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SYSC_HUMAN_1_477

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

Composition of the binding site

Protein chains monomer
A1 (SYSC_HUMAN):271, 273, 302, 304, 316:318, 321, 323, 325, 391:394, 427:429, 432, 434, 435271, 273, 302, 304, 316:318, 321, 323, 325, 391:394, 427:429, 432, 434, 435

Full PDB list

3vbb, 4l87

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
2
7
1
E
2
7
3
R
3
0
2
E
3
0
4
F
3
1
6
R
3
1
7
V
3
1
8
F
3
2
1
K
3
2
3
E
3
2
5
E
3
9
1
L
3
9
2
V
3
9
3
S
3
9
4
N
4
2
7
T
4
2
9
A
4
3
2
T
4
3
4
R
4
3
5
[1]3vbb.a mg1 . . . . . . . . . . . . . . . . . . .
[1]3vbb.b none . . . . . . . . . . . . . . . . . . .
[1]4l87.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

[download in TSV format]
   
PDB.ch
A1
T
2
7
1
E
2
7
3
R
3
0
2
E
3
0
4
F
3
1
6
R
3
1
7
V
3
1
8
F
3
2
1
K
3
2
3
E
3
2
5
E
3
9
1
L
3
9
2
V
3
9
3
S
3
9
4
N
4
2
7
A
4
2
8
T
4
2
9
A
4
3
2
T
4
3
4
R
4
3
5
[1]3vbb.a . . . . . . . . . . . . . . . . * . . .
[1]3vbb.b . . . . . . . . . . . . . . . . * . . .
[1]4l87.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
3vbb.a:mg
3vbb.b is apo
4l87.a:ssa
[1] 3vbb.a
0
- 1.7
[1] 3vbb.b 0
-
1.7
[1] 4l87.a 0 -
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
3vbb.a
3vbb.b
4l87.a
[1] 3vbb.a
0
.05 .09
[1] 3vbb.b .05
0
.09
[1] 4l87.a .09 .09
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

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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
3vbb.a
3vbb.b
4l87.a
[1] 3vbb.a
0
0.6 0.8
[1] 3vbb.b 0.6
0
0.5
[1] 4l87.a 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

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
3vbb.a
3vbb.b
4l87.a
[1] 3vbb.a
0
1.6 1.8
[1] 3vbb.b 1.6
0
1.2
[1] 4l87.a 1.8 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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