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HOD_PAENT_1_276

1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase [AB hydrolase superfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (HOD_PAENT):D: AB hydrolase-1 (36, 38, 100:102, 136, 140, 143)
R: Substrate binding (36, 38)
R: Substrate binding (100, 101)
156, 160, 177, 185, 188, 192, 251, 252
36, 38, 100:102, 136, 140, 143, 156, 160, 177, 185, 188, 192, 251, 252

Full PDB list

2wj3, 2wj4, 2wj6, 2wm2, 4cfs (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
3
6
H
3
8
H
1
0
0
S
1
0
1
H
1
0
2
L
1
4
3
L
1
5
6
W
1
6
0
M
1
7
7
W
1
8
5
S
1
8
8
I
1
9
2
H
2
5
1
[1]2wj3.a none . . . . . . . . . . . . .
[1]2wj4.a hqd13 . . . . . . . . . . . . .
[1]2wj6.a zz813 . . . . . . . . . . . . .
[1]4cfs.a hqd13 . . . . . . . . . . . . A

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
W
3
6
H
3
8
H
1
0
0
S
1
0
1
H
1
0
2
F
1
3
6
L
1
4
0
L
1
4
3
L
1
5
6
W
1
6
0
M
1
7
7
W
1
8
5
S
1
8
8
I
1
9
2
H
2
5
1
F
2
5
2
[1]2wj3.a . . . . . . . . . . . . . . . .
[1]2wj4.a . . . . . . . . . . . . . . . .
[1]2wj6.a . . . . . . . . . . . . . . . .
[1]4cfs.a . . . . . . . . . . . . . . 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
2wj3.a is apo
2wj4.a:hqd
2wj6.a:zz8
4cfs.a:hqd
[1] 2wj3.a
-
0 0.2 0.1
[1] 2wj4.a -
0
0.1 0
[1] 2wj6.a - 0.2
0
0.1
[1] 4cfs.a - 0 0.2
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
2wj3.a
2wj4.a
2wj6.a
4cfs.a
[1] 2wj3.a
0
.01 .03 .02
[1] 2wj4.a .01
0
.02 .01
[1] 2wj6.a .03 .02
0
.03
[1] 4cfs.a .02 .01 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2wj3.a
2wj4.a
2wj6.a
4cfs.a
[1] 2wj3.a
0
0.1 0.2 0.2
[1] 2wj4.a 0.1
0
0.2 0.2
[1] 2wj6.a 0.2 0.2
0
0.2
[1] 4cfs.a 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2wj3.a
2wj4.a
2wj6.a
4cfs.a
[1] 2wj3.a
0
0.1 0.3 0.2
[1] 2wj4.a 0.1
0
0.3 0.2
[1] 2wj6.a 0.3 0.3
0
0.3
[1] 4cfs.a 0.2 0.2 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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