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SYT_ECOLI_239_642

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYT_ECOLI):R: Catalytic (308, 309, 312, 313, 316, 317, 331, 332, 334, 335, 363, 365, 373:376, 379, 381, 383, 385, 426, 428, 459:462, 465, 479, 480, 482, 484, 486, 489, 511:513, 516, 517, 519, 520)
R: Contacts 3'-CCA of tRNA (313, 316, 317)
R: Contacts mRNA operator (489)
308, 309, 312, 313, 316, 317, 331, 332, 334, 335, 363, 365, 373:376, 379, 381, 383, 385, 426, 428, 459:462, 465, 479, 480, 482, 484, 486, 489, 511:513, 516, 517, 519, 520
Metals (Me):Zn

Full PDB list

1evk, 1evl, 1fyf, 1kog, 1qf6, 4hwo, 4hwp, 4hwr, 4hws, 4p3o, 4p3p (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
3
0
8
H
3
0
9
N
3
1
2
Y
3
1
3
A
3
1
6
M
3
1
7
P
3
3
1
M
3
3
2
C
3
3
4
R
3
6
3
E
3
6
5
L
3
7
3
M
3
7
4
R
3
7
5
V
3
7
6
F
3
7
9
Q
3
8
1
D
3
8
3
H
3
8
5
A
4
6
0
Y
4
6
2
K
4
6
5
Q
4
7
9
C
4
8
0
T
4
8
2
Q
4
8
4
D
4
8
6
L
4
8
9
H
5
1
1
R
5
1
2
A
5
1
3
G
5
1
6
S
5
1
7
E
5
1
9
R
5
2
0
[1]1evk.b T8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1fyf.a ssa29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1kog.a tsb30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hwo.a 40928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hwp.a x1629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hwr.b 1b226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hws.a 1b329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]1evk.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]4p3p.b 2cr35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[3]1qf6.a A,amp45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
3
0
8
H
3
0
9
N
3
1
2
Y
3
1
3
A
3
1
6
M
3
1
7
P
3
3
1
M
3
3
2
C
3
3
4
P
3
3
5
R
3
6
3
E
3
6
5
L
3
7
3
M
3
7
4
R
3
7
5
V
3
7
6
F
3
7
9
Q
3
8
1
D
3
8
3
H
3
8
5
K
4
2
6
I
4
2
8
G
4
5
9
A
4
6
0
F
4
6
1
Y
4
6
2
K
4
6
5
Q
4
7
9
C
4
8
0
T
4
8
2
Q
4
8
4
D
4
8
6
L
4
8
9
H
5
1
1
R
5
1
2
A
5
1
3
G
5
1
6
S
5
1
7
E
5
1
9
R
5
2
0
[1]1evk.b . . . * * . . * . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]1fyf.a . . . * * . . * . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]1kog.a . . . * . . . . . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]4hwo.a . . . * . . . * . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]4hwp.a . . . * . . . * . . . . . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]4hwr.b . . . * . . . * . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[1]4hws.a . . . * . . . * . . . * . . . . . . . . . . . * * * . . . . * . . . . . . . . . Zn
[2]1evk.a . . . * . . . . . . * . . . . . . * . . . . . . . . . . . . . . . . . . . . . . Zn
