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PTN6_HUMAN_243_533_pep

Tyrosine-protein phosphatase non-receptor type 6 [Protein-tyrosine phosphatase family. Non-receptor class 2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTN6_HUMAN):D: Tyrosine-protein phosphatase (254:258, 275:279, 282, 358:360, 419, 420, 453:459, 492, 495:497, 500)
R: Substrate binding (453:459)
55, 56, 58:62, 67:71, 74, 254:258, 275:279, 282, 358:360, 419, 420, 453:459, 492, 495:497, 500

Full PDB list

1fpr, 1gwz, 2b3o, 3ps5, 4gry, 4grz, 4gs0, 4hjp, 4hjq (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
2
5
4
K
2
5
7
R
2
7
5
Y
2
7
6
K
2
7
7
N
2
7
8
I
2
7
9
F
2
8
2
R
3
5
8
K
3
6
0
C
4
5
3
S
4
5
4
A
4
5
5
G
4
5
6
I
4
5
7
G
4
5
8
R
4
5
9
R
4
9
2
S
4
9
6
G
4
9
7
Q
5
0
0
[1]1fpr.a EDTLTptrADLD85 . . . . . . . . . . S . . . . . . . . . .
[1]4gs0.b unk.unk.fty.unk33 - - . . . . . . . . . . . . . . . . . . .
[1]4hjq.b none . . . . . . . . . . S . . . . . . . . . .
[2]2b3o.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
Q
5
5
N
5
6
G
5
8
D
5
9
F
6
0
Y
6
1
D
6
2
E
6
7
K
6
8
F
6
9
A
7
0
T
7
1
E
7
4
Q
2
5
4
E
2
5
5
V
2
5
6
K
2
5
7
N
2
5
8
R
2
7
5
Y
2
7
6
K
2
7
7
N
2
7
8
I
2
7
9
F
2
8
2
R
3
5
8
N
3
5
9
K
3
6
0
D
4
1
9
H
4
2
0
C
4
5
3
S
4
5
4
A
4
5
5
G
4
5
6
I
4
5
7
G
4
5
8
R
4
5
9
R
4
9
2
R
4
9
5
S
4
9
6
G
4
9
7
Q
5
0
0
[1]1fpr.a - - - - - - - - - - - - - . . . . . . . . . . . . . . . . S . . . * . . . . . . .
[1]4gs0.b - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . .
[1]4hjq.b - - - - - - - - - - - - - . * . . . . . . . . . . . . . . S . . . . . . . . . . .
[2]2b3o.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
1fpr.a:EDTLTptrADLD
4gs0.b:unk.unk.fty.unk
4hjq.b is apo
2b3o.a is apo
[1] 1fpr.a
1.7
1.7 - -
[1] 4gs0.b 4.1
0
- -
[1] 4hjq.b 6.8 1.2
-
-
[2] 2b3o.a 22 15 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1fpr.a
4gs0.b
4hjq.b
2b3o.a
[1] 1fpr.a
0
.09 .20 .65
[1] 4gs0.b .09
0
.15 .65
[1] 4hjq.b .20 .15
0
.70
[2] 2b3o.a .65 .65 .70
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.4 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
1fpr.a
4gs0.b
4hjq.b
2b3o.a
[1] 1fpr.a
0
2.1 3.2 2.8
[1] 4gs0.b 2.1
0
1.4 0.7
[1] 4hjq.b 3.2 1.4
0
1.9
[2] 2b3o.a 2.8 0.7 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1fpr.a
4gs0.b
4hjq.b
2b3o.a
[1] 1fpr.a
0
2.9 4.3 3.8
[1] 4gs0.b 2.9
0
2.2 1.4
[1] 4hjq.b 4.3 2.2
0
2.6
[2] 2b3o.a 3.8 1.4 2.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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