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SYY_ECOLI_3_322

Tyrosine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYY_ECOLI):37:41, 48, 50, 51, 53, 54, 71, 76, 81, 126, 175, 179, 182, 195, 197:201, 225:22837:41, 48, 50, 51, 53, 54, 71, 76, 81, 126, 175, 179, 182, 195, 197:201, 225:228

Full PDB list

1vbm, 1vbn, 1wq3, 1wq4, 1x8x, 2yxn, 4oud (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
3
7
C
3
8
G
3
9
F
4
0
D
4
1
G
5
0
H
5
1
V
5
3
P
5
4
L
7
1
T
7
6
D
8
1
N
1
2
6
Y
1
7
5
Q
1
7
9
D
1
8
2
Q
1
9
5
G
1
9
7
G
1
9
8
D
2
0
0
Q
2
0
1
V
2
2
5
P
2
2
6
L
2
2
7
I
2
2
8
[1]1vbm.a ysa35 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1vbn.b ysa35 V . . . . . . . . . . . . . . . C . . . . . . . .
[1]1wq3.a iyr14 V . . . . . . . . . . . . . . . C . . . . . . . .
[1]1wq4.a Y13 V . . . . . . . . . . . . . . . C . . . . . . . .
[1]2yxn.a azy16 V . . . . . . . . . . . . . . . C . . . . . . . .
[1]4oud.a Y13 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oud.b none . . . . . . . . . . . . . . . . . . . . . . . . .

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
Y
3
7
C
3
8
G
3
9
F
4
0
D
4
1
H
4
8
G
5
0
H
5
1
V
5
3
P
5
4
L
7
1
T
7
6
D
8
1
N
1
2
6
Y
1
7
5
Q
1
7
9
D
1
8
2
Q
1
9
5
G
1
9
7
G
1
9
8
S
1
9
9
D
2
0
0
Q
2
0
1
V
2
2
5
P
2
2
6
L
2
2
7
I
2
2
8
[1]1vbm.a * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1vbn.b V . . . . . . . . . . . . . . . . C . . . . . . . . .
[1]1wq3.a V . . . . . . . . . . . . . . . . C . . . . . . . . .
[1]1wq4.a V . . . . . . . . . . . . . . . . C . . . . . . . . .
[1]2yxn.a V . . . . . . . . . . . . . . . . C . . . . . . . . .
[1]4oud.a * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oud.b * . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1vbm.a:ysa
1vbn.b:ysa
1wq3.a:iyr
1wq4.a:Y
2yxn.a:azy
4oud.a:Y
4oud.b is apo
[1] 1vbm.a
0
0.1 1.0 0.2 1.6 0.1 -
[1] 1vbn.b 0.1
0.1
0.2 0.1 0.2 0 -
[1] 1wq3.a 0.7 1.1
0
0 0 0 -
[1] 1wq4.a 0.9 0.9 0.1
0.1
0 0.1 -
[1] 2yxn.a 1.3 1.2 0.1 0.1
0
0.1 -
[1] 4oud.a 1.3 1.0 1.2 0.2 1.5
0.2
-
[1] 4oud.b 2.0 1.2 1.5 0 1.5 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
1vbm.a
1vbn.b
1wq3.a
1wq4.a
2yxn.a
4oud.a
4oud.b
[1] 1vbm.a
0
.07 .10 .10 .11 .06 .10
[1] 1vbn.b .07
0
.05 .05 .06 .12 .15
[1] 1wq3.a .10 .05
0
.01 .01 .13 .17
[1] 1wq4.a .10 .05 .01
0
.01 .11 .16
[1] 2yxn.a .11 .06 .01 .01
0
.13 .17
[1] 4oud.a .06 .12 .13 .11 .13
0
.06
[1] 4oud.b .10 .15 .17 .16 .17 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1vbm.a
1vbn.b
1wq3.a
1wq4.a
2yxn.a
4oud.a
4oud.b
[1] 1vbm.a
0
0.3 0.7 0.6 0.7 0.6 2.5
[1] 1vbn.b 0.3
0
0.7 0.6 0.7 0.7 2.4
[1] 1wq3.a 0.7 0.7
0
0.2 0.1 0.9 2.5
[1] 1wq4.a 0.6 0.6 0.2
0
0.3 0.8 2.5
[1] 2yxn.a 0.7 0.7 0.1 0.3
0
1.0 2.6
[1] 4oud.a 0.6 0.7 0.9 0.8 1.0
0
2.3
[1] 4oud.b 2.5 2.4 2.5 2.5 2.6 2.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1vbm.a
1vbn.b
1wq3.a
1wq4.a
2yxn.a
4oud.a
4oud.b
[1] 1vbm.a
0
0.5 1.0 0.8 1.1 1.0 2.8
[1] 1vbn.b 0.5
0
0.9 0.6 0.9 1.0 2.9
[1] 1wq3.a 1.0 0.9
0
0.6 0.2 1.2 3.0
[1] 1wq4.a 0.8 0.6 0.6
0
0.6 1.1 2.9
[1] 2yxn.a 1.1 0.9 0.2 0.6
0
1.3 3.0
[1] 4oud.a 1.0 1.0 1.2 1.1 1.3
0
2.7
[1] 4oud.b 2.8 2.9 3.0 2.9 3.0 2.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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