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.

SYMC_HUMAN_1_219

Methionine--tRNA ligase, cytoplasmic [Class-I aminoacyl-tRNA synthetase family] / Eukaryotic translation elongation factor 1 epsilon-1 (MCA3_HUMAN)

Composition of the binding site

Protein chains heterodimer [domain annotation]
A1 (SYMC_HUMAN):2, 29:312, 29:31
B1 (MCA3_HUMAN):D: GST C-terminal (157, 158)12, 157, 158

Full PDB list

4bl7, 4bvx, 4bvy (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 B1
R
2
L
2
9
S
3
1
K
1
2
Q
1
5
7
H
1
5
8
[1]4bvx.a i3c16 . . . . . .
[2]4bl7.a none . . . . . .

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 B1
R
2
L
2
9
I
3
0
S
3
1
K
1
2
Q
1
5
7
H
1
5
8
[1]4bvx.a . . . . . . .
[2]4bl7.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
4bvx.a:i3c
4bl7.a is apo
[1] 4bvx.a
0.2
-
[2] 4bl7.a 2.1
-
[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
4bvx.a
4bl7.a
[1] 4bvx.a
0
.30
[2] 4bl7.a .30
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4bvx.a
4bl7.a
[1] 4bvx.a
0
0.7
[2] 4bl7.a 0.7
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

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
4bvx.a
4bl7.a
[1] 4bvx.a
0
1.4
[2] 4bl7.a 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...