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SYTC_HUMAN_320_723

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

Composition of the binding site

Protein chains monomer
A1 (SYTC_HUMAN):386:388, 391, 392, 411, 413, 442, 460, 462, 464, 506, 537:540, 543, 545, 546, 557:560, 562, 564, 567, 590:592, 595386:388, 391, 392, 411, 413, 442, 460, 462, 464, 506, 537:540, 543, 545, 546, 557:560, 562, 564, 567, 590:592, 595
Metals (Me):Zn

Full PDB list

4hwt, 4p3n, 4ttv

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
S
3
8
6
G
3
8
7
H
3
8
8
M
4
1
1
C
4
1
3
R
4
4
2
Q
4
6
0
D
4
6
2
H
4
6
4
F
5
3
9
Y
5
4
0
D
5
4
5
I
5
4
6
Q
5
5
7
C
5
5
8
A
5
5
9
T
5
6
0
Q
5
6
2
D
5
6
4
L
5
6
7
H
5
9
0
R
5
9
1
[1]4p3n.a 2cr35 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4ttv.a bc934 . . . . . . . . . . . . . . . . . . . . . . Zn
[2]4hwt.a 1b226 . . . . . . . . . . . . . . . . . . . . . . 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
S
3
8
6
G
3
8
7
H
3
8
8
H
3
9
1
Y
3
9
2
M
4
1
1
C
4
1
3
R
4
4
2
Q
4
6
0
D
4
6
2
H
4
6
4
L
5
0
6
G
5
3
7
A
5
3
8
F
5
3
9
Y
5
4
0
K
5
4
3
D
5
4
5
I
5
4
6
Q
5
5
7
C
5
5
8
A
5
5
9
T
5
6
0
Q
5
6
2
D
5
6
4
L
5
6
7
H
5
9
0
R
5
9
1
A
5
9
2
G
5
9
5
[1]4p3n.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4ttv.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[2]4hwt.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
4p3n.a:2cr
4ttv.a:bc9
4hwt.a:1b2
[1] 4p3n.a
0.2
0.1 3.0
[1] 4ttv.a 0.2
0.1
2.9
[2] 4hwt.a 9.7 9.8
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4p3n.a
4ttv.a
4hwt.a
[1] 4p3n.a
0
.02 .43
[1] 4ttv.a .02
0
.42
[2] 4hwt.a .43 .42
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
4p3n.a
4ttv.a
4hwt.a
[1] 4p3n.a
0
0.3 1.9
[1] 4ttv.a 0.3
0
2.0
[2] 4hwt.a 1.9 2.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
4p3n.a
4ttv.a
4hwt.a
[1] 4p3n.a
0
0.8 2.3
[1] 4ttv.a 0.8
0
2.3
[2] 4hwt.a 2.3 2.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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