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SYTM_YEAST_24_462

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

Composition of the binding site

Protein chains monomer
A1 (SYTM_YEAST):131, 133, 162, 164, 173:175, 178, 180, 182, 184, 270, 287, 288, 290, 292, 319:321, 324, 325, 328131, 133, 162, 164, 173:175, 178, 180, 182, 184, 270, 287, 288, 290, 292, 319:321, 324, 325, 328
Metals (Me):Zn

Full PDB list

3ugq, 3uh0, 4eo4, 4yye (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
M
1
3
1
C
1
3
3
R
1
6
2
E
1
6
4
T
1
7
3
R
1
7
4
L
1
7
5
F
1
7
8
Q
1
8
0
D
1
8
2
H
1
8
4
Y
2
7
0
Q
2
8
7
V
2
8
8
T
2
9
0
Q
2
9
2
H
3
1
9
G
3
2
4
S
3
2
5
R
3
2
8
[1]3ugq.a none . . . . . . . . . . . . . . . . . . . . Zn
[1]3uh0.a tsb30 . . . . . . . . . . . . . . . . . . . . Zn
[1]4eo4.a ssa29 . . . . . . . . . . . . . . . . . . . . Zn

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 Me
M
1
3
1
C
1
3
3
R
1
6
2
E
1
6
4
T
1
7
3
R
1
7
4
L
1
7
5
F
1
7
8
Q
1
8
0
D
1
8
2
H
1
8
4
Y
2
7
0
Q
2
8
7
V
2
8
8
T
2
9
0
Q
2
9
2
H
3
1
9
R
3
2
0
A
3
2
1
G
3
2
4
S
3
2
5
R
3
2
8
[1]3ugq.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3uh0.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4eo4.a . . . . . . . . . . . . . . . . . . . . . . Zn

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
3ugq.a is apo
3uh0.a:tsb
4eo4.a:ssa
[1] 3ugq.a
-
0.4 0.6
[1] 3uh0.a -
0
0.2
[1] 4eo4.a - 0
0.2
[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
3ugq.a
3uh0.a
4eo4.a
[1] 3ugq.a
0
.03 .03
[1] 3uh0.a .03
0
0
[1] 4eo4.a .03 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3ugq.a
3uh0.a
4eo4.a
[1] 3ugq.a
0
0.6 0.7
[1] 3uh0.a 0.6
0
0.2
[1] 4eo4.a 0.7 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

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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
3ugq.a
3uh0.a
4eo4.a
[1] 3ugq.a
0
1.2 1.2
[1] 3uh0.a 1.2
0
0.6
[1] 4eo4.a 1.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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