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.

SYP_ENTFA_1_572

Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYP_ENTFA):109, 111, 140, 142, 150:152, 155, 157, 159, 161, 202, 407:410, 412, 440:442, 444, 447109, 111, 140, 142, 150:152, 155, 157, 159, 161, 202, 407:410, 412, 440:442, 444, 447
Metals (Me):Mn

Full PDB list

2j3l, 2j3m

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
1
0
9
E
1
1
1
R
1
4
0
E
1
4
2
L
1
5
0
R
1
5
1
G
1
5
2
F
1
5
5
M
1
5
7
D
1
5
9
Y
1
6
1
M
2
0
2
E
4
0
7
I
4
0
8
G
4
0
9
H
4
1
0
F
4
1
2
C
4
4
0
Y
4
4
1
G
4
4
2
G
4
4
4
R
4
4
7
[1]2j3l.a p5a30 . . . . . . . . . . . . . . . . . . . . . .
[1]2j3m.a atp,pri38 . . . . . . . . . . . - . . . . . . . . . . Mn

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 Me
T
1
0
9
E
1
1
1
R
1
4
0
E
1
4
2
L
1
5
0
R
1
5
1
G
1
5
2
F
1
5
5
M
1
5
7
D
1
5
9
Y
1
6
1
M
2
0
2
E
4
0
7
I
4
0
8
G
4
0
9
H
4
1
0
F
4
1
2
C
4
4
0
Y
4
4
1
G
4
4
2
G
4
4
4
R
4
4
7
[1]2j3l.a . . . . . . . . . . . . . . . . . . . . . .
[1]2j3m.a . . . . . . . . . . . - . . . . . . . . . . Mn

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
2j3l.a:p5a
2j3m.a:atp,pri
[1] 2j3l.a
0
0.5
[1] 2j3m.a 0
0.3
[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
2j3l.a
2j3m.a
[1] 2j3l.a
0
.03
[1] 2j3m.a .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
2j3l.a
2j3m.a
[1] 2j3l.a
0
0.4
[1] 2j3m.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
2j3l.a
2j3m.a
[1] 2j3l.a
0
0.7
[1] 2j3m.a 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...