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AROD_SALTY_1_252

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROD_SALTY):R: 3-dehydroquinate binding (46, 48)
21, 80, 82, 143, 145, 170, 172, 203, 205, 213, 225, 231:234, 236
21, 46, 48, 80, 82, 143, 145, 170, 172, 203, 205, 213, 225, 231:234, 236

Full PDB list

3l2i, 3lb0, 3m7w, 3nnt, 3o1n, 3oex, 3s42, 4gfs, 4guf, 4gug, 4guh, 4gui, 4guj, 4iuo (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
2
1
E
4
6
R
4
8
R
8
2
H
1
4
3
K
1
7
0
A
1
7
2
M
2
0
3
M
2
0
5
R
2
1
3
F
2
2
5
S
2
3
2
A
2
3
3
Q
2
3
6
[1]3lb0.a none . . . . . . . . . . . . . .
[1]3m7w.b dqa12 . . . . . * . . . . . . . .
[1]3nnt.a dqa13 . . . . . M . . . . . . . .
[1]3o1n.a none . . . . . . . . . . . . . A
[1]3s42.a mla7 . . . . . . . . . . . . . .
[1]4gfs.b ni1 . . . . . . . . . . . - . .
[1]4guh.a 3ds11 . . . . . * . . . . . . . .
[1]4gui.a qic13 . . . . . . . . . . . . . .
[1]4guj.a skm12 . . . . . . . . . . . . . .
[1]4iuo.a qic13 . . . . . M . . . . . . . .

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
S
2
1
E
4
6
R
4
8
T
8
0
R
8
2
H
1
4
3
F
1
4
5
K
1
7
0
A
1
7
2
M
2
0
3
M
2
0
5
R
2
1
3
F
2
2
5
A
2
3
1
S
2
3
2
A
2
3
3
P
2
3
4
Q
2
3
6
[1]3lb0.a . . . . . . . . . . . . . . . . . .
[1]3m7w.b . . . . . . . * . . . . . . . . . .
[1]3nnt.a . . . . . . . M . . . . . . . . . .
[1]3o1n.a . . . . . . . * . * . . . . . . . A
[1]3s42.a . . . . . . . * . . . . . . . . . .
[1]4gfs.b . . . . . * . * . . . . . - - . . .
[1]4guh.a . . . . . . . * . . . . . . . . . .
[1]4gui.a . . . . . . . . . . . . . . . . . .
[1]4guj.a . . . . . . . . . . . . . . . . . .
[1]4iuo.a . . . . . . . M . . . . . . . . . .

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
3lb0.a is apo
3m7w.b:dqa
3nnt.a:dqa
3o1n.a is apo
3s42.a:mla
4gfs.b:ni
4guh.a:3ds
4gui.a:qic
4guj.a:skm
4iuo.a:qic
[1] 3lb0.a
-
0.4 0.4 - 0.2 0 0.4 0.4 0.2 0.4
[1] 3m7w.b -
0.6
0.9 - 0.4 0.1 0.6 0.8 0.7 0.8
[1] 3nnt.a - 0.1
0
- 0.1 0 0.2 0.2 0 0.1
[1] 3o1n.a - 1.1 1.4
-
0.5 0.1 1.1 0.8 0.8 1.0
[1] 3s42.a - 0.5 1.0 -
0
0.1 0.5 0.5 0.4 0.5
[1] 4gfs.b - 1.2 1.6 - 1.0
0.2
1.2 1.7 1.5 1.9
[1] 4guh.a - 0.6 0.9 - 0.2 0.1
0.6
0.7 0.4 0.7
[1] 4gui.a - 0 0 - 0.2 0 0.1
0
0 0
[1] 4guj.a - 0 0.3 - 0.2 0 0 0
0
0
[1] 4iuo.a - 0 0 - 0.2 0 0 0 0
0.1
[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
3lb0.a
3m7w.b
3nnt.a
3o1n.a
3s42.a
4gfs.b
4guh.a
4gui.a
4guj.a
4iuo.a
[1] 3lb0.a
0
.05 .04 .09 .06 .11 .03 .03 .03 .03
[1] 3m7w.b .05
0
.08 .07 .05 .07 .02 .07 .06 .06
[1] 3nnt.a .04 .08
0
.11 .08 .12 .06 .03 .03 .02
[1] 3o1n.a .09 .07 .11
0
.03 .09 .06 .12 .10 .11
[1] 3s42.a .06 .05 .08 .03
0
.08 .04 .08 .08 .07
[1] 4gfs.b .11 .07 .12 .09 .08
0
.09 .14 .13 .13
[1] 4guh.a .03 .02 .06 .06 .04 .09
0
.06 .04 .05
[1] 4gui.a .03 .07 .03 .12 .08 .14 .06
0
.02 .01
[1] 4guj.a .03 .06 .03 .10 .08 .13 .04 .02
0
.02
[1] 4iuo.a .03 .06 .02 .11 .07 .13 .05 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3lb0.a
3m7w.b
3nnt.a
3o1n.a
3s42.a
4gfs.b
4guh.a
4gui.a
4guj.a
4iuo.a
[1] 3lb0.a
0
0.4 0.3 0.7 0.6 2.2 0.4 0.4 0.4 0.4
[1] 3m7w.b 0.4
0
0.5 0.6 0.5 2.1 0.4 0.3 0.4 0.3
[1] 3nnt.a 0.3 0.5
0
0.7 0.6 2.0 0.6 0.5 0.6 0.5
[1] 3o1n.a 0.7 0.6 0.7
0
0.6 1.9 0.7 0.7 0.7 0.6
[1] 3s42.a 0.6 0.5 0.6 0.6
0
2.0 0.6 0.5 0.5 0.5
[1] 4gfs.b 2.2 2.1 2.0 1.9 2.0
0
2.2 2.2 2.2 2.2
[1] 4guh.a 0.4 0.4 0.6 0.7 0.6 2.2
0
0.2 0.1 0.2
[1] 4gui.a 0.4 0.3 0.5 0.7 0.5 2.2 0.2
0
0.2 0.2
[1] 4guj.a 0.4 0.4 0.6 0.7 0.5 2.2 0.1 0.2
0
0.2
[1] 4iuo.a 0.4 0.3 0.5 0.6 0.5 2.2 0.2 0.2 0.2
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

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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
3lb0.a
3m7w.b
3nnt.a
3o1n.a
3s42.a
4gfs.b
4guh.a
4gui.a
4guj.a
4iuo.a
[1] 3lb0.a
0
0.5 0.3 0.9 0.7 2.1 0.4 0.3 0.4 0.3
[1] 3m7w.b 0.5
0
0.5 0.9 0.7 2.1 0.4 0.5 0.5 0.4
[1] 3nnt.a 0.3 0.5
0
0.9 0.7 2.0 0.6 0.4 0.6 0.5
[1] 3o1n.a 0.9 0.9 0.9
0
0.8 1.8 0.9 0.9 0.9 0.9
[1] 3s42.a 0.7 0.7 0.7 0.8
0
1.9 0.7 0.7 0.7 0.6
[1] 4gfs.b 2.1 2.1 2.0 1.8 1.9
0
2.2 2.1 2.2 2.1
[1] 4guh.a 0.4 0.4 0.6 0.9 0.7 2.2
0
0.4 0.3 0.3
[1] 4gui.a 0.3 0.5 0.4 0.9 0.7 2.1 0.4
0
0.3 0.2
[1] 4guj.a 0.4 0.5 0.6 0.9 0.7 2.2 0.3 0.3
0
0.2
[1] 4iuo.a 0.3 0.4 0.5 0.9 0.6 2.1 0.3 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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