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AROQ_HELPY_1_167

3-dehydroquinate dehydratase [Type-II 3-dehydroquinase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (AROQ_HELPY):R: Substrate binding (103, 104)
9:11, 13:19, 22, 76, 78, 79, 82, 102, 106, 109, 113
9:11, 13:19, 22, 76, 78, 79, 82, 102:104, 106, 109, 113
A2 (AROQ_HELPY):89, 92, 9389, 92, 93

Full PDB list

1j2y, 2c4v, 2c4w, 2c57, 2wks, 2xb9, 2xd9, 2xda, 4b6r, 4b6s

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
N
1
0
L
1
1
M
1
3
L
1
4
R
1
7
D
1
8
P
1
9
Y
2
2
N
7
6
G
7
8
A
7
9
H
8
2
H
1
0
2
L
1
0
3
T
1
0
4
I
1
0
6
R
1
1
3
D
8
9
M
9
2
L
9
3
[1]2c4w.a gaj24 . . . . . . . . . . . . . . . . . - - -
[1]2c57.b fa112 . . . . . - - - . . . . . . . . . . . .
[1]2wks.a cb624 . . . . . . . . . . . . . . . . . . . .
[1]2xb9.a xnw22 . . . . . . . . . . . . . . . . . . . .
[1]2xd9.a xd918 . . . . . . . . . . . . . . . . . . . .
[1]2xda.a jps20 . . . . . . . . . . . . . . . . . - - -
[1]4b6r.a 9zt22 . . . . . . . . . . . . . . . . . . . .
[1]4b6s.b 2hn25 . . . . . . . . . . . . . . . . . . . .
[2]1j2y.a dqa13 . . . . . . . . . . . . . . . . . - - -
[2]2c4v.a none . . . . . . . . . . . . . . . . . - - -

