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YOPH_YERPS_188_468

Tyrosine-protein phosphatase YopH [Protein-tyrosine phosphatase family. Non-receptor class subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (YOPH_YERPS):D: Tyrosine-protein phosphatase (205, 229:232, 356:358, 402:410, 443, 446, 447, 450)205, 229:232, 356:358, 402:410, 443, 446, 447, 450

Full PDB list

1lyv, 1pa9, 1qz0, 1xxp, 1xxv, 1ypt, 1ytn, 1yts, 1ytw, 2i42, 2y2f, 2ydu, 3blt, 3blu, 3bm8, 3f99, 3f9a, 3f9b, 3u96, 4yaa, 4z6b, 4zi4, 4zn5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
2
9
R
2
3
0
D
2
3
1
I
2
3
2
D
3
5
6
Q
3
5
7
H
4
0
2
C
4
0
3
R
4
0
4
A
4
0
5
G
4
0
6
V
4
0
7
G
4
0
8
R
4
0
9
T
4
1
0
I
4
4
3
Q
4
4
6
K
4
4
7
Q
4
5
0
[1]1lyv.a none . . . . . . . S . . . . . . . . . . .
[1]1pa9.a csn15 . . . . . . . . . . . . . . . . . . .
[1]1qz0.a DEftyLnh244 . . . . . . . . . . . . . . . . . . .
[1]1xxp.a ptr16 . . . . . . . S . . . . . . . . . . .
[1]1ytn.a none . . . . . . . . . . . . . . . . . . .
[1]1ytw.a wo45 . . . . . . . . . . . . . . . . . . .
[1]2i42.a v1 . . . . . . . . . . . . . . . . . . .
[1]2y2f.a yi122 . . . . . . . . . . . . . . . . . . .
[1]2ydu.a 79w16 . . . . . . . . . . . . . . . . . . .
[1]3blu.a pvs11 . . . . . . . * . . . . . . . . . . .
[1]3bm8.a psy12 . . . . A . . * . . . . . . . . . . .
[1]3f9b.a pdv9 . . . . . . . . . . . . . . . . . . .
[1]3u96.b csn15 . . . . . F . . . . . . . . . . . . .
[1]4zi4.a dvg13 . . . . . . . . . . . . . . . . . . .
[2]3blt.a psy12 . . . . . . . * . . . . . . . . . . .

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
2
0
5
F
2
2
9
R
2
3
0
D
2
3
1
I
2
3
2
D
3
5
6
Q
3
5
7
T
3
5
8
H
4
0
2
C
4
0
3
R
4
0
4
A
4
0
5
G
4
0
6
V
4
0
7
G
4
0
8
R
4
0
9
T
4
1
0
I
4
4
3
Q
4
4
6
K
4
4
7
Q
4
5
0
[1]1lyv.a . . . . . * * . . S . . . . . . . . * . .
[1]1pa9.a . . . . . . * . . * . . . . . . . . . . .
[1]1qz0.a . . . * . . . . . * . . . . . . . . . . .
[1]1xxp.a . . . * . . . . . S . . . . . . . . . . .
[1]1ytn.a . . * . . * . . . * . . . . . . . . . . .
[1]1ytw.a . . * . . * . . . * . . . . . . . . . . .
[1]2i42.a . . . . . * . . . * . . . . . . . . * . .
[1]2y2f.a . . . . . . . . . * . . . . . . . . . . .
[1]2ydu.a . . . . . * . . . * . . . . . . . . * . .
[1]3blu.a . . * . . * . . . * . . . . . . . . * . .
[1]3bm8.a . . * . . A . . . * . . . . . . . . * . .
[1]3f9b.a . . * * . . . . . * . . . . . . . . * . .
[1]3u96.b . . * . . . F . . * . . . . . . . . . . .
[1]4zi4.a . . . . . . . . . * . . . . . . . . * . .
