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SYT_ECOLI_1_239

Threonine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYT_ECOLI):R: Correctly edits mischarged seryl- tRNA(Thr) (73, 76, 77, 94:96, 104, 156, 159, 164, 168:171, 180:183)
R: N2 domain, the editing domain (73, 76, 77, 94:96, 104, 156, 159, 164, 168:171, 180:183)
73, 76, 77, 94:96, 104, 156, 159, 164, 168:171, 180:183

Full PDB list

1qf6, 1tje, 1tke, 1tkg, 1tky (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
7
3
A
7
6
H
7
7
I
9
4
G
9
5
P
9
6
Y
1
0
4
K
1
5
6
I
1
5
9
I
1
6
4
D
1
6
8
K
1
6
9
P
1
7
0
G
1
7
1
D
1
8
0
M
1
8
1
C
1
8
2
R
1
8
3
[1]1tje.a none . . . . . . . . . . . . . . . . . .
[1]1tke.a S7 . . . . . . . . . . . . . . . . . .
[1]1tkg.a ssa29 . . . . . . . . . . . . . . . . . .
[1]1tky.a a3s25 . . . . . . . . . . . . . . . . . .

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

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PDB.ch
A1
H
7
3
A
7
6
H
7
7
I
9
4
G
9
5
P
9
6
Y
1
0
4
K
1
5
6
I
1
5
9
I
1
6
4
D
1
6
8
K
1
6
9
P
1
7
0
G
1
7
1
D
1
8
0
M
1
8
1
C
1
8
2
R
1
8
3
[1]1tje.a . . . . . . . . . . . . . . . . . .
[1]1tke.a . . . . . . . . . . . . . . . . . .
[1]1tkg.a . . . . . . . . . . . . . . . . . .
[1]1tky.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
1tje.a is apo
1tke.a:S
1tkg.a:ssa
1tky.a:a3s
[1] 1tje.a
-
0.1 0.1 0.2
[1] 1tke.a -
0
0.2 0.2
[1] 1tkg.a - 0.1
0
0.1
[1] 1tky.a - 0.1 0.1
0.1
[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
1tje.a
1tke.a
1tkg.a
1tky.a
[1] 1tje.a
0
.01 .01 .01
[1] 1tke.a .01
0
.01 .01
[1] 1tkg.a .01 .01
0
.01
[1] 1tky.a .01 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1tje.a
1tke.a
1tkg.a
1tky.a
[1] 1tje.a
0
0.1 0.3 0.1
[1] 1tke.a 0.1
0
0.3 0.1
[1] 1tkg.a 0.3 0.3
0
0.3
[1] 1tky.a 0.1 0.1 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1tje.a
1tke.a
1tkg.a
1tky.a
[1] 1tje.a
0
0.2 1.0 0.3
[1] 1tke.a 0.2
0
1.0 0.3
[1] 1tkg.a 1.0 1.0
0
1.0
[1] 1tky.a 0.3 0.3 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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