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PTPRB_HUMAN_1666_1972

Receptor-type tyrosine-protein phosphatase beta [Protein-tyrosine phosphatase family. Receptor class 3 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTPRB_HUMAN):D: Tyrosine-protein phosphatase (1715, 1732:1736, 1809, 1811, 1870, 1871, 1904:1906, 1908:1910, 1945, 1948)
R: Substrate binding (1904:1906, 1908:1910)
1715, 1732:1736, 1809, 1811, 1870, 1871, 1904:1906, 1908:1910, 1945, 1948

Full PDB list

2ahs, 2h02, 2h03, 2h04, 2hc1, 2hc2, 2i3r, 2i3u, 2i4e, 2i4g, 2i4h, 2i5x (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
R
1
7
1
5
Y
1
7
3
3
N
1
7
3
4
N
1
7
3
5
I
1
7
3
6
R
1
8
0
9
K
1
8
1
1
D
1
8
7
0
H
1
8
7
1
C
1
9
0
4
S
1
9
0
5
A
1
9
0
6
V
1
9
0
8
G
1
9
0
9
R
1
9
1
0
H
1
9
4
5
Q
1
9
4
8
[1]2h02.a 2un28 . . . . . . . . . . . . . . . . .
[1]2h03.a 3un33 . . . . . . . . . . . . . . . . .
[1]2h04.a 4un32 . . . . . . . . . . . . . . . . .
[1]2hc1.a none . . . . . . . . . . . . . . . . .
[1]2i4e.b v1 . . . . . . . . . . . . . . . . .
[1]2i4g.a ua137 . . . . . . . . . . . . . . . . .
[1]2i5x.b ua513 . . . . . . . . . . . . . . . . .

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
R
1
7
1
5
R
1
7
3
2
Y
1
7
3
3
N
1
7
3
4
N
1
7
3
5
I
1
7
3
6
R
1
8
0
9
K
1
8
1
1
D
1
8
7
0
H
1
8
7
1
C
1
9
0
4
S
1
9
0
5
A
1
9
0
6
V
1
9
0
8
G
1
9
0
9
R
1
9
1
0
H
1
9
4
5
Q
1
9
4
8
[1]2h02.a . . . . . . . . . . . . . . . . * .
[1]2h03.a . . . . . . . . . . . . . . . . * .
[1]2h04.a . . . . . . * . . . . . . . . . * .
[1]2hc1.a . . . . . . . . . . . . . * . . * .
[1]2i4e.b . . . . . . . . . . . . . . . . * .
[1]2i4g.a . . . . . . . . . . . . . . . . . .
[1]2i5x.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
2h02.a:2un
2h03.a:3un
2h04.a:4un
2hc1.a is apo
2i4e.b:v
2i4g.a:ua1
2i5x.b:ua5
[1] 2h02.a
0
0.2 0.3 - 0.1 2.5 0
[1] 2h03.a 0
0
0 - 0.1 2.9 0
[1] 2h04.a 0 1.3
0
- 0.1 2.8 0.1
[1] 2hc1.a 0.8 0.8 0.9
-
0.1 3.3 0.7
[1] 2i4e.b 0.8 1.0 0.9 -
0.1
3.1 1.0
[1] 2i4g.a 0 0.2 0.3 - 0.1
0
0
[1] 2i5x.b 0 0.1 0.2 - 0.1 2.3
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
2h02.a
2h03.a
2h04.a
2hc1.a
2i4e.b
2i4g.a
2i5x.b
[1] 2h02.a
0
.06 .11 .06 .04 .15 .01
[1] 2h03.a .06
0
.08 .11 .09 .17 .05
[1] 2h04.a .11 .08
0
.16 .12 .22 .09
[1] 2hc1.a .06 .11 .16
0
.06 .18 .07
[1] 2i4e.b .04 .09 .12 .06
0
.18 .05
[1] 2i4g.a .15 .17 .22 .18 .18
0
.14
[1] 2i5x.b .01 .05 .09 .07 .05 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
2h02.a
2h03.a
2h04.a
2hc1.a
2i4e.b
2i4g.a
2i5x.b
[1] 2h02.a
0
0.4 0.4 1.5 0.2 0.5 0.2
[1] 2h03.a 0.4
0
0.3 1.5 0.4 0.6 0.4
[1] 2h04.a 0.4 0.3
0
1.5 0.4 0.6 0.4
[1] 2hc1.a 1.5 1.5 1.5
0
1.5 1.4 1.4
[1] 2i4e.b 0.2 0.4 0.4 1.5
0
0.5 0.2
[1] 2i4g.a 0.5 0.6 0.6 1.4 0.5
0
0.4
[1] 2i5x.b 0.2 0.4 0.4 1.4 0.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2h02.a
2h03.a
2h04.a
2hc1.a
2i4e.b
2i4g.a
2i5x.b
[1] 2h02.a
0
2.2 1.6 2.6 1.4 2.5 1.3
[1] 2h03.a 2.2
0
1.2 2.1 1.7 1.5 1.6
[1] 2h04.a 1.6 1.2
0
2.3 1.3 1.8 1.1
[1] 2hc1.a 2.6 2.1 2.3
0
2.3 2.4 2.2
[1] 2i4e.b 1.4 1.7 1.3 2.3
0
2.0 0.6
[1] 2i4g.a 2.5 1.5 1.8 2.4 2.0
0
2.0
[1] 2i5x.b 1.3 1.6 1.1 2.2 0.6 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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