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SYQ_ECOLI_2_552

Glutamine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYQ_ECOLI):31:35, 37, 41, 43, 44, 46, 47, 67, 212, 216, 229:231, 234, 259, 261, 262, 269:271, 304, 305, 30831:35, 37, 41, 43, 44, 46, 47, 67, 212, 216, 229:231, 234, 259, 261, 262, 269:271, 304, 305, 308

Full PDB list

1euq, 1euy, 1exd, 1gtr, 1gts, 1nyl, 1o0b, 1o0c, 1qrs, 1qrt, 1qru, 1qtq, 1zjw, 2rd2, 2re8, 4jxx, 4jxz, 4jyz (redundant Pocketome entry); 1gsg (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
3
1
F
3
2
P
3
3
P
3
4
E
3
5
H
4
1
G
4
3
H
4
4
K
4
6
S
4
7
D
6
7
Y
2
1
2
H
2
1
6
C
2
3
0
T
2
3
1
F
2
3
4
F
2
5
9
R
2
6
1
L
2
6
2
M
2
6
9
K
2
7
1
A
3
0
5
R
3
0
8
[1]1exd.a so4A27 . . . . . . . . . . . . . . . . . . . . . . .
[1]1gts.a amp23 . . . . . . . . . . . . . . . . . . . . . . .
[1]1nyl.a none . . . . . . . . . . . . . . . . . . . . . . .
[1]1o0b.a amp,Q29 . . . . . . . . . . . . . . . . . . . . . . .
[1]1o0c.a amp,E33 . . . . . . . . . . . . . . . . . . . . . . .
[1]1qtq.a qsi32 . . . . . . . . . . . . . . . . . . . . . . .
[1]2rd2.a qsi32 . . . . . . . . . . . . . R . . . . . . . . .
[1]2re8.a gsu32 . . . . . . . . . . . . . R . . . . . . . . .
[1]4jxz.a atp31 . . . . . . . . . . . . . . . . . . . . . . .

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
R
3
1
F
3
2
P
3
3
P
3
4
E
3
5
N
3
7
H
4
1
G
4
3
H
4
4
K
4
6
S
4
7
D
6
7
Y
2
1
2
H
2
1
6
L
2
2
9
C
2
3
0
T
2
3
1
F
2
3
4
F
2
5
9
R
2
6
1
L
2
6
2
M
2
6
9
S
2
7
0
K
2
7
1
A
3
0
4
A
3
0
5
R
3
0
8
[1]1exd.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1gts.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nyl.a . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]1o0b.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1o0c.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1qtq.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2rd2.a . . . . . . . . . . . . . . . R . . . . . . . . . . .
[1]2re8.a . . . . . . . . . . . . . . . R . . . . . . . . . . .
[1]4jxz.a . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1exd.a:so4A
1gts.a:amp
1nyl.a is apo
1o0b.a:Q,amp
1o0c.a:E,amp
1qtq.a:qsi
2rd2.a:qsi
2re8.a:gsu
4jxz.a:atp
[1] 1exd.a
0.1
0.1 - 0.1 0.4 0 0.1 0 0.3
[1] 1gts.a 0.2
0
- 0.2 1.1 0.3 0.3 0.4 0
[1] 1nyl.a 0.2 0.3
-
0.7 1.8 1.2 0.9 0.8 0.3
[1] 1o0b.a 0.3 0.1 -
0
0.6 0 0 0 0
[1] 1o0c.a 0.1 0 - 0
0.1
0 0 0 0.2
[1] 1qtq.a 0.2 0.1 - 0.1 0.7
0
0 0 0.2
[1] 2rd2.a 0.3 0.1 - 0 0.6 0
0
0 0
[1] 2re8.a 0.2 0.1 - 0.1 1.0 0 0.1
0
0.1
[1] 4jxz.a 0.1 0.1 - 0 0.8 0 0.2 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
1exd.a
1gts.a
1nyl.a
1o0b.a
1o0c.a
1qtq.a
2rd2.a
2re8.a
4jxz.a
[1] 1exd.a
0
.04 .08 .02 .01 .02 .01 .02 .02
[1] 1gts.a .04
0
.07 .04 .04 .04 .04 .04 .04
[1] 1nyl.a .08 .07
0
.09 .09 .08 .09 .07 .07
[1] 1o0b.a .02 .04 .09
0
.02 .01 .01 .02 .02
[1] 1o0c.a .01 .04 .09 .02
0
.03 .02 .04 .04
[1] 1qtq.a .02 .04 .08 .01 .03
0
.01 .01 .01
[1] 2rd2.a .01 .04 .09 .01 .02 .01
0
.02 .02
[1] 2re8.a .02 .04 .07 .02 .04 .01 .02
0
.01
[1] 4jxz.a .02 .04 .07 .02 .04 .01 .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1exd.a
1gts.a
1nyl.a
1o0b.a
1o0c.a
1qtq.a
2rd2.a
2re8.a
4jxz.a
[1] 1exd.a
0
0.3 1.0 0.5 0.3 0.4 0.4 0.4 0.2
[1] 1gts.a 0.3
0
1.0 0.5 0.3 0.4 0.4 0.4 0.3
[1] 1nyl.a 1.0 1.0
0
1.1 1.0 1.0 1.0 1.0 1.0
[1] 1o0b.a 0.5 0.5 1.1
0
0.4 0.2 0.2 0.2 0.4
[1] 1o0c.a 0.3 0.3 1.0 0.4
0
0.3 0.3 0.3 0.3
[1] 1qtq.a 0.4 0.4 1.0 0.2 0.3
0
0.2 0.2 0.3
[1] 2rd2.a 0.4 0.4 1.0 0.2 0.3 0.2
0
0.1 0.3
[1] 2re8.a 0.4 0.4 1.0 0.2 0.3 0.2 0.1
0
0.3
[1] 4jxz.a 0.2 0.3 1.0 0.4 0.3 0.3 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1exd.a
1gts.a
1nyl.a
1o0b.a
1o0c.a
1qtq.a
2rd2.a
2re8.a
4jxz.a
[1] 1exd.a
0
0.8 1.3 0.5 0.4 0.4 0.5 0.5 0.5
[1] 1gts.a 0.8
0
1.3 0.8 0.7 0.7 0.7 0.7 0.7
[1] 1nyl.a 1.3 1.3
0
1.4 1.3 1.3 1.3 1.3 1.3
[1] 1o0b.a 0.5 0.8 1.4
0
0.4 0.3 0.3 0.3 0.5
[1] 1o0c.a 0.4 0.7 1.3 0.4
0
0.3 0.3 0.4 0.5
[1] 1qtq.a 0.4 0.7 1.3 0.3 0.3
0
0.2 0.3 0.4
[1] 2rd2.a 0.5 0.7 1.3 0.3 0.3 0.2
0
0.2 0.5
[1] 2re8.a 0.5 0.7 1.3 0.3 0.4 0.3 0.2
0
0.5
[1] 4jxz.a 0.5 0.7 1.3 0.5 0.5 0.4 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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