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SYP_THET8_1_477

Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYP_THET8):111, 113, 142, 144, 150:153, 156, 158, 160, 162, 205, 225, 227, 228, 230, 258:260, 262:264111, 113, 142, 144, 150:153, 156, 158, 160, 162, 205, 225, 227, 228, 230, 258:260, 262:264

Full PDB list

1h4q, 1h4s, 1h4t, 1hc7

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
1
1
1
E
1
1
3
R
1
4
2
E
1
4
4
F
1
5
0
L
1
5
1
R
1
5
2
T
1
5
3
F
1
5
6
W
1
5
8
E
1
6
0
H
1
6
2
F
2
0
5
Q
2
2
5
G
2
2
7
T
2
2
8
H
2
3
0
S
2
5
8
W
2
5
9
G
2
6
0
S
2
6
2
R
2
6
4
[1]1h4q.a atp,pri38 . . . . . . . . . . . . . . . . . . . . . .
[1]1h4s.a psd30 . . . . . . . . . . . . . . . . . . . . . .
[1]1h4t.a P8 . . . . . . . . . . . . . . . . . . . . . .
[1]1hc7.c 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
T
1
1
1
E
1
1
3
R
1
4
2
E
1
4
4
F
1
5
0
L
1
5
1
R
1
5
2
T
1
5
3
F
1
5
6
W
1
5
8
E
1
6
0
H
1
6
2
F
2
0
5
Q
2
2
5
G
2
2
7
T
2
2
8
H
2
3
0
S
2
5
8
W
2
5
9
G
2
6
0
S
2
6
2
W
2
6
3
R
2
6
4
[1]1h4q.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1h4s.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1h4t.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1hc7.c . . . . . . . . . . . . . . . . . . . . . . .

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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1h4q.a:atp,pri
1h4s.a:psd
1h4t.a:P
1hc7.c is apo
[1] 1h4q.a
0.1
0.2 0.1 -
[1] 1h4s.a 0.7
0.2
0.1 -
[1] 1h4t.a 0.7 0.8
0.2
-
[1] 1hc7.c 0.3 0.9 0
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1h4q.a
1h4s.a
1h4t.a
1hc7.c
[1] 1h4q.a
0
.03 .05 .05
[1] 1h4s.a .03
0
.04 .07
[1] 1h4t.a .05 .04
0
.04
[1] 1hc7.c .05 .07 .04
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

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1h4q.a
1h4s.a
1h4t.a
1hc7.c
[1] 1h4q.a
0
0.8 0.4 0.5
[1] 1h4s.a 0.8
0
0.9 0.8
[1] 1h4t.a 0.4 0.9
0
0.5
[1] 1hc7.c 0.5 0.8 0.5
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

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1h4q.a
1h4s.a
1h4t.a
1hc7.c
[1] 1h4q.a
0
0.8 0.7 0.7
[1] 1h4s.a 0.8
0
1.1 1.1
[1] 1h4t.a 0.7 1.1
0
0.7
[1] 1hc7.c 0.7 1.1 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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