If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

SYT_PYRAB_1_145

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYT_PYRAB):R: Editing domain (11, 19, 20, 43:45, 79:83, 88, 89, 94, 98, 117:121)11, 19, 20, 43:45, 79:83, 88, 89, 94, 98, 117:121

Full PDB list

1y2q, 2hkz, 2hl0, 2hl1, 2hl2, 3pd2, 3pd3, 3pd4, 3pd5, 4rrq, 4rrr, 4s02, 4s03, 4s0i, 4s0j, 4s0k, 4s0l (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
1
9
L
2
0
I
4
3
S
4
4
V
4
5
Y
7
9
P
8
0
F
8
1
A
8
2
H
8
3
L
8
8
A
8
9
A
9
4
L
9
8
F
1
1
7
G
1
1
8
Y
1
1
9
Y
1
2
0
K
1
2
1
[1]1y2q.a none . . . . . . . . . . . . . . . . . . .
[1]2hkz.a S7 . . . . . . . . . . . . . . . . . . .
[1]2hl0.a a3s25 . . . . . . . . . . . . . . . . . . .
[1]2hl2.b ssa29 . . . . . . . . . . . . . . . . . . .
[1]3pd3.b a3t26 . . . . . . . . . . . . . . . . . . .
[1]3pd4.a a3g23 . . . . . . . . . . . . . . . . . . .
[1]3pd5.a tsb30 . . . . . . . . . . . . . . . . . . .
[1]4rrq.b a3s25 . . . . . . . . . . . . . . . . . . M
[1]4rrr.b a3t26 . . . . . . . . . . . . . . . . . . M
[1]4s02.a none . . . . . A . W . - . . . . . . . . I
[1]4s03.a none . . . . . I . W . . . . . . . . . . I
[1]4s0i.a none . . . . . S . W . . . . . . . . . . I
[1]4s0l.a none . . . . . V . W . . . . . . . . . . I

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
I
1
1
A
1
9
L
2
0
I
4
3
S
4
4
V
4
5
Y
7
9
P
8
0
F
8
1
A
8
2
H
8
3
L
8
8
A
8
9
A
9
4
L
9
8
F
1
1
7
G
1
1
8
Y
1
1
9
Y
1
2
0
K
1
2
1
[1]1y2q.a . . . . . . . . . . . . . . . . . . . .
[1]2hkz.a . . . . . . . . . . . . . . . * . . . .
[1]2hl0.a . . . . . . . . . . . . . . . . . . * .
[1]2hl2.b . . . . . . . . . . . . . . . . . . . .
[1]3pd3.b . . . . . . . . . . . . . . . . . . . .
[1]3pd4.a . . . . . . . . . . . . . . . . . . . .
[1]3pd5.a . . . . . . . . . . . . . . . . . . . .
[1]4rrq.b . . . . . . . . . . . . . . . . . . * M
[1]4rrr.b . . . . . . . . . . . . . . . . . . . M
[1]4s02.a * . . . . . A . W . - . . . . . . . . I
[1]4s03.a * . . . . . I . W . . . . . . . . . . I
[1]4s0i.a * . . . . . S . W . . . . . . . . . . I
[1]4s0l.a * . . . . . V . W . . . . . . . . . . I

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1y2q.a is apo
2hkz.a:S
2hl0.a:a3s
2hl2.b:ssa
3pd3.b:a3t
3pd4.a:a3g
3pd5.a:tsb
4rrq.b:a3s
4rrr.b:a3t
4s02.a is apo
4s03.a is apo
4s0i.a is apo
4s0l.a is apo
[1] 1y2q.a
-
0 1.3 0.7 0.8 0.7 0.7 0.8 0.8 - - - -
[1] 2hkz.a -
0
1.5 0.7 1.0 0.7 0.7 0.8 1.0 - - - -
[1] 2hl0.a - 0
0
0.6 0.5 0.1 0.4 0 0.2 - - - -
[1] 2hl2.b - 0 0.4
0
0.1 0.1 0.1 0.2 0.2 - - - -
[1] 3pd3.b - 0.1 0.1 0.1
0
0 0 0.1 0 - - - -
[1] 3pd4.a - 0 0.2 0 0
0
0 0 0 - - - -
[1] 3pd5.a - 0 0.1 0 0 0
0
0.1 0 - - - -
[1] 4rrq.b - 0 0.1 0.6 0.1 0 0.4
0
0.1 - - - -
[1] 4rrr.b - 0 0.1 0.2 0 0 0.1 0.1
0
- - - -
[1] 4s02.a - 0 0.4 0.1 0.6 0.3 0.3 0.2 0.6
-
- - -
[1] 4s03.a - 0 0.7 0.3 0.2 0.2 0.2 0.3 0.2 -
-
- -
[1] 4s0i.a - 0 0.9 0.3 0.5 0.2 0.4 0.3 0.5 - -
-
-
[1] 4s0l.a - 0 0.4 0.1 0.2 0.1 0.2 0.2 0.2 - - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1y2q.a
2hkz.a
2hl0.a
2hl2.b
3pd3.b
3pd4.a
3pd5.a
4rrq.b
4rrr.b
4s02.a
4s03.a
4s0i.a
4s0l.a
[1] 1y2q.a
0
.01 .10 .06 .07 .07 .06 .09 .07 .07 .04 .03 .05
[1] 2hkz.a .01
0
.11 .06 .08 .07 .07 .10 .08 .08 .04 .03 .05
[1] 2hl0.a .10 .11
0
.06 .04 .05 .04 .01 .04 .05 .07 .08 .06
[1] 2hl2.b .06 .06 .06
0
.03 .01 .02 .05 .03 .03 .03 .04 .01
[1] 3pd3.b .07 .08 .04 .03
0
.02 .01 .03 .01 .04 .04 .05 .03
[1] 3pd4.a .07 .07 .05 .01 .02
0
.01 .04 .02 .04 .04 .05 .02
[1] 3pd5.a .06 .07 .04 .02 .01 .01
0
.03 .01 .04 .04 .05 .02
[1] 4rrq.b .09 .10 .01 .05 .03 .04 .03
0
.03 .05 .06 .07 .05
[1] 4rrr.b .07 .08 .04 .03 .01 .02 .01 .03
0
.04 .04 .05 .03
[1] 4s02.a .07 .08 .05 .03 .04 .04 .04 .05 .04
0
.04 .05 .03
[1] 4s03.a .04 .04 .07 .03 .04 .04 .04 .06 .04 .04
0
.01 .02
[1] 4s0i.a .03 .03 .08 .04 .05 .05 .05 .07 .05 .05 .01
0
.03
[1] 4s0l.a .05 .05 .06 .01 .03 .02 .02 .05 .03 .03 .02 .03
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

