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PTN7_HUMAN_64_360_pep

Tyrosine-protein phosphatase non-receptor type 7 [Protein-tyrosine phosphatase family. Non-receptor class subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTN7_HUMAN):D: Tyrosine-protein phosphatase (124:128, 257, 258, 291:297, 335)
R: Substrate binding (291:297)
124:128, 257, 258, 291:297, 335

Full PDB list

1zc0, 2a3k, 2gp0, 2hvl, 2qdc, 2qdm, 2qdp, 3d42, 3d44, 3o4s, 3o4t, 3o4u (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
1
2
4
Y
1
2
5
K
1
2
6
T
1
2
7
I
1
2
8
D
2
5
7
H
2
5
8
C
2
9
1
S
2
9
2
A
2
9
3
G
2
9
4
I
2
9
5
G
2
9
6
R
2
9
7
Q
3
3
5
[1]2a3k.a none . . . . . . . . . . . . . . .
[1]2qdc.a none . . . . . A . . . . . . . . .
[1]2qdm.a none . . . . . A . S . . . . . . A
[1]2qdp.a none . . . . . . . S . . . . . . .
[1]3d42.a TEptrV39 . . . D . . . S . . . . . . .
[1]3d44.a DEptrV40 . . . D . . . S . . . . . . .

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
2
4
Y
1
2
5
K
1
2
6
T
1
2
7
I
1
2
8
D
2
5
7
H
2
5
8
C
2
9
1
S
2
9
2
A
2
9
3
G
2
9
4
I
2
9
5
G
2
9
6
R
2
9
7
Q
3
3
5
[1]2a3k.a . . . . . . . . . . . . . . .
[1]2qdc.a . . . . . A . . . . . . . . .
[1]2qdm.a . . . . . A . S . . . . . . A
[1]2qdp.a . . . . . . . S . . . . . . .
[1]3d42.a . . . D . . . S . . . . . . .
[1]3d44.a . . . D . . . S . . . . . . .

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
2a3k.a is apo
2qdc.a is apo
2qdm.a is apo
2qdp.a is apo
3d42.a:TEptrV
3d44.a:DEptrV
[1] 2a3k.a
-
- - - 0.1 0.1
[1] 2qdc.a -
-
- - 0.4 0.5
[1] 2qdm.a - -
-
- 0 0.1
[1] 2qdp.a - - -
-
0.4 0.4
[1] 3d42.a - - - -
0.1
0.4
[1] 3d44.a - - - - 0
0.1
[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
2a3k.a
2qdc.a
2qdm.a
2qdp.a
3d42.a
3d44.a
[1] 2a3k.a
0
.05 .01 .04 .03 .02
[1] 2qdc.a .05
0
.05 .03 .07 .05
[1] 2qdm.a .01 .05
0
.03 .02 .01
[1] 2qdp.a .04 .03 .03
0
.05 .03
[1] 3d42.a .03 .07 .02 .05
0
.03
[1] 3d44.a .02 .05 .01 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2a3k.a
2qdc.a
2qdm.a
2qdp.a
3d42.a
3d44.a
[1] 2a3k.a
0
0.4 0.3 0.4 0.3 0.3
[1] 2qdc.a 0.4
0
0.3 0.2 0.3 0.3
[1] 2qdm.a 0.3 0.3
0
0.3 0.2 0.3
[1] 2qdp.a 0.4 0.2 0.3
0
0.3 0.3
[1] 3d42.a 0.3 0.3 0.2 0.3
0
0.2
[1] 3d44.a 0.3 0.3 0.3 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2a3k.a
2qdc.a
2qdm.a
2qdp.a
3d42.a
3d44.a
[1] 2a3k.a
0
1.0 1.2 1.1 0.9 0.9
[1] 2qdc.a 1.0
0
1.0 0.2 0.8 0.6
[1] 2qdm.a 1.2 1.0
0
0.8 1.0 1.0
[1] 2qdp.a 1.1 0.2 0.8
0
0.8 0.7
[1] 3d42.a 0.9 0.8 1.0 0.8
0
0.6
[1] 3d44.a 0.9 0.6 1.0 0.7 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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