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SYI_THET8_384_821

Isoleucine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYI_THET8):45, 46, 54, 56, 57, 59, 85, 521, 550, 551, 553, 554, 558, 581:584, 59245, 46, 54, 56, 57, 59, 85, 521, 550, 551, 553, 554, 558, 581:584, 592
Metals (Me):Zn

Full PDB list

1ile, 1jzq, 1jzs

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
4
5
P
4
6
H
5
4
G
5
6
H
5
7
Q
5
9
S
5
2
1
E
5
5
0
G
5
5
1
D
5
5
3
Q
5
5
4
W
5
5
8
H
5
8
1
G
5
8
2
L
5
8
3
I
5
8
4
M
5
9
2
[1]1ile.a none . . . . . . . . . . . . . . . . . Zn
[1]1jzq.a ila31 . . . . . . . . . . . . . . . . . Zn
[1]1jzs.a mrc35 . . . . . . . . . . . . . . . . . Zn

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
4
5
P
4
6
H
5
4
G
5
6
H
5
7
Q
5
9
D
8
5
S
5
2
1
E
5
5
0
G
5
5
1
D
5
5
3
Q
5
5
4
W
5
5
8
H
5
8
1
G
5
8
2
L
5
8
3
I
5
8
4
M
5
9
2
[1]1ile.a . . . . . . . . . . . . . . . . . . Zn
[1]1jzq.a . . . . . . . . . . . . . . . . . . Zn
[1]1jzs.a . . . . . . . . . . . . . . . . . . Zn

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
1ile.a is apo
1jzq.a:ila
1jzs.a:mrc
[1] 1ile.a
-
0.2 0.1
[1] 1jzq.a -
0
0
[1] 1jzs.a - 0.3
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
1ile.a
1jzq.a
1jzs.a
[1] 1ile.a
0
.01 .02
[1] 1jzq.a .01
0
.02
[1] 1jzs.a .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

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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
1ile.a
1jzq.a
1jzs.a
[1] 1ile.a
0
0.4 0.5
[1] 1jzq.a 0.4
0
0.4
[1] 1jzs.a 0.5 0.4
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

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
1ile.a
1jzq.a
1jzs.a
[1] 1ile.a
0
0.7 0.8
[1] 1jzq.a 0.7
0
0.6
[1] 1jzs.a 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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