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SYWC_YEAST_1_432

Tryptophan--tRNA ligase, cytoplasmic [Class-I aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYWC_YEAST):28, 29, 106:110, 117, 119, 120, 123, 141, 143, 146, 147, 213, 230, 253:256, 258, 259, 261:263, 284:286, 295, 29628, 29, 106:110, 117, 119, 120, 123, 141, 143, 146, 147, 213, 230, 253:256, 258, 259, 261:263, 284:286, 295, 296

Full PDB list

2ip1, 3kt0, 3kt3, 3kt6, 3kt8

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
0
6
T
1
0
7
G
1
0
8
R
1
0
9
G
1
1
0
G
1
1
9
H
1
2
0
P
1
2
3
E
1
4
1
T
1
4
3
E
1
4
6
K
1
4
7
Q
2
3
0
I
2
5
3
C
2
5
5
A
2
5
6
D
2
5
8
Q
2
5
9
Y
2
6
2
F
2
6
3
R
2
8
4
F
2
8
5
F
2
8
6
K
2
9
5
M
2
9
6
[1]2ip1.a pg413 . . . . . . . . . . . . . . . . . . . . . . . - -
[1]3kt0.a emn14 . . . . . . . . . . . . . . . . . . . . . . . - -
[1]3kt3.a tym37 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kt6.b W15 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kt8.c ltn15 . . . . . . . . . . . . . . . . . . . . . . . . .

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
8
P
2
9
Y
1
0
6
T
1
0
7
G
1
0
8
R
1
0
9
G
1
1
0
H
1
1
7
G
1
1
9
H
1
2
0
P
1
2
3
E
1
4
1
T
1
4
3
E
1
4
6
K
1
4
7
F
2
1
3
Q
2
3
0
I
2
5
3
P
2
5
4
C
2
5
5
A
2
5
6
D
2
5
8
Q
2
5
9
P
2
6
1
Y
2
6
2
F
2
6
3
R
2
8
4
F
2
8
5
F
2
8
6
K
2
9
5
M
2
9
6
[1]2ip1.a - - * . . . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]3kt0.a - - * . . . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]3kt3.a . * . . . . . . . . . . . . . . * . . . . . * . * . . . . . .
[1]3kt6.b . * . . . . . . . . . . . . . . * . . . . . * . * . . . . . .
[1]3kt8.c . * . . . . . . . . . . . . . . * . . . . . * . * . . . . . .

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
2ip1.a:pg4
3kt0.a:emn
3kt3.a:tym
3kt6.b:W
3kt8.c:ltn
[1] 2ip1.a
0
0 1.4 1.3 1.1
[1] 3kt0.a 0
0
1.2 1.0 1.0
[1] 3kt3.a 4.4 4.2
0
0 0
[1] 3kt6.b 4.7 4.1 0.5
0
0
[1] 3kt8.c 4.9 4.5 0.7 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
2ip1.a
3kt0.a
3kt3.a
3kt6.b
3kt8.c
[1] 2ip1.a
0
.01 .23 .25 .27
[1] 3kt0.a .01
0
.23 .24 .26
[1] 3kt3.a .23 .23
0
.07 .09
[1] 3kt6.b .25 .24 .07
0
.02
[1] 3kt8.c .27 .26 .09 .02
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
2ip1.a
3kt0.a
3kt3.a
3kt6.b
3kt8.c
[1] 2ip1.a
0
0.3 1.7 1.8 1.7
[1] 3kt0.a 0.3
0
1.6 1.6 1.5
[1] 3kt3.a 1.7 1.6
0
0.6 0.6
[1] 3kt6.b 1.8 1.6 0.6
0
0.2
[1] 3kt8.c 1.7 1.5 0.6 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2ip1.a
3kt0.a
3kt3.a
3kt6.b
3kt8.c
[1] 2ip1.a
0
0.7 2.2 2.2 2.1
[1] 3kt0.a 0.7
0
2.0 2.0 1.9
[1] 3kt3.a 2.2 2.0
0
0.8 0.8
[1] 3kt6.b 2.2 2.0 0.8
0
0.3
[1] 3kt8.c 2.1 1.9 0.8 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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