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
1y2q.a
2hkz.a
2hl0.a
2hl2.b
3pd3.b
3pd4.a
3pd5.a
4rrq.b
4rrr.b
4s02.a
4s03.a
4s0i.a
4s0l.a
[1] 1y2q.a
0
0.1 0.7 0.4 0.7 0.4 0.4 0.7 0.7 0.7 0.5 0.5 0.5
[1] 2hkz.a 0.1
0
0.7 0.4 0.7 0.4 0.4 0.6 0.7 0.7 0.4 0.5 0.5
[1] 2hl0.a 0.7 0.7
0
0.7 0.3 0.5 0.7 0.2 0.3 0.7 0.7 0.7 0.9
[1] 2hl2.b 0.4 0.4 0.7
0
0.6 0.4 0.2 0.7 0.7 0.6 0.4 0.5 0.6
[1] 3pd3.b 0.7 0.7 0.3 0.6
0
0.5 0.6 0.3 0.1 0.7 0.7 0.7 0.9
[1] 3pd4.a 0.4 0.4 0.5 0.4 0.5
0
0.4 0.5 0.6 0.7 0.5 0.6 0.7
[1] 3pd5.a 0.4 0.4 0.7 0.2 0.6 0.4
0
0.6 0.7 0.6 0.4 0.5 0.5
[1] 4rrq.b 0.7 0.6 0.2 0.7 0.3 0.5 0.6
0
0.3 0.7 0.7 0.7 0.8
[1] 4rrr.b 0.7 0.7 0.3 0.7 0.1 0.6 0.7 0.3
0
0.7 0.7 0.8 0.9
[1] 4s02.a 0.7 0.7 0.7 0.6 0.7 0.7 0.6 0.7 0.7
0
0.5 0.5 0.6
[1] 4s03.a 0.5 0.4 0.7 0.4 0.7 0.5 0.4 0.7 0.7 0.5
0
0.3 0.3
[1] 4s0i.a 0.5 0.5 0.7 0.5 0.7 0.6 0.5 0.7 0.8 0.5 0.3
0
0.3
[1] 4s0l.a 0.5 0.5 0.9 0.6 0.9 0.7 0.5 0.8 0.9 0.6 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1y2q.a
2hkz.a
2hl0.a
2hl2.b
3pd3.b
3pd4.a
3pd5.a
4rrq.b
4rrr.b
4s02.a
4s03.a
4s0i.a
4s0l.a
[1] 1y2q.a
0
0.6 1.1 0.5 1.1 0.9 0.5 1.2 1.1 1.2 0.9 0.7 0.8
[1] 2hkz.a 0.6
0
1.2 0.8 1.0 0.9 0.7 1.2 1.1 1.2 1.0 0.8 0.9
[1] 2hl0.a 1.1 1.2
0
1.0 0.8 1.1 0.9 0.7 0.8 1.1 1.2 1.1 1.2
[1] 2hl2.b 0.5 0.8 1.0
0
1.0 0.9 0.4 1.1 1.0 1.1 1.0 0.8 0.9
[1] 3pd3.b 1.1 1.0 0.8 1.0
0
0.8 0.9 0.5 0.3 1.1 1.1 1.1 1.3
[1] 3pd4.a 0.9 0.9 1.1 0.9 0.8
0
0.8 1.0 0.9 1.1 1.0 1.0 1.1
[1] 3pd5.a 0.5 0.7 0.9 0.4 0.9 0.8
0
1.1 1.0 1.0 0.9 0.7 0.8
[1] 4rrq.b 1.2 1.2 0.7 1.1 0.5 1.0 1.1
0
0.5 1.0 1.2 1.1 1.3
[1] 4rrr.b 1.1 1.1 0.8 1.0 0.3 0.9 1.0 0.5
0
1.0 1.1 1.1 1.3
[1] 4s02.a 1.2 1.2 1.1 1.1 1.1 1.1 1.0 1.0 1.0
0
1.3 1.4 1.5
[1] 4s03.a 0.9 1.0 1.2 1.0 1.1 1.0 0.9 1.2 1.1 1.3
0
0.7 0.8
[1] 4s0i.a 0.7 0.8 1.1 0.8 1.1 1.0 0.7 1.1 1.1 1.4 0.7
0
0.6
[1] 4s0l.a 0.8 0.9 1.2 0.9 1.3 1.1 0.8 1.3 1.3 1.5 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...