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PTPRG_HUMAN_823_1128

Receptor-type tyrosine-protein phosphatase gamma [Protein-tyrosine phosphatase family. Receptor class 5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTPRG_HUMAN):D: Tyrosine-protein phosphatase 1 (950, 1023, 1026:1032, 1038, 1041, 1042, 1065, 1066, 1069, 1070, 1073, 1104:1108, 1110, 1111, 1114)
R: Substrate binding (1065, 1066)
841, 844, 845
841, 844, 845, 950, 1023, 1026:1032, 1038, 1041, 1042, 1065, 1066, 1069, 1070, 1073, 1104:1108, 1110, 1111, 1114

Full PDB list

2h4v, 2hy3, 2nlk, 2pbn, 3qcb, 3qcc, 3qcd, 3qce, 3qcf, 3qcg, 3qch, 3qci, 3qcj, 3qck, 3qcl, 3qcm, 3qcn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
8
4
1
Q
8
4
5
I
9
5
0
Y
1
0
2
3
W
1
0
2
6
G
1
0
3
0
V
1
0
3
1
P
1
0
3
2
V
1
0
3
8
F
1
0
4
1
G
1
0
6
5
R
1
0
6
6
T
1
0
6
9
Y
1
0
7
0
I
1
0
7
3
Q
1
1
0
4
T
1
1
0
5
E
1
1
0
7
Q
1
1
0
8
I
1
1
1
0
F
1
1
1
1
[1]3qch.a nx222 . . . . . . . . . . . . . . . . . . . . .
[1]3qci.a nx328 . . . . . . . . . . . . . . . . . . . . .
[1]3qcj.a nx432 . . . . . . . . . . . . . . . . . . . . .
[1]3qck.a nx519 . . . . . . . . . . . . . . . . . . . . .
[1]3qcl.a nxv24 . . . . . . . . . . . . . . . . . . . . .
[1]3qcm.a nxw36 . . . . . . . . . . . . . . . . . . . . .
[2]2hy3.a none . . . . . . . . . . . . . . . . . . . . .
[2]3qce.a nxy18 . . . . . . . . . . . . . . . . . . . . .
[2]3qcg.a nx118 . . . . . . . . . . . . . . . . . . . . .
[3]3qcd.a 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

[download in TSV format]
   
PDB.ch
A1
Y
8
4
1
N
8
4
4
Q
8
4
5
I
9
5
0
Y
1
0
2
3
W
1
0
2
6
P
1
0
2
7
D
1
0
2
8
M
1
0
2
9
G
1
0
3
0
V
1
0
3
1
P
1
0
3
2
V
1
0
3
8
F
1
0
4
1
V
1
0
4
2
G
1
0
6
5
R
1
0
6
6
T
1
0
6
9
Y
1
0
7
0
I
1
0
7
3
Q
1
1
0
4
T
1
1
0
5
E
1
1
0
6
E
1
1
0
7
Q
1
1
0
8
I
1
1
1
0
F
1
1
1
1
D
1
1
1
4
[1]3qch.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3qci.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3qcj.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3qck.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3qcl.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3qcm.a . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[2]2hy3.a . . . . . * . . * * * . . . . . . . . . . . . . . . . .
[2]3qce.a . . . . . * . . . * * . . . . . . . . . . . . . . . . .
[2]3qcg.a . . . . . * . . . * * . . . . . . . . . . . . . . . . .
[3]3qcd.a . . . . . * * * * * * . . . . . . . . . * . . . . . . .