[2]4p3p.b . . . * . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[3]1qf6.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
1evk.b:T
1fyf.a:ssa
1kog.a:tsb
4hwo.a:409
4hwp.a:x16
4hwr.b:1b2
4hws.a:1b3
1evk.a is apo
4p3p.b:2cr
1qf6.a:A,amp
[1] 1evk.b
0.1
0.2 0.2 0.2 1.2 0.2 0.3 - 11 5.0
[1] 1fyf.a 0.1
0
0.3 0.2 1.9 0.3 0.5 - 11 5.2
[1] 1kog.a 0.3 0.2
0.1
0.6 1.9 0.7 0.9 - 12 4.5
[1] 4hwo.a 0.1 0.5 0.3
0
1.6 0.3 0.2 - 11 5.2
[1] 4hwp.a 0.1 0.4 0.3 0
0.1
0.3 0.1 - 11 5.0
[1] 4hwr.b 0.1 0.6 0.7 0.2 1.8
0.1
0.4 - 11 4.9
[1] 4hws.a 0.1 0.4 0.2 0 1.6 0.3
0.1
- 11 5.0
[2] 1evk.a 0.1 1.5 2.3 2.0 2.0 1.9 1.9
-
1.2 5.5
[2] 4p3p.b 0.1 0.5 1.1 0.6 1.2 0.5 0.7 -
0
5.3
[3] 1qf6.a 0 0 0.4 0.1 1.6 0.3 0.3 - 9.9
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
1evk.b
1fyf.a
1kog.a
4hwo.a
4hwp.a
4hwr.b
4hws.a
1evk.a
4p3p.b
1qf6.a
[1] 1evk.b
0
.08 .10 .07 .08 .07 .07 .40 .34 .30
[1] 1fyf.a .08
0
.09 .07 .11 .08 .07 .43 .33 .31
[1] 1kog.a .10 .09
0
.10 .12 .12 .10 .43 .34 .31
[1] 4hwo.a .07 .07 .10
0
.05 .06 0 .43 .35 .29
[1] 4hwp.a .08 .11 .12 .05
0
.09 .05 .42 .35 .33
[1] 4hwr.b .07 .08 .12 .06 .09
0
.06 .43 .36 .29
[1] 4hws.a .07 .07 .10 0 .05 .06
0
.43 .35 .29
[2] 1evk.a .40 .43 .43 .43 .42 .43 .43
0
.14 .40
[2] 4p3p.b .34 .33 .34 .35 .35 .36 .35 .14
0
.38
[3] 1qf6.a .30 .31 .31 .29 .33 .29 .29 .40 .38
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1evk.b
1fyf.a
1kog.a
4hwo.a
4hwp.a
4hwr.b
4hws.a
1evk.a
4p3p.b
1qf6.a
[1] 1evk.b
0
0.5 0.7 0.5 0.5 0.5 0.5 2.0 2.4 0.9
[1] 1fyf.a 0.5
0
0.5 0.2 0.2 0.3 0.2 2.0 2.4 0.8
[1] 1kog.a 0.7 0.5
0
0.5 0.5 0.5 0.5 2.1 2.6 1.0
[1] 4hwo.a 0.5 0.2 0.5
0
0.1 0.3 0.1 2.0 2.4 0.8
[1] 4hwp.a 0.5 0.2 0.5 0.1
0
0.3 0.1 2.0 2.4 0.8
[1] 4hwr.b 0.5 0.3 0.5 0.3 0.3
0
0.3 2.1 2.5 0.8
[1] 4hws.a 0.5 0.2 0.5 0.1 0.1 0.3
0
2.0 2.4 0.7
[2] 1evk.a 2.0 2.0 2.1 2.0 2.0 2.1 2.0
0
0.7 1.6
[2] 4p3p.b 2.4 2.4 2.6 2.4 2.4 2.5 2.4 0.7
0
2.0
[3] 1qf6.a 0.9 0.8 1.0 0.8 0.8 0.8 0.7 1.6 2.0
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
1evk.b
1fyf.a
1kog.a
4hwo.a
4hwp.a
4hwr.b
4hws.a
1evk.a
4p3p.b
1qf6.a
[1] 1evk.b
0
1.1 1.0 1.0 1.1 0.9 1.0 2.5 2.9 1.4
[1] 1fyf.a 1.1
0
0.9 0.6 0.7 0.7 0.6 2.5 2.8 1.3
[1] 1kog.a 1.0 0.9
0
0.8 0.9 0.9 0.9 2.7 3.1 1.3
[1] 4hwo.a 1.0 0.6 0.8
0
0.4 0.6 0.3 2.5 2.9 1.2
[1] 4hwp.a 1.1 0.7 0.9 0.4
0
0.7 0.5 2.5 2.9 1.3
[1] 4hwr.b 0.9 0.7 0.9 0.6 0.7
0
0.5 2.5 2.9 1.3
[1] 4hws.a 1.0 0.6 0.9 0.3 0.5 0.5
0
2.4 2.8 1.2
[2] 1evk.a 2.5 2.5 2.7 2.5 2.5 2.5 2.4
0
1.4 2.2
[2] 4p3p.b 2.9 2.8 3.1 2.9 2.9 2.9 2.8 1.4
0
2.7
[3] 1qf6.a 1.4 1.3 1.3 1.2 1.3 1.3 1.2 2.2 2.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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