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AROQ_STRCO_2_157

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

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (AROQ_STRCO):R: Substrate binding (108, 109)
16:18, 20:25, 29, 80, 82, 83, 86, 107, 111, 114, 118
16:18, 20:25, 29, 80, 82, 83, 86, 107:109, 111, 114, 118
A2 (AROQ_STRCO):93, 9793, 97

Full PDB list

1d0i, 1gtz, 1gu0, 1gu1, 1v1j, 2bt4, 2cjf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
P
1
6
N
1
7
L
1
8
L
2
0
L
2
1
G
2
2
R
2
4
Y
2
9
N
8
0
A
8
2
A
8
3
H
8
6
H
1
0
7
I
1
0
8
S
1
0
9
I
1
1
1
R
1
1
8
D
9
3
T
9
7
[1]1d0i.c none . . . . . . . . . . . . . . . . . . .
[1]1gtz.a dhk12 . . . . . . A . . . . . . . . . . . .
[1]1gu1.a fa112 . . . . . . . . . . . . . . . . . . .
[1]1v1j.a fa313 . . . . . . . . . . . . . . . . . . .
[1]2bt4.a ca222 . . . . . . . . . . . . . . . . . . .
[1]2cjf.b rp425 . . . . . . . . . . . . . . . . . . .

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 A2
P
1
6
N
1
7
L
1
8
L
2
0
L
2
1
G
2
2
Q
2
3
R
2
4
Q
2
5
Y
2
9
N
8
0
A
8
2
A
8
3
H
8
6
H
1
0
7
I
1
0
8
S
1
0
9
I
1
1
1
R
1
1
4
R
1
1
8
D
9
3
T
9
7
[1]1d0i.c . . . . . . . . . . . . . . . . . . . . . .
[1]1gtz.a . . . . . . . A . . . . . . . . . . . . . .
[1]1gu1.a . . . . . . . . . . . . . . . . . . . . . .
[1]1v1j.a . . . . . . . * . . . . . . . . . . . . . .
[1]2bt4.a . . . . . . . . . . . . . . . . . . . . . .
[1]2cjf.b . . . . . . . . . . . . . . . . . . . . . .

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
1d0i.c is apo
1gtz.a:dhk
1gu1.a:fa1
1v1j.a:fa3
2bt4.a:ca2
2cjf.b:rp4
[1] 1d0i.c
-
0.4 0.1 0 0.6 0.2
[1] 1gtz.a -
0.1
0 0 0.6 0.8
[1] 1gu1.a - 0.1
0
0 0.3 0.2
[1] 1v1j.a - 0.1 0
0
2.7 3.7
[1] 2bt4.a - 0.2 0.1 0.2
0.1
0.1
[1] 2cjf.b - 0.1 0 0.1 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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1d0i.c
1gtz.a
1gu1.a
1v1j.a
2bt4.a
2cjf.b
[1] 1d0i.c
0
.04 .01 .17 .03 .03
[1] 1gtz.a .04
0
.03 .14 .05 .03
[1] 1gu1.a .01 .03
0
.15 .03 .01
[1] 1v1j.a .17 .14 .15
0
.18 .17
[1] 2bt4.a .03 .05 .03 .18
0
.02
[1] 2cjf.b .03 .03 .01 .17 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1d0i.c
1gtz.a
1gu1.a
1v1j.a
2bt4.a
2cjf.b
[1] 1d0i.c
0
0.6 0.4 0.3 0.4 0.4
[1] 1gtz.a 0.6
0
0.6 0.4 0.7 0.7
[1] 1gu1.a 0.4 0.6
0
0.3 0.3 0.3
[1] 1v1j.a 0.3 0.4 0.3
0
0.4 0.4
[1] 2bt4.a 0.4 0.7 0.3 0.4
0
0.3
[1] 2cjf.b 0.4 0.7 0.3 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1d0i.c
1gtz.a
1gu1.a
1v1j.a
2bt4.a
2cjf.b
[1] 1d0i.c
0
0.8 0.8 0.6 0.7 0.8
[1] 1gtz.a 0.8
0
0.8 0.5 0.8 0.9
[1] 1gu1.a 0.8 0.8
0
1.1 0.6 0.6
[1] 1v1j.a 0.6 0.5 1.1
0
1.3 1.4
[1] 2bt4.a 0.7 0.8 0.6 1.3
0
0.4
[1] 2cjf.b 0.8 0.9 0.6 1.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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