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SYT_STAAW_1_645

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYT_STAAW):R: Catalytic (313, 334:336, 363, 365, 367, 376:378, 381, 383, 385, 387, 468, 471, 485, 486, 488, 490, 517, 518, 522, 523, 526)313, 334:336, 363, 365, 367, 376:378, 381, 383, 385, 387, 468, 471, 485, 486, 488, 490, 517, 518, 522, 523, 526
Metals (Me):Zn

Full PDB list

1nyq, 1nyr

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
M
3
3
4
N
3
3
5
C
3
3
6
R
3
6
5
E
3
6
7
R
3
7
7
V
3
7
8
M
3
8
1
L
3
8
3
D
3
8
5
H
3
8
7
Y
4
6
8
K
4
7
1
T
4
8
5
L
4
8
6
T
4
8
8
Q
4
9
0
H
5
1
7
R
5
1
8
S
5
2
2
T
5
2
3
R
5
2
6
[1]1nyq.a tsb30 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1nyr.a atp,T39 . . . . . . . . . . . . . . . . . . . . . . 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
Y
3
1
3
M
3
3
4
N
3
3
5
C
3
3
6
M
3
6
3
R
3
6
5
E
3
6
7
Q
3
7
6
R
3
7
7
V
3
7
8
M
3
8
1
L
3
8
3
D
3
8
5
H
3
8
7
Y
4
6
8
K
4
7
1
T
4
8
5
L
4
8
6
T
4
8
8
Q
4
9
0
H
5
1
7
R
5
1
8
S
5
2
2
T
5
2
3
R
5
2
6
[1]1nyq.a . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1nyr.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
1nyq.a:tsb
1nyr.a:T,atp
[1] 1nyq.a
0.2
0.6
[1] 1nyr.a 0.1
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
1nyq.a
1nyr.a
[1] 1nyq.a
0
.02
[1] 1nyr.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1nyq.a
1nyr.a
[1] 1nyq.a
0
0.4
[1] 1nyr.a 0.4
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
1nyq.a
1nyr.a
[1] 1nyq.a
0
0.8
[1] 1nyr.a 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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