2
7
9
Y
3
3
7
[1]1gax.b . . . . . . . . . . . . . . . . . .
[1]1wk9.a . . . . . . . . . . . . . . . . . .
[1]1wka.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
1gax.b:A
1wk9.a:tsb
1wka.a is apo
[1] 1gax.b
0.3
1.4 -
[1] 1wk9.a 0.3
0.2
-
[1] 1wka.a 1.0 0.3
-
[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
1gax.b
1wk9.a
1wka.a
[1] 1gax.b
0
.09 .13
[1] 1wk9.a .09
0
.04
[1] 1wka.a .13 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1gax.b
1wk9.a
1wka.a
[1] 1gax.b
0
1.4 1.4
[1] 1wk9.a 1.4
0
0.2
[1] 1wka.a 1.4 0.2
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
1gax.b
1wk9.a
1wka.a
[1] 1gax.b
0
2.0 1.8
[1] 1wk9.a 2.0
0
1.0
[1] 1wka.a 1.8 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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