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ARS_PSEAE_1_536

Arylsulfatase [Sulfatase family]

Composition of the binding site

Protein chains monomer
A1 (ARS_PSEAE):50, 51, 72, 74, 115, 138, 139, 160, 211, 212, 321, 323, 325, 328, 331, 375, 376, 46350, 51, 72, 74, 115, 138, 139, 160, 211, 212, 321, 323, 325, 328, 331, 375, 376, 463
Metals (Me):Ca

Full PDB list

1hdh, 4cxk, 4cxs, 4cxu, 4cyr, 4cys, 5aj9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
C
5
1
M
7
2
E
7
4
H
1
1
5
G
1
3
8
A
1
3
9
T
1
6
0
H
2
1
1
W
2
1
2
E
3
2
1
A
3
2
3
L
3
2
5
F
3
3
1
K
3
7
5
A
3
7
6
F
4
6
3
[1]1hdh.b none * . . . . . . . . . . . . . . . Ca
[1]4cxk.a none * V . . . . . . . . . . . . . . Ca
[1]4cxs.a sv710 * . . . . . . . . . . . . . . . Ca
[1]4cxu.a 62y17 * . . . . . . . . . . . . . . . Ca
[1]4cyr.a none * . . . . . . . . . . . . . . . Ca
[1]4cys.a sv710 * V . . . . . . . . . . . . . . Ca

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
T
5
0
C
5
1
M
7
2
E
7
4
H
1
1
5
G
1
3
8
A
1
3
9
T
1
6
0
H
2
1
1
W
2
1
2
E
3
2
1
A
3
2
3
L
3
2
5
F
3
2
8
F
3
3
1
K
3
7
5
A
3
7
6
F
4
6
3
[1]1hdh.b . * . . . . . . . . . . . . . . . . Ca
[1]4cxk.a A * V . . . . . . . . . . . . . . . Ca
[1]4cxs.a A * . . . . . . . . . . . . . . . . Ca
[1]4cxu.a A * . . . . . . . . . . . . . . . . Ca
[1]4cyr.a A * . . . . . . . . . . . . . . . . Ca
[1]4cys.a A * V . . . . . . . . . . . . . . . Ca

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
1hdh.b is apo
4cxk.a is apo
4cxs.a:sv7
4cxu.a:62y
4cyr.a is apo
4cys.a:sv7
[1] 1hdh.b
-
- 0.2 0.3 - 0.2
[1] 4cxk.a -
-
0.2 0.2 - 0.2
[1] 4cxs.a - -
0.2
0.3 - 0.2
[1] 4cxu.a - - 0.2
0
- 0.2
[1] 4cyr.a - - 0.3 0.2
-
0.3
[1] 4cys.a - - 0.2 0.1 -
0.2
[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
1hdh.b
4cxk.a
4cxs.a
4cxu.a
4cyr.a
4cys.a
[1] 1hdh.b
0
.02 .03 .03 .02 .02
[1] 4cxk.a .02
0
.02 .01 .01 0
[1] 4cxs.a .03 .02
0
.01 .02 .02
[1] 4cxu.a .03 .01 .01
0
.01 .01
[1] 4cyr.a .02 .01 .02 .01
0
.01
[1] 4cys.a .02 0 .02 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1hdh.b
4cxk.a
4cxs.a
4cxu.a
4cyr.a
4cys.a
[1] 1hdh.b
0
0.2 0.3 0.2 0.2 0.7
[1] 4cxk.a 0.2
0
0.2 0.2 0.1 0.6
[1] 4cxs.a 0.3 0.2
0
0.2 0.2 0.6
[1] 4cxu.a 0.2 0.2 0.2
0
0.2 0.7
[1] 4cyr.a 0.2 0.1 0.2 0.2
0
0.6
[1] 4cys.a 0.7 0.6 0.6 0.7 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1hdh.b
4cxk.a
4cxs.a
4cxu.a
4cyr.a
4cys.a
[1] 1hdh.b
0
0.3 0.5 0.5 0.4 0.7
[1] 4cxk.a 0.3
0
0.4 0.2 0.3 0.6
[1] 4cxs.a 0.5 0.4
0
0.5 0.3 0.6
[1] 4cxu.a 0.5 0.2 0.5
0
0.5 0.7
[1] 4cyr.a 0.4 0.3 0.3 0.5
0
0.6
[1] 4cys.a 0.7 0.6 0.6 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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