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SYK_HUMAN_69_583

Lysine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYK_HUMAN):277, 278, 299, 301, 323, 325, 330:333, 335, 337, 339, 341, 445, 453, 485, 487, 494:499, 501, 546:548, 550, 553, 564277, 278, 299, 301, 323, 325, 330:333, 335, 337, 339, 341, 445, 453, 485, 487, 494:499, 501, 546:548, 550, 553, 564

Full PDB list

3bju, 4dpg, 4ycu, 4ycw, 6chd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
2
7
7
A
2
7
8
A
2
9
9
E
3
0
1
R
3
2
3
E
3
2
5
T
3
3
0
H
3
3
1
N
3
3
2
F
3
3
5
T
3
3
7
E
3
3
9
Y
3
4
1
E
4
8
7
E
4
9
4
I
4
9
5
C
4
9
6
N
4
9
7
A
4
9
8
Y
4
9
9
E
5
0
1
G
5
4
6
W
5
4
7
G
5
4
8
G
5
5
0
R
5
5
3
I
5
6
4
[1]3bju.a atp,ca,ca,ca,K44 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dpg.a apc,K,mg38 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ycu.a K,krs31 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ycw.f K,krs30 . . . . . . . . . . S . . . . . . . . . . . . . . . .
[1]6chd.a kaa32 . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
G
2
7
7
A
2
7
8
A
2
9
9
E
3
0
1
R
3
2
3
E
3
2
5
T
3
3
0
H
3
3
1
N
3
3
2
P
3
3
3
F
3
3
5
T
3
3
7
E
3
3
9
Y
3
4
1
D
4
4
5
E
4
5
3
R
4
8
5
E
4
8
7
E
4
9
4
I
4
9
5
C
4
9
6
N
4
9
7
A
4
9
8
Y
4
9
9
E
5
0
1
G
5
4
6
W
5
4
7
G
5
4
8
G
5
5
0
R
5
5
3
I
5
6
4
[1]3bju.a . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dpg.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ycu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ycw.f . . . . . . . . . . . S . . . . . . . . . . . . . . . . . . .
[1]6chd.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
3bju.a:K,atp,ca
4dpg.a:K,apc,mg
4ycu.a:K,krs
4ycw.f:K,krs
6chd.a:kaa
[1] 3bju.a
0.4
1.0 0.8 0.7 0.3
[1] 4dpg.a 0.7
0.1
0.6 0.6 0.3
[1] 4ycu.a 0.8 0.6
0
0.3 0.2
[1] 4ycw.f 1.4 1.2 0.3
0.3
0.3
[1] 6chd.a 0.7 1.3 1.2 1.4
0.3
[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
3bju.a
4dpg.a
4ycu.a
4ycw.f
6chd.a
[1] 3bju.a
0
.05 .05 .07 .04
[1] 4dpg.a .05
0
.03 .05 .08
[1] 4ycu.a .05 .03
0
.04 .06
[1] 4ycw.f .07 .05 .04
0
.09
[1] 6chd.a .04 .08 .06 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3bju.a
4dpg.a
4ycu.a
4ycw.f
6chd.a
[1] 3bju.a
0
0.7 0.3 0.4 0.4
[1] 4dpg.a 0.7
0
0.7 0.8 0.9
[1] 4ycu.a 0.3 0.7
0
0.3 0.5
[1] 4ycw.f 0.4 0.8 0.3
0
0.5
[1] 6chd.a 0.4 0.9 0.5 0.5
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

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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
3bju.a
4dpg.a
4ycu.a
4ycw.f
6chd.a
[1] 3bju.a
0
0.9 0.7 0.8 0.9
[1] 4dpg.a 0.9
0
1.0 1.1 1.2
[1] 4ycu.a 0.7 1.0
0
0.7 1.0
[1] 4ycw.f 0.8 1.1 0.7
0
0.9
[1] 6chd.a 0.9 1.2 1.0 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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