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SYS_PYRHO_1_455

Serine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYS_PYRHO):R: Serine binding (252, 254)
283, 285, 297:299, 302, 304, 306, 370:373, 404:406, 409, 411, 412
252, 254, 283, 285, 297:299, 302, 304, 306, 370:373, 404:406, 409, 411, 412

Full PDB list

2dq0, 2zr2, 2zr3

Pocket contact map

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PDB.ch
   
ligand
A1
T
2
5
2
E
2
5
4
R
2
8
3
E
2
8
5
F
2
9
7
R
2
9
8
V
2
9
9
F
3
0
2
K
3
0
4
E
3
0
6
E
3
7
0
V
3
7
1
V
3
7
2
S
3
7
3
N
4
0
4
S
4
0
5
T
4
0
6
A
4
0
9
S
4
1
1
R
4
1
2
[1]2dq0.a ssa29 . . . . . . . . . . . . . . . . . . . .
[1]2zr2.a amp23 . . . . . . . . . . . . . . . . . . . .
[1]2zr3.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

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PDB.ch
A1
T
2
5
2
E
2
5
4
R
2
8
3
E
2
8
5
F
2
9
7
R
2
9
8
V
2
9
9
F
3
0
2
K
3
0
4
E
3
0
6
E
3
7
0
V
3
7
1
V
3
7
2
S
3
7
3
N
4
0
4
S
4
0
5
T
4
0
6
A
4
0
9
S
4
1
1
R
4
1
2
[1]2dq0.a . . . . . . . . . . . . . . . . . . . .
[1]2zr2.a . . . . . . . . . . . . . . . . . . . .
[1]2zr3.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2dq0.a:ssa
2zr2.a:amp
2zr3.a is apo
[1] 2dq0.a
0.2
0.1 -
[1] 2zr2.a 0.4
0.1
-
[1] 2zr3.a 1.7 0.8
-
[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
2dq0.a
2zr2.a
2zr3.a
[1] 2dq0.a
0
.02 .08
[1] 2zr2.a .02
0
.07
[1] 2zr3.a .08 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
2dq0.a
2zr2.a
2zr3.a
[1] 2dq0.a
0
0.1 0.2
[1] 2zr2.a 0.1
0
0.2
[1] 2zr3.a 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2dq0.a
2zr2.a
2zr3.a
[1] 2dq0.a
0
0.2 0.8
[1] 2zr2.a 0.2
0
0.7
[1] 2zr3.a 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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