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_RHOPA_2_438

Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 2 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYP_RHOPA):109, 111, 140, 142, 149:152, 155, 157, 159, 161, 202, 209, 282:285, 287, 315:319, 322109, 111, 140, 142, 149:152, 155, 157, 159, 161, 202, 209, 282:285, 287, 315:319, 322

Full PDB list

2i4l, 2i4m, 2i4n, 2i4o (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
1
0
9
E
1
1
1
R
1
4
0
E
1
4
2
V
1
4
9
M
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
I
2
0
2
E
2
8
2
V
2
8
3
G
2
8
4
Q
2
8
5
F
2
8
7
S
3
1
5
Y
3
1
6
G
3
1
7
G
3
1
9
R
3
2
2
[1]2i4m.a none . . . . . . . . . . . . . . . . . . . . . . .
[1]2i4m.b psd30 . . . . . . . . . . . . . . . . . . . . . . .
[1]2i4n.a 5ca29 . . . . . . . . . . . . . . . . . . . . . . .
[1]2i4o.a atp,mg,mg33 . . . . . . . . . . . . . . . . . . . . . . .
[1]2i4o.b atp,mg,mg,mg34 . . . . . . . . . . . . . . . . . . . . . . .

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
T
1
0
9
E
1
1
1
R
1
4
0
E
1
4
2
V
1
4
9
M
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
I
2
0
2
E
2
0
9
E
2
8
2
V
2
8
3
G
2
8
4
Q
2
8
5
F
2
8
7
S
3
1
5
Y
3
1
6
G
3
1
7
V
3
1
8
G
3
1
9
R
3
2
2
[1]2i4m.a . . . . . . . . . . . . . . * . . * . . . . . . .
[1]2i4m.b . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2i4n.a . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2i4o.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2i4o.b . . . . . . . . . . . . . . . . . . . . . . . . .

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
2i4m.a is apo
2i4m.b:psd
2i4n.a:5ca
2i4o.a:atp,mg
2i4o.b:atp,mg
[1] 2i4m.a
-
2.1 2.0 2.0 2.4
[1] 2i4m.b -
0.1
0.7 1.1 1.2
[1] 2i4n.a - 0.1
0.1
0.4 0.8
[1] 2i4o.a - 0 0.2
0.2
0.3
[1] 2i4o.b - 0 0.2 0.2
0.1
[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
2i4m.a
2i4m.b
2i4n.a
2i4o.a
2i4o.b
[1] 2i4m.a
0
.07 .10 .10 .10
[1] 2i4m.b .07
0
.04 .05 .06
[1] 2i4n.a .10 .04
0
.04 .05
[1] 2i4o.a .10 .05 .04
0
.01
[1] 2i4o.b .10 .06 .05 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
2i4m.a
2i4m.b
2i4n.a
2i4o.a
2i4o.b
[1] 2i4m.a
0
2.3 2.2 0.4 0.4
[1] 2i4m.b 2.3
0
0.3 2.3 2.5
[1] 2i4n.a 2.2 0.3
0
2.3 2.5
[1] 2i4o.a 0.4 2.3 2.3
0
0.3
[1] 2i4o.b 0.4 2.5 2.5 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2i4m.a
2i4m.b
2i4n.a
2i4o.a
2i4o.b
[1] 2i4m.a
0
2.5 2.5 1.2 1.2
[1] 2i4m.b 2.5
0
0.7 2.8 3.0
[1] 2i4n.a 2.5 0.7
0
2.7 2.9
[1] 2i4o.a 1.2 2.8 2.7
0
0.5
[1] 2i4o.b 1.2 3.0 2.9 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...