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SYWC_HUMAN_91_471

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

Composition of the binding site

Protein chains monomer
A1 (SYWC_HUMAN):87, 130, 159:163, 165, 166, 168:178, 194, 196, 199, 200, 284, 307, 309, 310, 312, 313, 317, 338:343, 349:353, 385, 387, 402, 406, 408, 441, 442, 445, 44887, 130, 159:163, 165, 166, 168:178, 194, 196, 199, 200, 284, 307, 309, 310, 312, 313, 317, 338:343, 349:353, 385, 387, 402, 406, 408, 441, 442, 445, 448

Full PDB list

1o5t, 1r6t, 1r6u, 1ulh, 2ake, 2azx, 2dr2, 2quh, 2qui, 2quj, 2quk, 5uji, 5ujj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
5
9
T
1
6
0
G
1
6
1
R
1
6
2
G
1
6
3
S
1
6
5
A
1
6
8
H
1
7
0
V
1
7
1
G
1
7
2
H
1
7
3
L
1
7
4
I
1
7
5
P
1
7
6
I
1
7
8
Q
1
9
4
T
1
9
6
E
1
9
9
K
2
0
0
Q
2
8
4
I
3
0
7
C
3
0
9
A
3
1
0
D
3
1
2
Q
3
1
3
F
3
1
7
T
3
3
8
F
3
3
9
F
3
4
0
K
3
4
9
M
3
5
0
S
3
5
1
A
3
5
2
S
3
5
3
F
4
0
6
E
4
0
8
L
4
4
1
I
4
4
2
H
4
4
5
R
4
4
8
[1]1r6t.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . .
[1]1r6u.a tym37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1ulh.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2azx.a WW30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2azx.b W15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2dr2.a W15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2quh.b WW30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qui.a atp,ltn46 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qui.b ltn15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2quj.a tym37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5uji.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . .
[1]5ujj.a mg,tym38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
P
8
7
H
1
3
0
Y
1
5
9
T
1
6
0
G
1
6
1
R
1
6
2
G
1
6
3
S
1
6
5
S
1
6
6
A
1
6
8
M
1
6
9
H
1
7
0
V
1
7
1
G
1
7
2
H
1
7
3
L
1
7
4
I
1
7
5
P
1
7
6
F
1
7
7
I
1
7
8
Q
1
9
4
T
1
9
6
E
1
9
9
K
2
0
0
Q
2
8
4
I
3
0
7
C
3
0
9
A
3
1
0
D
3
1
2
Q
3
1
3
F
3
1
7
T
3
3
8
F
3
3
9
F
3
4
0
P
3
4
1
A
3
4
2
L
3
4
3
K
3
4
9
M
3
5
0
S
3
5
1
A
3
5
2
S
3
5
3
E
3
8
5
H
3
8
7
Y
4
0
2
F
4
0
6
E
4
0
8
L
4
4
1
I
4
4
2
H
4
4
5
R
4
4
8
[1]1r6t.b - . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . * . . .
[1]1r6u.a . . . . . . . . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . * . . .
[1]1ulh.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . * . . .
[1]2azx.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]2azx.b . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . * . . .
[1]2dr2.a - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2quh.b - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]2qui.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]2qui.b - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . * . . .
[1]2quj.a - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . .
[1]5uji.a - R . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . * . . - - - - - . . . . . * . . .
[1]5ujj.a . R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .

