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EPHB_MYCTO_1_356

Epoxide hydrolase B [AB hydrolase superfamily. Epoxide hydrolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPHB_MYCTO):D: AB hydrolase-1 (36, 104, 105, 108)
136, 137, 164, 165, 189, 193, 226, 272, 275, 333, 334
36, 104, 105, 108, 136, 137, 164, 165, 189, 193, 226, 272, 275, 333, 334

Full PDB list

2e3j, 2zjf

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
6
D
1
0
4
W
1
0
5
P
1
0
8
V
1
3
6
I
1
3
7
Y
1
6
4
Q
1
6
5
L
1
8
9
V
1
9
3
L
2
2
6
Y
2
7
2
H
3
3
3
W
3
3
4
[1]2e3j.a none . . . . . . . . . . . . . .
[1]2zjf.a bsu16 . . . . . . . . . . . . . .

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
F
3
6
D
1
0
4
W
1
0
5
P
1
0
8
V
1
3
6
I
1
3
7
Y
1
6
4
Q
1
6
5
L
1
8
9
V
1
9
3
L
2
2
6
Y
2
7
2
I
2
7
5
H
3
3
3
W
3
3
4
[1]2e3j.a . . . . . * . . . . . . . . .
[1]2zjf.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
2e3j.a is apo
2zjf.a:bsu
[1] 2e3j.a
-
1.2
[1] 2zjf.a -
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
2e3j.a
2zjf.a
[1] 2e3j.a
0
.07
[1] 2zjf.a .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
2e3j.a
2zjf.a
[1] 2e3j.a
0
0.2
[1] 2zjf.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2e3j.a
2zjf.a
[1] 2e3j.a
0
0.6
[1] 2zjf.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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