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LYPA1_HUMAN_3_230

Acyl-protein thioesterase 1 [AB hydrolase superfamily. AB hydrolase 2 family]

Composition of the binding site

Protein chains monomer
A1 (LYPA1_HUMAN):30, 63, 75, 77:82, 84, 145, 146, 149, 176:178, 181, 184, 18530, 63, 75, 77:82, 84, 145, 146, 149, 176:178, 181, 184, 185

Full PDB list

1fj2, 5sym

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
3
0
I
7
5
G
7
7
L
7
8
S
7
9
P
8
0
E
8
4
W
1
4
5
L
1
4
6
R
1
4
9
L
1
7
6
V
1
7
7
F
1
8
1
L
1
8
4
T
1
8
5
[1]5sym.b 71q28 . . . . . . . . . . . . . . .
[2]1fj2.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
L
3
0
L
6
3
I
7
5
G
7
7
L
7
8
S
7
9
P
8
0
D
8
1
S
8
2
E
8
4
W
1
4
5
L
1
4
6
R
1
4
9
L
1
7
6
V
1
7
7
P
1
7
8
F
1
8
1
L
1
8
4
T
1
8
5
[1]5sym.b . . . . . . . . . . . . . . . . . . .
[2]1fj2.b . . . . * . * . . . . . . . . . * * .

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
5sym.b:71q
1fj2.b is apo
[1] 5sym.b
0
-
[2] 1fj2.b 9.2
-
[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
5sym.b
1fj2.b
[1] 5sym.b
0
.48
[2] 1fj2.b .48
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
5sym.b
1fj2.b
[1] 5sym.b
0
1.2
[2] 1fj2.b 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
5sym.b
1fj2.b
[1] 5sym.b
0
1.6
[2] 1fj2.b 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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