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AROD_SALTI_1_252

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROD_SALTI):R: 3-dehydroquinate binding (46, 48)
21, 23, 80, 82, 143, 170, 172, 203, 205, 213, 225, 231:234, 236
21, 23, 46, 48, 80, 82, 143, 170, 172, 203, 205, 213, 225, 231:234, 236

Full PDB list

1gqn, 1l9w, 1qfe, 4clm, 4cnn, 4cno, 4cnp, 4uio (redundant Pocketome entry)

Pocket contact map

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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]1l9w.b dhs11 . . . . . . . . . . . . . .
[1]4clm.b wpl13 . . . . . * . . . . . . . .
[1]4cnn.b none . . . . . . . . . . . - - .
[1]4cno.a 9py14 . . . . . . . . . . . - - .
[1]4cnp.b 9c414 . . . . . . . . . . . . . .
[1]4uio.a vau14 . . . . . * . . . . . . . .

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
M
2
3
E
4
6
R
4
8
T
8
0
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
A
2
3
1
S
2
3
2
A
2
3
3
P
2
3
4
Q
2
3
6
[1]1l9w.b . . . . . . . * . . . . . . * . . *
[1]4clm.b . . . . . . . * . . . . . . * * . .
[1]4cnn.b . . . . . . . * . . . . . - - - . .
[1]4cno.a . . . . . . . * . . . . . - - - . .
[1]4cnp.b . . . . . . . . . . . . . . * * . .
[1]4uio.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
1l9w.b:dhs
4clm.b:wpl
4cnn.b is apo
4cno.a:9py
4cnp.b:9c4
4uio.a:vau
[1] 1l9w.b
0.2
1.0 - 3.3 0.8 0.9
[1] 4clm.b 0.2
0.7
- 3.0 0.4 0.6
[1] 4cnn.b 0.2 1.1
-
1.3 1.0 1.1
[1] 4cno.a 0.5 1.0 -
0
0.9 1.3
[1] 4cnp.b 0.1 0.8 - 3.4
0.2
0.6
[1] 4uio.a 0.2 0.8 - 2.7 0.4
0.6
[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
1l9w.b
4clm.b
4cnn.b
4cno.a
4cnp.b
4uio.a
[1] 1l9w.b
0
.06 .12 .24 .06 .05
[1] 4clm.b .06
0
.13 .21 .03 .02
[1] 4cnn.b .12 .13
0
.13 .15 .11
[1] 4cno.a .24 .21 .13
0
.24 .19
[1] 4cnp.b .06 .03 .15 .24
0
.05
[1] 4uio.a .05 .02 .11 .19 .05
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
1l9w.b
4clm.b
4cnn.b
4cno.a
4cnp.b
4uio.a
[1] 1l9w.b
0
0.3 0.6 1.4 0.4 0.2
[1] 4clm.b 0.3
0
0.5 1.4 0.2 0.3
[1] 4cnn.b 0.6 0.5
0
1.1 0.6 0.6
[1] 4cno.a 1.4 1.4 1.1
0
1.5 1.4
[1] 4cnp.b 0.4 0.2 0.6 1.5
0
0.4
[1] 4uio.a 0.2 0.3 0.6 1.4 0.4
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
1l9w.b
4clm.b
4cnn.b
4cno.a
4cnp.b
4uio.a
[1] 1l9w.b
0
0.4 0.8 1.7 0.5 0.4
[1] 4clm.b 0.4
0
0.6 1.7 0.3 0.3
[1] 4cnn.b 0.8 0.6
0
1.4 0.7 0.7
[1] 4cno.a 1.7 1.7 1.4
0
1.7 1.6
[1] 4cnp.b 0.5 0.3 0.7 1.7
0
0.4
[1] 4uio.a 0.4 0.3 0.7 1.6 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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