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AGAL_HUMAN_32_429

Alpha-galactosidase A [Glycosyl hydrolase 27 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AGAL_HUMAN):R: Substrate binding (203, 206, 207)
47, 92, 93, 134, 142, 143, 168, 170, 172, 227, 230, 231
47, 92, 93, 134, 142, 143, 168, 170, 172, 203, 206, 207, 227, 230, 231

Full PDB list

1r46, 1r47, 3gxn, 3gxp, 3gxt, 3hg2, 3hg3, 3hg4, 3hg5, 3lx9, 3lxa, 3lxb, 3lxc, 3s5y, 3s5z, 3tv8, 4nxs (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
4
7
D
9
2
D
9
3
Y
1
3
4
C
1
4
2
K
1
6
8
D
1
7
0
C
1
7
2
E
2
0
3
L
2
0
6
Y
2
0
7
R
2
2
7
A
2
3
0
D
2
3
1
[1]1r46.a none . . . . . . . . . . . . . .
[1]3gxt.a noj11 . . . . . . . . . . . . . .
[1]3hg3.a gla-glc23 . . . . . . A . . . . . . .
[1]3hg4.a 7jz12 . . . . . . * . . . . . . .
[1]3lx9.a none . . . . . . . . S A . . . .
[1]3lxa.a gla12 . . . . . . . . S A . . . .
[1]3s5y.a dgj11 . . . . . . . . . . . . . .
[1]3s5z.a gla12 . . . . . . . . . . . . . .
[1]3tv8.a dgj11 . . . . . . A . . . . . . .
[1]4nxs.b 2oz21 . . . . . . . . . . . . . .

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
4
7
D
9
2
D
9
3
Y
1
3
4
C
1
4
2
A
1
4
3
K
1
6
8
D
1
7
0
C
1
7
2
E
2
0
3
L
2
0
6
Y
2
0
7
R
2
2
7
A
2
3
0
D
2
3
1
[1]1r46.a . . . . . . . . . . . . . . .
[1]3gxt.a . . . . . . . . . . . . . . .
[1]3hg3.a . . . . . . . A . . . . . . .
[1]3hg4.a . . . . . . . * . . . . . . .
[1]3lx9.a . . . . . . . . . S A . . . .
[1]3lxa.a . . . . . . . * . S A . . . .
[1]3s5y.a . . . . . . . . . . . . . . .
[1]3s5z.a . . . . . . . . . . . . . . .
[1]3tv8.a . . . . . . . A . . . . . . .
[1]4nxs.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
1r46.a is apo
3gxt.a:noj
3hg3.a:gla-glc
3hg4.a:7jz
3lx9.a is apo
3lxa.a:gla
3s5y.a:dgj
3s5z.a:gla
3tv8.a:dgj
4nxs.b:2oz
[1] 1r46.a
-
0.6 0.2 0.9 - 0.1 0.2 0.3 0.3 0.3
[1] 3gxt.a -
0.2
0 0.8 - 0 0 0 0.1 0.2
[1] 3hg3.a - 0.5
0
0.4 - 0.1 0.2 0.1 0.1 0.5
[1] 3hg4.a - 0.4 0.1
0.9
- 0.2 0.1 0.1 0.1 0.7
[1] 3lx9.a - 0.4 0 0.4
-
0.1 0 0 0.1 0.5
[1] 3lxa.a - 0.4 0.1 0.6 -
0.1
0 0.1 0.1 0.6
[1] 3s5y.a - 0.4 0.2 1.0 - 0.1
0
0.1 0.2 0.4
[1] 3s5z.a - 0.4 0 0.8 - 0.1 0
0
0 0.4
[1] 3tv8.a - 0.4 0 0.4 - 0.2 0.1 0
0.1
0.6
[1] 4nxs.b - 0.2 0.1 0.9 - 0 0.1 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
1r46.a
3gxt.a
3hg3.a
3hg4.a
3lx9.a
3lxa.a
3s5y.a
3s5z.a
3tv8.a
4nxs.b
[1] 1r46.a
0
.04 .06 .11 .06 .08 .04 .03 .07 .04
[1] 3gxt.a .04
0
.05 .09 .05 .07 .03 .02 .06 .01
[1] 3hg3.a .06 .05
0
.11 .07 .07 .05 .04 .01 .06
[1] 3hg4.a .11 .09 .11
0
.06 .05 .07 .07 .10 .09
[1] 3lx9.a .06 .05 .07 .06
0
.02 .05 .04 .08 .06
[1] 3lxa.a .08 .07 .07 .05 .02
0
.05 .06 .09 .07
[1] 3s5y.a .04 .03 .05 .07 .05 .05
0
.01 .05 .03
[1] 3s5z.a .03 .02 .04 .07 .04 .06 .01
0
.04 .03
[1] 3tv8.a .07 .06 .01 .10 .08 .09 .05 .04
0
.07
[1] 4nxs.b .04 .01 .06 .09 .06 .07 .03 .03 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1r46.a
3gxt.a
3hg3.a
3hg4.a
3lx9.a
3lxa.a
3s5y.a
3s5z.a
3tv8.a
4nxs.b
[1] 1r46.a
0
0.4 0.4 0.4 0.5 0.4 0.4 0.4 0.4 0.4
[1] 3gxt.a 0.4
0
0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.4
[1] 3hg3.a 0.4 0.4
0
0.3 0.3 0.3 0.3 0.3 0.3 0.4
[1] 3hg4.a 0.4 0.4 0.3
0
0.3 0.3 0.2 0.2 0.2 0.2
[1] 3lx9.a 0.5 0.4 0.3 0.3
0
0.2 0.3 0.3 0.3 0.4
[1] 3lxa.a 0.4 0.3 0.3 0.3 0.2
0
0.2 0.2 0.3 0.4
[1] 3s5y.a 0.4 0.3 0.3 0.2 0.3 0.2
0
0.2 0.2 0.3
[1] 3s5z.a 0.4 0.3 0.3 0.2 0.3 0.2 0.2
0
0.2 0.3
[1] 3tv8.a 0.4 0.3 0.3 0.2 0.3 0.3 0.2 0.2
0
0.2
[1] 4nxs.b 0.4 0.4 0.4 0.2 0.4 0.4 0.3 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
1r46.a
3gxt.a
3hg3.a
3hg4.a
3lx9.a
3lxa.a
3s5y.a
3s5z.a
3tv8.a
4nxs.b
[1] 1r46.a
0
0.6 0.6 0.8 0.7 0.7 0.6 0.6 0.5 0.8
[1] 3gxt.a 0.6
0
0.7 0.6 0.6 0.6 0.4 0.4 0.4 0.8
[1] 3hg3.a 0.6 0.7
0
0.7 0.4 0.3 0.6 0.6 0.5 0.7
[1] 3hg4.a 0.8 0.6 0.7
0
0.5 0.6 0.5 0.5 0.5 0.8
[1] 3lx9.a 0.7 0.6 0.4 0.5
0
0.3 0.5 0.5 0.5 0.6
[1] 3lxa.a 0.7 0.6 0.3 0.6 0.3
0
0.6 0.5 0.5 0.6
[1] 3s5y.a 0.6 0.4 0.6 0.5 0.5 0.6
0
0.2 0.3 0.7
[1] 3s5z.a 0.6 0.4 0.6 0.5 0.5 0.5 0.2
0
0.3 0.7
[1] 3tv8.a 0.5 0.4 0.5 0.5 0.5 0.5 0.3 0.3
0
0.7
[1] 4nxs.b 0.8 0.8 0.7 0.8 0.6 0.6 0.7 0.7 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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