If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

SYYM_HUMAN_28_377

Tyrosine--tRNA ligase, mitochondrial [Class-I aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYYM_HUMAN):77:81, 88, 90, 91, 93, 94, 111, 116, 121, 173, 221, 225, 228, 241, 243, 244, 246, 247, 272:27477:81, 88, 90, 91, 93, 94, 111, 116, 121, 173, 221, 225, 228, 241, 243, 244, 246, 247, 272:274

Full PDB list

2pid, 3zxi

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
7
7
G
7
9
F
8
0
D
8
1
H
8
8
G
9
0
H
9
1
A
9
4
L
1
1
1
T
1
1
6
D
1
2
1
N
1
7
3
Y
2
2
1
Q
2
2
5
D
2
2
8
Q
2
4
1
G
2
4
3
G
2
4
4
D
2
4
6
Q
2
4
7
P
2
7
2
L
2
7
3
I
2
7
4
[1]2pid.b ysa35 . . . . . . . . . . . . . . . . . . . . . . .
[1]3zxi.a tya34 . . . . . . . . . . . . . . . . . . . . . . .

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
Y
7
7
C
7
8
G
7
9
F
8
0
D
8
1
H
8
8
G
9
0
H
9
1
L
9
3
A
9
4
L
1
1
1
T
1
1
6
D
1
2
1
N
1
7
3
Y
2
2
1
Q
2
2
5
D
2
2
8
Q
2
4
1
G
2
4
3
G
2
4
4
D
2
4
6
Q
2
4
7
P
2
7
2
L
2
7
3
I
2
7
4
[1]2pid.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zxi.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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2pid.b:ysa
3zxi.a:tya
[1] 2pid.b
0.1
0.2
[1] 3zxi.a 0.3
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2pid.b
3zxi.a
[1] 2pid.b
0
.02
[1] 3zxi.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

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
2pid.b
3zxi.a
[1] 2pid.b
0
0.3
[1] 3zxi.a 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

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
2pid.b
3zxi.a
[1] 2pid.b
0
0.8
[1] 3zxi.a 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...