[2]3blt.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
1lyv.a is apo
1pa9.a:csn
1qz0.a:DEftyLnh2
1xxp.a:ptr
1ytn.a is apo
1ytw.a:wo4
2i42.a:v
2y2f.a:yi1
2ydu.a:79w
3blu.a:pvs
3bm8.a:psy
3f9b.a:pdv
3u96.b:csn
4zi4.a:dvg
3blt.a:psy
[1] 1lyv.a
-
1.3 1.7 0.9 - 0.1 0 1.6 1.4 1.5 1.0 1.7 1.0 2.3 2.4
[1] 1pa9.a -
0
0.6 0.3 - 0.1 0.1 0.5 0.3 1.4 0.8 1.3 0.2 1.7 1.9
[1] 1qz0.a - 0
0
0.3 - 0 0.1 0.9 0 1.3 0.5 0.8 0 0.8 1.9
[1] 1xxp.a - 0.1 0.2
0
- 0 0 1.1 0.2 1.0 0.5 0.8 0 1.0 1.9
[1] 1ytn.a - 0.5 2.7 0.6
-
0.2 0.1 1.2 0.8 1.4 0.8 1.6 0.4 1.8 2.3
[1] 1ytw.a - 0.3 2.3 0.5 -
0
0.1 1.3 0.4 1.2 0.8 1.3 0.3 2.0 2.3
[1] 2i42.a - 1.2 2.0 0.8 - 0.1
0.1
2.2 0.8 1.2 1.1 1.4 1.0 2.3 2.4
[1] 2y2f.a - 0 0.1 0.2 - 0 0.1
0
0 1.2 0.5 0.6 0 0.9 1.9
[1] 2ydu.a - 0.9 1.0 0.4 - 0 0.1 1.2
0.3
1.3 0.9 1.0 0.7 1.5 2.0
[1] 3blu.a - 0.9 2.8 0.5 - 0 0 1.6 1.0
0.8
0.5 1.5 0.7 2.1 1.4
[1] 3bm8.a - 0.5 2.1 0.6 - 0.1 0.3 1.3 0.7 1.5
0.5
0.8 0.5 1.1 2.0
[1] 3f9b.a - 1.3 1.6 0.2 - 0 0.1 1.6 0.2 1.2 0.7
0.2
0.8 0.1 2.0
[1] 3u96.b - 0 1.8 0.5 - 0 0.1 0.2 0.1 1.4 0.8 0.9
0.1
1.5 2.0
[1] 4zi4.a - 1.5 1.9 0.5 - 0 0.1 1.4 0.2 1.2 0.7 0.3 1.0
0.1
2.0
[2] 3blt.a - 0.9 4.3 0.4 - 0 0 2.0 0.8 0.5 0.4 1.3 0.5 1.9
0.8
[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
1lyv.a
1pa9.a
1qz0.a
1xxp.a
1ytn.a
1ytw.a
2i42.a
2y2f.a
2ydu.a
3blu.a
3bm8.a
3f9b.a
3u96.b
4zi4.a
3blt.a
[1] 1lyv.a
0
.09 .18 .16 .15 .16 .06 .13 .07 .16 .16 .21 .18 .21 .30
[1] 1pa9.a .09
0
.10 .09 .16 .16 .13 .06 .08 .20 .15 .20 .10 .20 .30
[1] 1qz0.a .18 .10
0
.04 .21 .16 .15 .05 .13 .27 .15 .14 .16 .18 .31
[1] 1xxp.a .16 .09 .04
0
.20 .14 .11 .07 .13 .23 .15 .15 .17 .19 .27
[1] 1ytn.a .15 .16 .21 .20
0
.09 .16 .17 .11 .11 .11 .19 .11 .18 .20
[1] 1ytw.a .16 .16 .16 .14 .09
0
.13 .17 .15 .14 .11 .16 .12 .18 .16
[1] 2i42.a .06 .13 .15 .11 .16 .13
0
.13 .09 .15 .15 .18 .23 .18 .24
[1] 2y2f.a .13 .06 .05 .07 .17 .17 .13
0
.09 .22 .13 .17 .11 .18 .31
[1] 2ydu.a .07 .08 .13 .13 .11 .15 .09 .09
0
.16 .14 .17 .19 .18 .28
[1] 3blu.a .16 .20 .27 .23 .11 .14 .15 .22 .16
0
.13 .21 .19 .19 .15
[1] 3bm8.a .16 .15 .15 .15 .11 .11 .15 .13 .14 .13
0
.10 .13 .10 .22
[1] 3f9b.a .21 .20 .14 .15 .19 .16 .18 .17 .17 .21 .10
0
.20 .05 .28
[1] 3u96.b .18 .10 .16 .17 .11 .12 .23 .11 .19 .19 .13 .20
0
.20 .26
[1] 4zi4.a .21 .20 .18 .19 .18 .18 .18 .18 .18 .19 .10 .05 .20
0
.27
[2] 3blt.a .30 .30 .31 .27 .20 .16 .24 .31 .28 .15 .22 .28 .26 .27
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1lyv.a
1pa9.a
1qz0.a
1xxp.a
1ytn.a
