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ASM_MOUSE_83_164

Sphingomyelin phosphodiesterase [Acid sphingomyelinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ASM_MOUSE):D: Saposin B-type (83, 84, 93, 94, 96, 97, 100, 101, 103, 104, 106, 107, 109:111, 113, 114, 117, 131:138, 143, 149, 158, 159)
82
82:84, 93, 94, 96, 97, 100, 101, 103, 104, 106, 107, 109:111, 113, 114, 117, 131:138, 143, 149, 158, 159

Full PDB list

5fi9, 5fib, 5fic

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
9
3
A
9
6
L
9
7
G
1
0
0
L
1
0
1
V
1
1
0
L
1
4
9
[1]5fib.b none . . . . . . .
[1]5fic.a 6e022 . . . . . . .
[2]5fi9.b none . . . . . . .

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
W
8
2
Q
8
3
N
8
4
L
9
3
F
9
4
A
9
6
L
9
7
G
1
0
0
L
1
0
1
K
1
0
3
E
1
0
4
N
1
0
6
V
1
0
7
R
1
0
9
V
1
1
0
G
1
1
1
V
1
1
3
A
1
1
4
I
1
1
7
S
1
3
1
A
1
3
2
V
1
3
3
H
1
3
4
L
1
3
5
F
1
3
6
E
1
3
7
D
1
3
8
V
1
4
3
L
1
4
9
L
1
5
8
L
1
5
9
[1]5fib.b K L . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5fic.a - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5fi9.b K L . . . . . . . . . . . . * . . . . . * . . * * * . . . . .

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
5fib.b is apo
5fic.a:6e0
5fi9.b is apo
[1] 5fib.b
-
0 -
[1] 5fic.a -
0
-
[2] 5fi9.b - 14
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
5fib.b
5fic.a
5fi9.b
[1] 5fib.b
0
0 .43
[1] 5fic.a 0
0
.43
[2] 5fi9.b .43 .43
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.0 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
5fib.b
5fic.a
5fi9.b
[1] 5fib.b
0
2.6 16
[1] 5fic.a 2.6
0
15
[2] 5fi9.b 16 15
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.6 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
5fib.b
5fic.a
5fi9.b
[1] 5fib.b
0
3.0 16
[1] 5fic.a 3.0
0
15
[2] 5fi9.b 16 15
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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