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
1r6t.b is apo
1r6u.a:tym
1ulh.b is apo
2azx.a:WW
2azx.b:W
2dr2.a:W
2quh.b:WW
2qui.a:atp,ltn
2qui.b:ltn
2quj.a:tym
5uji.a is apo
5ujj.a:mg,tym
[1] 1r6t.b
-
0.3 - 1.5 0.1 0.2 0.3 1.0 0.3 0.2 - 0.2
[1] 1r6u.a -
0.1
- 1.7 0 0 0.1 1.4 0 0 - 0.1
[1] 1ulh.b - 0.1
-
1.7 0 0 0.1 1.1 0 0.1 - 0.1
[1] 2azx.a - 0.8 -
0
0 0 0.1 0.5 0.1 0.3 - 0.4
[1] 2azx.b - 0.5 - 1.8
0
0 0.1 1.1 0 0.2 - 0.2
[1] 2dr2.a - 0.7 - 0.6 0
0
0 0.8 0 0.3 - 0.7
[1] 2quh.b - 0.8 - 1.8 0 0
0
1.2 0 0.3 - 0.6
[1] 2qui.a - 0.8 - 1.6 0 0 0
0.4
0 0.3 - 0.4
[1] 2qui.b - 0.9 - 1.6 0 0 0 1.5
0
0.2 - 0.7
[1] 2quj.a - 0.4 - 1.2 0 0 0 1.4 0
0
- 0.4
[1] 5uji.a - 2.2 - 3.3 0.7 0.7 0.8 1.9 0.7 1.6
-
2.4
[1] 5ujj.a - 0.2 - 2.1 0 0 0.1 1.4 0 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
1r6t.b
1r6u.a
1ulh.b
2azx.a
2azx.b
2dr2.a
2quh.b
2qui.a
2qui.b
2quj.a
5uji.a
5ujj.a
[1] 1r6t.b
0
.04 .05 .06 .05 .05 .06 .04 .06 .05 .10 .04
[1] 1r6u.a .04
0
.04 .07 .05 .07 .06 .05 .05 .06 .11 .04
[1] 1ulh.b .05 .04
0
.06 .04 .07 .05 .04 .05 .05 .11 .04
[1] 2azx.a .06 .07 .06
0
.05 .04 .06 .04 .07 .06 .14 .08
[1] 2azx.b .05 .05 .04 .05
0
.06 .02 .03 .05 .04 .11 .05
[1] 2dr2.a .05 .07 .07 .04 .06
0
.05 .04 .05 .05 .13 .07
[1] 2quh.b .06 .06 .05 .06 .02 .05
0
.02 .04 .03 .12 .05
[1] 2qui.a .04 .05 .04 .04 .03 .04 .02
0
.03 .04 .11 .04
[1] 2qui.b .06 .05 .05 .07 .05 .05 .04 .03
0
.04 .12 .04
[1] 2quj.a .05 .06 .05 .06 .04 .05 .03 .04 .04
0
.13 .05
[1] 5uji.a .10 .11 .11 .14 .11 .13 .12 .11 .12 .13
0
.11
[1] 5ujj.a .04 .04 .04 .08 .05 .07 .05 .04 .04 .05 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1r6t.b
1r6u.a
1ulh.b
2azx.a
2azx.b
2dr2.a
2quh.b
2qui.a
2qui.b
2quj.a
5uji.a
5ujj.a
[1] 1r6t.b
0
1.0 1.3 1.2 1.3 1.4 1.4 1.4 1.3 1.3 8.0 1.4
[1] 1r6u.a 1.0
0
0.9 0.7 0.9 1.5 0.9 0.9 1.4 0.9 8.1 0.9
[1] 1ulh.b 1.3 0.9
0
0.9 1.1 1.2 0.5 0.7 1.0 0.5 5.1 0.5
[1] 2azx.a 1.2 0.7 0.9
0
0.7 1.3 0.8 0.9 1.1 0.8 8.0 0.8
[1] 2azx.b 1.3 0.9 1.1 0.7
0
1.4 0.9 1.0 1.3 1.0 8.1 1.1
[1] 2dr2.a 1.4 1.5 1.2 1.3 1.4
0
1.1 1.3 0.5 0.9 7.8 1.3
[1] 2quh.b 1.4 0.9 0.5 0.8 0.9 1.1
0
0.3 1.0 0.5 8.0 0.6
[1] 2qui.a 1.4 0.9 0.7 0.9 1.0 1.3 0.3
0
1.1 0.7 8.1 0.7
[1] 2qui.b 1.3 1.4 1.0 1.1 1.3 0.5 1.0 1.1
0
0.8 8.0 1.2
[1] 2quj.a 1.3 0.9 0.5 0.8 1.0 0.9 0.5 0.7 0.8
0
8.0 0.7
[1] 5uji.a 8.0 8.1 5.1 8.0 8.1 7.8 8.0 8.1 8.0 8.0
0
8.0
[1] 5ujj.a 1.4 0.9 0.5 0.8 1.1 1.3 0.6 0.7 1.2 0.7 8.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1r6t.b
1r6u.a
1ulh.b
2azx.a
2azx.b
2dr2.a
2quh.b
2qui.a
2qui.b
2quj.a
5uji.a
5ujj.a
[1] 1r6t.b
0
1.3 1.6 1.4 1.6 1.6 1.7 1.6 1.6 1.6 8.7 1.6
[1] 1r6u.a 1.3
0
1.2 1.0 1.3 1.8 1.3 1.3 1.5 1.2 8.8 1.1
[1] 1ulh.b 1.6 1.2
0
1.2 1.3 1.5 1.1 1.1 1.2 1.0 5.5 0.9
[1] 2azx.a 1.4 1.0 1.2
0
1.0 1.6 1.2 1.2 1.4 1.1 8.8 1.1
[1] 2azx.b 1.6 1.3 1.3 1.0
0
1.7 1.3 1.3 1.5 1.2 9.0 1.4
[1] 2dr2.a 1.6 1.8 1.5 1.6 1.7
0
1.6 1.6 0.8 1.4 8.6 1.7
[1] 2quh.b 1.7 1.3 1.1 1.2 1.3 1.6
0
0.6 1.3 0.7 8.8 1.2
[1] 2qui.a 1.6 1.3 1.1 1.2 1.3 1.6 0.6
0
1.3 0.8 8.9 1.2
[1] 2qui.b 1.6 1.5 1.2 1.4 1.5 0.8 1.3 1.3
0
0.9 8.7 1.4
[1] 2quj.a 1.6 1.2 1.0 1.1 1.2 1.4 0.7 0.8 0.9
0
7.9 1.1
[1] 5uji.a 8.7 8.8 5.5 8.8 9.0 8.6 8.8 8.9 8.7 7.9
0
8.7
[1] 5ujj.a 1.6 1.1 0.9 1.1 1.4 1.7 1.2 1.2 1.4 1.1 8.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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