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 A2
P
9
N
1
0
L
1
1
M
1
3
L
1
4
G
1
5
H
1
6
R
1
7
D
1
8
P
1
9
Y
2
2
N
7
6
G
7
8
A
7
9
H
8
2
H
1
0
2
L
1
0
3
T
1
0
4
I
1
0
6
R
1
0
9
R
1
1
3
D
8
9
M
9
2
L
9
3
[1]2c4w.a . . . . . . . . . . . . . . . . . . . . . - - -
[1]2c57.b . . . . . . . * - - - . . . . . . . . . . . . .
[1]2wks.a . . . . . . . . . . * . . . . . . . . . . . . .
[1]2xb9.a . . . . . . . . . . * . . . . . . . . . . . . .
[1]2xd9.a . . . . . . . . . . * . . . . . . . . . . . . *
[1]2xda.a . . . . . . . . . . * . . . . . . . . . . - - -
[1]4b6r.a . . . . . . . . . . * . . . . . . . . . . . . .
[1]4b6s.b . . . . . . . . . . * . . . . . . . . . . . . .
[2]1j2y.a . . . . . . . * . . * . . . . . . . . . . - - -
[2]2c4v.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
2c4w.a:gaj
2c57.b:fa1
2wks.a:cb6
2xb9.a:xnw
2xd9.a:xd9
2xda.a:jps
4b6r.a:9zt
4b6s.b:2hn
1j2y.a:dqa
2c4v.a is apo
[1] 2c4w.a
0
0.4 0.4 0.1 0.1 0.1 0.1 0.1 0.3 -
[1] 2c57.b 1.4
0
1.0 1.1 0.3 0.6 0.7 0.2 0.3 -
[1] 2wks.a 3.0 0.2
0
1.0 0.5 0.5 1.5 0.8 0.4 -
[1] 2xb9.a 2.3 0.2 0.2
0.3
0.2 0.1 0.4 0.2 0.3 -
[1] 2xd9.a 2.9 0.1 1.9 1.0
0
0.2 0.9 0.8 0.4 -
[1] 2xda.a 2.5 0.1 0.1 0.5 0
0
0.5 0.2 0.4 -
[1] 4b6r.a 1.9 0.1 0.3 0.4 0.1 0.1
0.1
0 0.4 -
[1] 4b6s.b 1.9 0.1 0.2 0.4 0.2 0.1 0.1
0
0.4 -
[2] 1j2y.a 6.4 0.4 4.7 4.8 2.2 3.2 5.3 4.0
0.2
-
[2] 2c4v.a 7.0 0.3 5.0 5.3 2.4 3.6 5.2 3.7 0.6
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
2c4w.a
2c57.b
2wks.a
2xb9.a
2xd9.a
2xda.a
4b6r.a
4b6s.b
1j2y.a
2c4v.a
[1] 2c4w.a
0
.09 .16 .12 .21 .12 .12 .11 .34 .37
[1] 2c57.b .09
0
.20 .15 .22 .16 .16 .14 .29 .32
[1] 2wks.a .16 .20
0
.06 .11 .06 .08 .07 .20 .24
[1] 2xb9.a .12 .15 .06
0
.11 .03 .04 .02 .23 .27
[1] 2xd9.a .21 .22 .11 .11
0
.09 .13 .12 .29 .32
[1] 2xda.a .12 .16 .06 .03 .09
0
.05 .05 .23 .26
[1] 4b6r.a .12 .16 .08 .04 .13 .05
0
.02 .26 .30
[1] 4b6s.b .11 .14 .07 .02 .12 .05 .02
0
.26 .29
[2] 1j2y.a .34 .29 .20 .23 .29 .23 .26 .26
0
.04
[2] 2c4v.a .37 .32 .24 .27 .32 .26 .30 .29 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
2c4w.a
2c57.b
2wks.a
2xb9.a
2xd9.a
2xda.a
4b6r.a
4b6s.b
1j2y.a
2c4v.a
[1] 2c4w.a
0
1.0 2.1 1.8 1.8 1.8 1.8 1.7 2.1 2.1
[1] 2c57.b 1.0
0
1.4 0.9 0.9 0.9 0.8 0.9 0.6 0.6
[1] 2wks.a 2.1 1.4
0
1.5 1.4 1.6 1.5 1.4 2.2 2.2
[1] 2xb9.a 1.8 0.9 1.5
0
0.7 0.5 0.6 0.6 1.1 1.1
[1] 2xd9.a 1.8 0.9 1.4 0.7
0
0.2 0.7 0.6 1.2 1.2
[1] 2xda.a 1.8 0.9 1.6 0.5 0.2
0
0.6 0.5 1.1 1.1
[1] 4b6r.a 1.8 0.8 1.5 0.6 0.7 0.6
0
0.6 1.0 1.0
[1] 4b6s.b 1.7 0.9 1.4 0.6 0.6 0.5 0.6
0
1.2 1.2
[2] 1j2y.a 2.1 0.6 2.2 1.1 1.2 1.1 1.0 1.2
0
0.4
[2] 2c4v.a 2.1 0.6 2.2 1.1 1.2 1.1 1.0 1.2 0.4
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
2c4w.a
2c57.b
2wks.a
2xb9.a
2xd9.a
2xda.a
4b6r.a
4b6s.b
1j2y.a
2c4v.a
[1] 2c4w.a
0
1.0 2.7 2.2 2.3 2.3 2.3 2.5 3.1 3.1
[1] 2c57.b 1.0
0
1.2 0.9 0.9 0.9 0.8 1.0 0.6 0.6
[1] 2wks.a 2.7 1.2
0
2.0 1.9 2.1 2.0 2.1 3.4 3.4
[1] 2xb9.a 2.2 0.9 2.0
0
1.0 0.8 0.8 1.3 2.2 2.2
[1] 2xd9.a 2.3 0.9 1.9 1.0
0
0.5 1.0 1.5 2.3 2.4
[1] 2xda.a 2.3 0.9 2.1 0.8 0.5
0
0.9 1.4 2.3 2.3
[1] 4b6r.a 2.3 0.8 2.0 0.8 1.0 0.9
0
1.2 2.4 2.4
[1] 4b6s.b 2.5 1.0 2.1 1.3 1.5 1.4 1.2
0
2.7 2.7
[2] 1j2y.a 3.1 0.6 3.4 2.2 2.3 2.3 2.4 2.7
0
0.6
[2] 2c4v.a 3.1 0.6 3.4 2.2 2.4 2.3 2.4 2.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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