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
3qch.a:nx2
3qci.a:nx3
3qcj.a:nx4
3qck.a:nx5
3qcl.a:nxv
3qcm.a:nxw
2hy3.a is apo
3qce.a:nxy
3qcg.a:nx1
3qcd.a is apo
[1] 3qch.a
0
0.2 0.3 0 0.2 0.3 - 0.2 0 -
[1] 3qci.a 0
0.1
0.4 0 0.3 0.3 - 0 0 -
[1] 3qcj.a 0 0.1
0
0 0 0.2 - 0 0 -
[1] 3qck.a 0 0 0.2
0
0 0.4 - 0 0 -
[1] 3qcl.a 0.1 0.2 0.4 0.1
0.1
0.2 - 0.2 0.1 -
[1] 3qcm.a 0.2 0.2 1.0 0.1 0.1
0.1
- 0.2 0 -
[2] 2hy3.a 6.8 6.5 7.7 7.1 7.6 8.3
-
5.8 6.2 -
[2] 3qce.a 4.6 4.8 5.1 5.6 6.2 5.9 -
3.7
4.8 -
[2] 3qcg.a 4.4 4.1 4.3 4.8 5.5 6.0 - 3.5
3.9
-
[3] 3qcd.a 12 15 16 9.7 10 9.6 - 8.4 9.4
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
3qch.a
3qci.a
3qcj.a
3qck.a
3qcl.a
3qcm.a
2hy3.a
3qce.a
3qcg.a
3qcd.a
[1] 3qch.a
0
.02 .02 .01 .01 .06 .31 .25 .21 .58
[1] 3qci.a .02
0
.02 .02 .03 .05 .30 .23 .23 .58
[1] 3qcj.a .02 .02
0
.02 .02 .06 .33 .25 .23 .60
[1] 3qck.a .01 .02 .02
0
.02 .06 .32 .24 .22 .58
[1] 3qcl.a .01 .03 .02 .02
0
.05 .31 .25 .21 .58
[1] 3qcm.a .06 .05 .06 .06 .05
0
.34 .26 .26 .59
[2] 2hy3.a .31 .30 .33 .32 .31 .34
0
.11 .13 .31
[2] 3qce.a .25 .23 .25 .24 .25 .26 .11
0
.05 .38
[2] 3qcg.a .21 .23 .23 .22 .21 .26 .13 .05
0
.40
[3] 3qcd.a .58 .58 .60 .58 .58 .59 .31 .38 .40
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
3qch.a
3qci.a
3qcj.a
3qck.a
3qcl.a
3qcm.a
2hy3.a
3qce.a
3qcg.a
3qcd.a
[1] 3qch.a
0
0.2 0.2 0.3 0.5 0.9 2.1 2.0 1.9 3.5
[1] 3qci.a 0.2
0
0.2 0.3 0.6 0.8 2.1 2.0 1.9 3.4
[1] 3qcj.a 0.2 0.2
0
0.2 0.5 0.9 2.1 2.1 2.0 3.5
[1] 3qck.a 0.3 0.3 0.2
0
0.4 0.9 2.1 2.1 2.0 3.5
[1] 3qcl.a 0.5 0.6 0.5 0.4
0
0.7 2.2 2.1 2.1 3.6
[1] 3qcm.a 0.9 0.8 0.9 0.9 0.7
0
2.3 2.1 2.1 3.6
[2] 2hy3.a 2.1 2.1 2.1 2.1 2.2 2.3
0
0.9 0.6 1.7
[2] 3qce.a 2.0 2.0 2.1 2.1 2.1 2.1 0.9
0
0.6 1.8
[2] 3qcg.a 1.9 1.9 2.0 2.0 2.1 2.1 0.6 0.6
0
1.7
[3] 3qcd.a 3.5 3.4 3.5 3.5 3.6 3.6 1.7 1.8 1.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
3qch.a
3qci.a
3qcj.a
3qck.a
3qcl.a
3qcm.a
2hy3.a
3qce.a
3qcg.a
3qcd.a
[1] 3qch.a
0
0.3 0.4 0.4 0.6 1.0 2.2 2.1 1.9 3.5
[1] 3qci.a 0.3
0
0.5 0.5 0.7 1.1 2.3 2.1 1.9 3.8
[1] 3qcj.a 0.4 0.5
0
0.3 0.6 1.2 2.4 2.1 2.0 3.9
[1] 3qck.a 0.4 0.5 0.3
0
0.5 1.1 2.3 2.1 2.0 3.9
[1] 3qcl.a 0.6 0.7 0.6 0.5
0
1.1 2.4 2.2 2.1 4.0
[1] 3qcm.a 1.0 1.1 1.2 1.1 1.1
0
2.5 2.1 2.2 4.0
[2] 2hy3.a 2.2 2.3 2.4 2.3 2.4 2.5
0
1.3 1.0 2.2
[2] 3qce.a 2.1 2.1 2.1 2.1 2.2 2.1 1.3
0
0.9 2.0
[2] 3qcg.a 1.9 1.9 2.0 2.0 2.1 2.2 1.0 0.9
0
2.2
[3] 3qcd.a 3.5 3.8 3.9 3.9 4.0 4.0 2.2 2.0 2.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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