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SYK_GEOSE_2_494

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

Composition of the binding site

Protein chains monomer
A1 (SYK_GEOSE):208, 209, 230, 232, 254, 256, 257, 259, 261:263, 266, 268, 270, 272, 367, 371, 403, 405, 412:417, 419, 464:466, 468, 471, 482208, 209, 230, 232, 254, 256, 257, 259, 261:263, 266, 268, 270, 272, 367, 371, 403, 405, 412:417, 419, 464:466, 468, 471, 482
Metals (Me):Mg

Full PDB list

3a74, 3e9h, 3e9i

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
2
0
8
A
2
0
9
A
2
3
0
E
2
3
2
R
2
5
4
E
2
5
6
G
2
5
7
S
2
5
9
R
2
6
1
H
2
6
2
N
2
6
3
F
2
6
6
M
2
6
8
E
2
7
0
Y
2
7
2
E
3
6
7
E
3
7
1
R
4
0
3
E
4
0
5
E
4
1
2
H
4
1
3
A
4
1
4
N
4
1
5
A
4
1
6
F
4
1
7
E
4
1
9
G
4
6
4
L
4
6
5
G
4
6
6
G
4
6
8
R
4
7
1
I
4
8
2
[1]3a74.a b4p,lyn63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3a74.d b4p,lyn,mg64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3e9h.a kaa,mg33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e9h.b kaa32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e9i.a xah33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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 Me
G
2
0
8
A
2
0
9
A
2
3
0
E
2
3
2
R
2
5
4
E
2
5
6
G
2
5
7
S
2
5
9
R
2
6
1
H
2
6
2
N
2
6
3
F
2
6
6
M
2
6
8
E
2
7
0
Y
2
7
2
E
3
6
7
E
3
7
1
R
4
0
3
E
4
0
5
E
4
1
2
H
4
1
3
A
4
1
4
N
4
1
5
A
4
1
6
F
4
1
7
E
4
1
9
G
4
6
4
L
4
6
5
G
4
6
6
G
4
6
8
R
4
7
1
I
4
8
2
[1]3a74.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3a74.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3e9h.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e9h.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e9i.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
3a74.a:b4p,lyn
3a74.d:b4p,lyn,mg
3e9h.a:kaa,mg
3e9h.b:kaa
3e9i.a:xah
[1] 3a74.a
0
0 0.2 0.1 0
[1] 3a74.d 0.2
0.2
0.1 0.1 0
[1] 3e9h.a 0.2 0.2
0
0.1 0
[1] 3e9h.b 0.3 0.3 0.1
0.1
0.2
[1] 3e9i.a 0.3 0.3 0.1 0.2
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
3a74.a
3a74.d
3e9h.a
3e9h.b
3e9i.a
[1] 3a74.a
0
.02 .01 .01 .02
[1] 3a74.d .02
0
.01 .01 .02
[1] 3e9h.a .01 .01
0
.01 .02
[1] 3e9h.b .01 .01 .01
0
.02
[1] 3e9i.a .02 .02 .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
3a74.a
3a74.d
3e9h.a
3e9h.b
3e9i.a
[1] 3a74.a
0
0.1 0.2 0.2 0.2
[1] 3a74.d 0.1
0
0.2 0.2 0.3
[1] 3e9h.a 0.2 0.2
0
0.2 0.2
[1] 3e9h.b 0.2 0.2 0.2
0
0.3
[1] 3e9i.a 0.2 0.3 0.2 0.3
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

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
3a74.a
3a74.d
3e9h.a
3e9h.b
3e9i.a
[1] 3a74.a
0
0.4 0.7 0.6 0.6
[1] 3a74.d 0.4
0
0.7 0.5 0.7
[1] 3e9h.a 0.7 0.7
0
0.5 0.7
[1] 3e9h.b 0.6 0.5 0.5
0
0.8
[1] 3e9i.a 0.6 0.7 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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