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PTP10_DROME_1248_1533

Tyrosine-protein phosphatase 10D [Protein-tyrosine phosphatase family. Receptor class subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTP10_DROME):D: Tyrosine-protein phosphatase (1302, 1304, 1305, 1380, 1468:1470, 1472:1474, 1509, 1512)
R: Substrate binding (1468:1470, 1472:1474)
1302, 1304, 1305, 1380, 1468:1470, 1472:1474, 1509, 1512

Full PDB list

3s3e, 3s3f, 3s3h, 3s3k

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
3
0
2
N
1
3
0
4
I
1
3
0
5
K
1
3
8
0
C
1
4
6
8
S
1
4
6
9
A
1
4
7
0
V
1
4
7
2
R
1
4
7
4
W
1
5
0
9
Q
1
5
1
2
[1]3s3e.a none . . . . . . . . . . .
[1]3s3f.b v1 . . . . . . . . . . .
[1]3s3h.b ptr16 . . . . . . . . . . .
[1]3s3k.b csn15 . . . . . . . . . . .

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
F
1
3
0
2
N
1
3
0
4
I
1
3
0
5
K
1
3
8
0
C
1
4
6
8
S
1
4
6
9
A
1
4
7
0
V
1
4
7
2
G
1
4
7
3
R
1
4
7
4
W
1
5
0
9
Q
1
5
1
2
[1]3s3e.a . . . . . . . . . . . .
[1]3s3f.b . * . . . . . . . . . .
[1]3s3h.b . . . . . . . . . . . .
[1]3s3k.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
3s3e.a is apo
3s3f.b:v
3s3h.b:ptr
3s3k.b:csn
[1] 3s3e.a
-
0 0.1 0.1
[1] 3s3f.b -
0
0.6 0.1
[1] 3s3h.b - 0
0.2
0.2
[1] 3s3k.b - 0 0.8
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
3s3e.a
3s3f.b
3s3h.b
3s3k.b
[1] 3s3e.a
0
.06 .03 .07
[1] 3s3f.b .06
0
.04 .02
[1] 3s3h.b .03 .04
0
.07
[1] 3s3k.b .07 .02 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3s3e.a
3s3f.b
3s3h.b
3s3k.b
[1] 3s3e.a
0
0.6 0.5 0.6
[1] 3s3f.b 0.6
0
0.7 0.3
[1] 3s3h.b 0.5 0.7
0
0.8
[1] 3s3k.b 0.6 0.3 0.8
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

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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
3s3e.a
3s3f.b
3s3h.b
3s3k.b
[1] 3s3e.a
0
0.6 0.6 0.7
[1] 3s3f.b 0.6
0
0.7 0.5
[1] 3s3h.b 0.6 0.7
0
0.7
[1] 3s3k.b 0.7 0.5 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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