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TP4A1_HUMAN_2_166

Protein tyrosine phosphatase type IVA 1 [Protein-tyrosine phosphatase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (TP4A1_HUMAN):D: Tyrosine-protein phosphatase (124, 128, 132)
R: Interaction with ATF5 (124, 128, 132)
14:16, 159, 160
14:16, 124, 128, 132, 159, 160

Full PDB list

1rxd, 1x24, 1xm2, 1zck, 1zcl, 3rz2, 5bx1, 5lxq, 5mmz (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
Y
1
4
K
1
5
N
1
6
M
1
2
4
F
1
3
2
R
1
5
9
[1]1rxd.a none . . . * . .
[1]5bx1.a 4xa27 . . . . . .
[1]5mmz.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
Y
1
4
K
1
5
N
1
6
M
1
2
4
D
1
2
8
F
1
3
2
R
1
5
9
F
1
6
0
[1]1rxd.a . . . * . . . .
[1]5bx1.a . . . . . . . .
[1]5mmz.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
1rxd.a is apo
5bx1.a:4xa
5mmz.b is apo
[1] 1rxd.a
-
0.9 -
[1] 5bx1.a -
0
-
[1] 5mmz.b - 0.3
-
[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
1rxd.a
5bx1.a
5mmz.b
[1] 1rxd.a
0
.11 .15
[1] 5bx1.a .11
0
.04
[1] 5mmz.b .15 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1rxd.a
5bx1.a
5mmz.b
[1] 1rxd.a
0
2.5 0.9
[1] 5bx1.a 2.5
0
0.9
[1] 5mmz.b 0.9 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1rxd.a
5bx1.a
5mmz.b
[1] 1rxd.a
0
4.2 1.5
[1] 5bx1.a 4.2
0
1.3
[1] 5mmz.b 1.5 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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