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.

SYYC_HUMAN_2_360

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

Composition of the binding site

Protein chains monomer
A1 (SYYC_HUMAN):39, 41:43, 72, 74, 77, 81, 152, 166, 170, 173, 182, 18839, 41:43, 72, 74, 77, 81, 152, 166, 170, 173, 182, 188

Full PDB list

1n3l, 1q11, 4q93, 4qbt, 5thh, 5thl (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
3
9
G
4
1
L
7
2
A
7
4
H
7
7
V
1
5
2
Y
1
6
6
Q
1
7
0
D
1
7
3
Q
1
8
2
Q
1
8
8
[1]1n3l.a none . . . . . . . . . . .
[1]1q11.a tye12 . . . . . . . . . . .
[1]4q93.a stl17 . . . . . . . . . . .
[1]5thh.a Y13 . . . . . . . . . . .
[2]5thl.a none . R . . . . . . . . .

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
3
9
G
4
1
T
4
2
A
4
3
L
7
2
A
7
4
H
7
7
D
8
1
V
1
5
2
Y
1
6
6
Q
1
7
0
D
1
7
3
Q
1
8
2
Q
1
8
8
[1]1n3l.a . . . . . . . . . * . . . .
[1]1q11.a . . . . . . . . . * . . . .
[1]4q93.a . . . . . . . . . . . . . .
[1]5thh.a . . . . . . . . . * . . . .
[2]5thl.a * R . . . . . . . . . . . .

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
1n3l.a is apo
1q11.a:tye
4q93.a:stl
5thh.a:Y
5thl.a is apo
[1] 1n3l.a
-
0.6 3.4 0.7 -
[1] 1q11.a -
0
3.3 0.1 -
[1] 4q93.a - 0.1
0.1
0.2 -
[1] 5thh.a - 0 3.2
0.2
-
[2] 5thl.a - 3.7 4.0 3.5
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1n3l.a
1q11.a
4q93.a
5thh.a
5thl.a
[1] 1n3l.a
0
.06 .26 .05 .51
[1] 1q11.a .06
0
.24 .01 .53
[1] 4q93.a .26 .24
0
.23 .30
[1] 5thh.a .05 .01 .23
0
.53
[2] 5thl.a .51 .53 .30 .53
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 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
1n3l.a
1q11.a
4q93.a
5thh.a
5thl.a
[1] 1n3l.a
0
1.8 0.5 1.8 0.3
[1] 1q11.a 1.8
0
1.6 0.1 1.7
[1] 4q93.a 0.5 1.6
0
1.6 0.5
[1] 5thh.a 1.8 0.1 1.6
0
1.7
[2] 5thl.a 0.3 1.7 0.5 1.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1n3l.a
1q11.a
4q93.a
5thh.a
5thl.a
[1] 1n3l.a
0
2.2 1.7 2.2 1.8
[1] 1q11.a 2.2
0
2.0 0.7 2.1
[1] 4q93.a 1.7 2.0
0
2.0 0.9
[1] 5thh.a 2.2 0.7 2.0
0
2.2
[2] 5thl.a 1.8 2.1 0.9 2.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...