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PTN5_HUMAN_280_563

Tyrosine-protein phosphatase non-receptor type 5 [Protein-tyrosine phosphatase family. Non-receptor class subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTN5_HUMAN):D: Tyrosine-protein phosphatase (328, 330, 331, 400, 402, 403, 458:461, 463, 467, 496:502, 540, 541, 544)
R: Substrate binding (496:502)
328, 330, 331, 400, 402, 403, 458:461, 463, 467, 496:502, 540, 541, 544

Full PDB list

2bij, 2bv5, 2cjz, 5ovr, 5ovx, 5ow1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
3
2
8
I
3
3
1
N
4
0
0
E
4
0
2
E
4
0
3
S
4
5
8
W
4
5
9
P
4
6
0
D
4
6
1
K
4
6
3
R
4
6
7
C
4
9
6
S
4
9
7
A
4
9
8
G
4
9
9
I
5
0
0
G
5
0
1
R
5
0
2
Q
5
4
0
T
5
4
1
Q
5
4
4
[1]2bij.a none . . . . - . . . . . . . . . . . . . . . .
[1]2bv5.a none . . . . . . . . . . . * . . . . . . . . .
[1]2cjz.a ptr16 . . - - - . . . . . . S . . . . . . . . .
[1]5ovr.a axk28 . . . . . . . . . . . . . . . . . . . . .
[1]5ovx.a ay528 . . . . . . . . . . . . . . . . . . . . .
[1]5ow1.a ay826 . . . . . . . . . . . . . . . . . . . . .

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
3
2
8
T
3
3
0
I
3
3
1
N
4
0
0
E
4
0
2
E
4
0
3
S
4
5
8
W
4
5
9
P
4
6
0
D
4
6
1
K
4
6
3
R
4
6
7
C
4
9
6
S
4
9
7
A
4
9
8
G
4
9
9
I
5
0
0
G
5
0
1
R
5
0
2
Q
5
4
0
T
5
4
1
Q
5
4
4
[1]2bij.a . . . . . - . . . . . * . . . . . . . . . .
[1]2bv5.a . . . . . . . . . . . * scy . . . . . . . . .
[1]2cjz.a . . . - - - . . . . . . S . . . . . . . . .
[1]5ovr.a . . . . . . . . . . . . . . . . . . . . . .
[1]5ovx.a . . . . . . . . . . . . . . . . . . . . . .
[1]5ow1.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
2bij.a is apo
2bv5.a is apo
2cjz.a:ptr
5ovr.a:axk
5ovx.a:ay5
5ow1.a:ay8
[1] 2bij.a
-
- 0.5 1.9 1.8 0.1
[1] 2bv5.a -
-
2.5 1.5 1.4 0
[1] 2cjz.a - -
0
0 0 0
[1] 5ovr.a - - 0.5
0
0.1 0
[1] 5ovx.a - - 0.8 0.1
0
0
[1] 5ow1.a - - 1.0 2.3 1.9
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
2bij.a
2bv5.a
2cjz.a
5ovr.a
5ovx.a
5ow1.a
[1] 2bij.a
0
.13 .11 .09 .10 .07
[1] 2bv5.a .13
0
.18 .16 .17 .17
[1] 2cjz.a .11 .18
0
.03 .04 .15
[1] 5ovr.a .09 .16 .03
0
.02 .13
[1] 5ovx.a .10 .17 .04 .02
0
.14
[1] 5ow1.a .07 .17 .15 .13 .14
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
2bij.a
2bv5.a
2cjz.a
5ovr.a
5ovx.a
5ow1.a
[1] 2bij.a
0
0.3 0.4 0.3 0.2 0.2
[1] 2bv5.a 0.3
0
0.5 0.4 0.4 0.3
[1] 2cjz.a 0.4 0.5
0
0.4 0.5 0.4
[1] 5ovr.a 0.3 0.4 0.4
0
0.1 0.2
[1] 5ovx.a 0.2 0.4 0.5 0.1
0
0.2
[1] 5ow1.a 0.2 0.3 0.4 0.2 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
2bij.a
2bv5.a
2cjz.a
5ovr.a
5ovx.a
5ow1.a
[1] 2bij.a
0
0.5 1.1 0.8 0.8 0.7
[1] 2bv5.a 0.5
0
1.0 0.8 0.8 0.6
[1] 2cjz.a 1.1 1.0
0
0.8 0.8 1.0
[1] 5ovr.a 0.8 0.8 0.8
0
0.2 0.8
[1] 5ovx.a 0.8 0.8 0.8 0.2
0
0.8
[1] 5ow1.a 0.7 0.6 1.0 0.8 0.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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