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ASM3B_MOUSE_18_435

Acid sphingomyelinase-like phosphodiesterase 3b [Acid sphingomyelinase family]

Composition of the binding site

Protein chains monomer
A1 (ASM3B_MOUSE):30, 93, 97, 134, 135, 242, 250, 277:279, 306, 308, 31030, 93, 97, 134, 135, 242, 250, 277:279, 306, 308, 310
Metals (Me):Zn

Full PDB list

5kar, 5kas

Pocket contact map

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PDB.ch
   
ligand
A1 Me
H
3
0
D
9
3
H
9
7
N
1
3
4
H
1
3
5
F
2
4
2
W
2
5
0
H
2
7
7
H
2
7
8
H
2
7
9
W
3
0
6
T
3
0
8
[1]5kar.a none . . . . . . . . . . . . Zn
[1]5kas.a pc,zn12 . . . . . . . . . . . . Zn

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 Me
H
3
0
D
9
3
H
9
7
N
1
3
4
H
1
3
5
F
2
4
2
W
2
5
0
H
2
7
7
H
2
7
8
H
2
7
9
W
3
0
6
T
3
0
8
L
3
1
0
[1]5kar.a . . . . . . . . . . . . . Zn
[1]5kas.a . . . . . . . . . . . . . Zn

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
5kar.a is apo
5kas.a:pc,zn
[1] 5kar.a
-
0.4
[1] 5kas.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
5kar.a
5kas.a
[1] 5kar.a
0
.02
[1] 5kas.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
5kar.a
5kas.a
[1] 5kar.a
0
0.1
[1] 5kas.a 0.1
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
5kar.a
5kas.a
[1] 5kar.a
0
0.1
[1] 5kas.a 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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