1ytw.a
2i42.a
2y2f.a
2ydu.a
3blu.a
3bm8.a
3f9b.a
3u96.b
4zi4.a
3blt.a
[1] 1lyv.a
0
0.2 0.4 0.4 0.3 0.3 0.2 0.3 0.2 0.3 0.4 1.4 0.3 1.5 0.4
[1] 1pa9.a 0.2
0
0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.4 1.3 0.2 1.5 0.4
[1] 1qz0.a 0.4 0.3
0
0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.5 1.3 0.3 1.5 0.4
[1] 1xxp.a 0.4 0.3 0.3
0
0.4 0.3 0.4 0.4 0.3 0.5 0.5 1.4 0.3 1.4 0.5
[1] 1ytn.a 0.3 0.3 0.3 0.4
0
0.3 0.2 0.3 0.2 0.4 0.5 1.4 0.3 1.5 0.4
[1] 1ytw.a 0.3 0.3 0.3 0.3 0.3
0
0.2 0.3 0.2 0.3 0.4 1.4 0.4 1.5 0.4
[1] 2i42.a 0.2 0.3 0.3 0.4 0.2 0.2
0
0.3 0.2 0.3 0.4 1.4 0.3 1.5 0.3
[1] 2y2f.a 0.3 0.3 0.3 0.4 0.3 0.3 0.3
0
0.2 0.3 0.5 1.4 0.4 1.5 0.4
[1] 2ydu.a 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.2
0
0.3 0.4 1.3 0.3 1.4 0.3
[1] 3blu.a 0.3 0.3 0.4 0.5 0.4 0.3 0.3 0.3 0.3
0
0.4 1.5 0.4 1.6 0.2
[1] 3bm8.a 0.4 0.4 0.5 0.5 0.5 0.4 0.4 0.5 0.4 0.4
0
1.4 0.5 1.6 0.5
[1] 3f9b.a 1.4 1.3 1.3 1.4 1.4 1.4 1.4 1.4 1.3 1.5 1.4
0
1.3 0.3 1.5
[1] 3u96.b 0.3 0.2 0.3 0.3 0.3 0.4 0.3 0.4 0.3 0.4 0.5 1.3
0
1.4 0.5
[1] 4zi4.a 1.5 1.5 1.5 1.4 1.5 1.5 1.5 1.5 1.4 1.6 1.6 0.3 1.4
0
1.6
[2] 3blt.a 0.4 0.4 0.4 0.5 0.4 0.4 0.3 0.4 0.3 0.2 0.5 1.5 0.5 1.6
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
1lyv.a
1pa9.a
1qz0.a
1xxp.a
1ytn.a
1ytw.a
2i42.a
2y2f.a
2ydu.a
3blu.a
3bm8.a
3f9b.a
3u96.b
4zi4.a
3blt.a
[1] 1lyv.a
0
1.1 1.1 1.1 0.9 1.1 0.8 1.4 0.4 0.9 1.1 2.4 0.9 2.4 1.2
[1] 1pa9.a 1.1
0
1.1 1.2 0.8 0.8 0.8 0.9 1.0 0.9 0.9 2.3 0.7 2.4 1.1
[1] 1qz0.a 1.1 1.1
0
1.0 1.0 0.9 0.8 1.3 1.0 1.0 0.8 2.1 0.9 2.2 1.0
[1] 1xxp.a 1.1 1.2 1.0
0
1.3 1.2 0.7 1.4 1.0 1.3 1.2 2.3 1.2 2.4 1.3
[1] 1ytn.a 0.9 0.8 1.0 1.3
0
0.7 0.8 1.1 0.8 0.8 0.9 2.3 0.7 2.4 0.9
[1] 1ytw.a 1.1 0.8 0.9 1.2 0.7
0
0.6 1.1 1.0 0.9 0.7 2.2 0.8 2.4 0.8
[1] 2i42.a 0.8 0.8 0.8 0.7 0.8 0.6
0
0.9 0.8 0.8 0.7 2.2 0.9 2.3 0.7
[1] 2y2f.a 1.4 0.9 1.3 1.4 1.1 1.1 0.9
0
1.3 1.1 1.1 2.4 1.0 2.4 1.2
[1] 2ydu.a 0.4 1.0 1.0 1.0 0.8 1.0 0.8 1.3
0
0.9 1.0 2.3 0.9 2.3 1.1
[1] 3blu.a 0.9 0.9 1.0 1.3 0.8 0.9 0.8 1.1 0.9
0
0.8 2.4 0.7 2.4 0.8
[1] 3bm8.a 1.1 0.9 0.8 1.2 0.9 0.7 0.7 1.1 1.0 0.8
0
2.1 0.8 2.1 0.7
[1] 3f9b.a 2.4 2.3 2.1 2.3 2.3 2.2 2.2 2.4 2.3 2.4 2.1
0
1.9 0.8 2.3
[1] 3u96.b 0.9 0.7 0.9 1.2 0.7 0.8 0.9 1.0 0.9 0.7 0.8 1.9
0
1.9 0.8
[1] 4zi4.a 2.4 2.4 2.2 2.4 2.4 2.4 2.3 2.4 2.3 2.4 2.1 0.8 1.9
0
2.4
[2] 3blt.a 1.2 1.1 1.0 1.3 0.9 0.8 0.7 1.2 1.1 0.8 0.7 2.3 0.8 2.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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