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SYS_THET8_1_421

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_THET8):R: Serine binding (225, 227)
256, 258, 270:272, 275, 277, 279, 345:348, 378:380, 383, 386
225, 227, 256, 258, 270:272, 275, 277, 279, 345:348, 378:380, 383, 386

Full PDB list

1ser, 1ses, 1set, 1sry (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
T
2
2
5
E
2
2
7
R
2
5
6
E
2
5
8
M
2
7
0
R
2
7
1
V
2
7
2
F
2
7
5
K
2
7
7
E
2
7
9
E
3
4
5
T
3
4
6
H
3
4
7
S
3
4
8
N
3
7
8
N
3
7
9
T
3
8
0
A
3
8
3
R
3
8
6
[1]1ser.a none . . . . . . . . . . . . . . . . . . .
[1]1ses.a ahx30 . . . . . . . . . . . . . . . . . . .
[1]1ses.b amp23 . . . . . . . . . . . . . . . . . . .
[1]1set.a ssa29 . . . . . . . . . . . . . . . . . . .

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
2
5
E
2
2
7
R
2
5
6
E
2
5
8
M
2
7
0
R
2
7
1
V
2
7
2
F
2
7
5
K
2
7
7
E
2
7
9
E
3
4
5
T
3
4
6
H
3
4
7
S
3
4
8
N
3
7
8
N
3
7
9
T
3
8
0
A
3
8
3
R
3
8
6
[1]1ser.a . . * . . . . . . . . . . . . . . . .
[1]1ses.a . . . . . . . . . . . . . . . . . . .
[1]1ses.b . . . . . . . . . . . . . . . . . . .
[1]1set.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
1ser.a is apo
1ses.a:ahx
1ses.b:amp
1set.a:ssa
[1] 1ser.a
-
3.0 2.6 3.1
[1] 1ses.a -
0.1
0.1 0.1
[1] 1ses.b - 0.4
0.1
0.4
[1] 1set.a - 0.1 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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1ser.a
1ses.a
1ses.b
1set.a
[1] 1ser.a
0
.16 .15 .16
[1] 1ses.a .16
0
.04 .01
[1] 1ses.b .15 .04
0
.03
[1] 1set.a .16 .01 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1ser.a
1ses.a
1ses.b
1set.a
[1] 1ser.a
0
0.5 0.5 0.5
[1] 1ses.a 0.5
0
0.2 0.2
[1] 1ses.b 0.5 0.2
0
0.2
[1] 1set.a 0.5 0.2 0.2
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

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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
1ser.a
1ses.a
1ses.b
1set.a
[1] 1ser.a
0
1.3 1.4 1.2
[1] 1ses.a 1.3
0
0.8 0.5
[1] 1ses.b 1.4 0.8
0
0.7
[1] 1set.a 1.2 0.5 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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