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PHP_SULSO_1_314

Aryldialkylphosphatase [Metallo-dependent hydrolases superfamily. Phosphotriesterase family]

Composition of the binding site

Protein chains homodimer
A1 (PHP_SULSO):22, 24, 27, 72, 97, 99, 137, 170, 199, 223, 226, 228, 229, 256, 258, 261, 263:268, 270, 271, 274, 275, 27822, 24, 27, 72, 97, 99, 137, 170, 199, 223, 226, 228, 229, 256, 258, 261, 263:268, 270, 271, 274, 275, 278
A2 (PHP_SULSO):104, 107, 108104, 107, 108
Metals (Me):Co/Fe

Full PDB list

2vc5, 2vc7, 3uf9, 4g2d, 4ker, 4kes, 4ket, 4keu, 4kev, 4kez, 4kf1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
H
2
4
V
2
7
L
7
2
Y
9
7
Y
9
9
K
1
3
7
H
1
7
0
H
1
9
9
R
2
2
3
L
2
2
6
L
2
2
8
F
2
2
9
D
2
5
6
C
2
5
8
I
2
6
1
W
2
6
3
T
2
6
5
A
2
6
6
K
2
6
7
P
2
6
8
Y
2
7
0
K
2
7
1
L
2
7
4
A
2
7
5
W
2
7
8
F
1
0
4
L
1
0
7
N
1
0
8
[1]2vc5.a none . . . . . * . . . . . . . . . . . . . . . . . . . . . . Co,Fe
[1]2vc7.b ht518 . . . . . * . . . . . . . . . . . . . . . . . . . . . . Co,Fe
[1]3uf9.c fst18 . . . . . * . . . . . . . . . . . . . . . . . . . . . . Co,Fe
[1]4g2d.a none . . . . . * . . . . . . . . . . . . R . L . . . . - - - Co,Fe
[1]4ker.c none . . . . . * . . . . . . . . . V . . . . . . . . . . . . Co,Fe
[1]4kes.a none . . . . . * . . . . . . . . . T . . . . . . . . . . . . Co,Fe
[1]4ket.b none . . . . . * . . . . . . . . . I . . . . . . . . . . . . Co,Fe
[1]4ket.d pg413 . . . . . * . . . . . . . . . I . . . . . . . . . . . . Co,Fe
[1]4keu.a none . . . . . * . . . . . . . . . M . . . . . . . . . . . . Co,Fe
[1]4kev.c none . . . . . * . . . . . . . . . L . . . . . . . . . . . . Co,Fe
[1]4kez.a none . . . . . * . . . . . . . . . F . . . . . . . . . . . . Co,Fe
[1]4kf1.d ht5,pg431 . . . . . * . . . . . . . . . I . . . . . . . . . . . . Co,Fe

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 A2 Me
H
2
2
H
2
4
V
2
7
L
7
2
Y
9
7
Y
9
9
K
1
3
7
H
1
7
0
H
1
9
9
R
2
2
3
L
2
2
6
L
2
2
8
F
2
2
9
D
2
5
6
C
2
5
8
I
2
6
1
W
2
6
3
G
2
6
4
T
2
6
5
A
2
6
6
K
2
6
7
P
2
6
8
Y
2
7
0
K
2
7
1
L
2
7
4
A
2
7
5
W
2
7
8
F
1
0
4
L
1
0
7
N
1
0
8
[1]2vc5.a . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . Co,Fe
[1]2vc7.b . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . Co,Fe
[1]3uf9.c . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . Co,Fe
[1]4g2d.a . . . . . . * . . . . . . . . . * . . . R . L . . . . - - - Co,Fe
[1]4ker.c . . . . . . * . . . . . . . . . V . . . . . . . . . . . . . Co,Fe
[1]4kes.a . . . . . . * . . . . . . . . . T . . . . . . . . . . . . . Co,Fe
[1]4ket.b . . . . . . * . . . . . . . . . I . . . . . . . . . . . . . Co,Fe
[1]4ket.d . . . . . . * . . . . . . . . . I . . . . . . . . . . . . . Co,Fe
[1]4keu.a . . . . . . * . . . . . . . . . M . . . . . . . . . . . . . Co,Fe
[1]4kev.c . . . . . . * . . . . . . . . . L . * * . . . . . . . . . . Co,Fe
[1]4kez.a . . . . . . * . . . . . . . . . F . . . . . . . . . . . . . Co,Fe
[1]4kf1.d . . . . . . * . . . . . . . . . I . . . . . . . . . . . . . Co,Fe

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
2vc5.a is apo
2vc7.b:ht5
3uf9.c:fst
4g2d.a is apo
4ker.c is apo
4kes.a is apo
4ket.b is apo
4ket.d:pg4
4keu.a is apo
4kev.c is apo
4kez.a is apo
4kf1.d:ht5,pg4
[1] 2vc5.a
-
0.3 0.5 - - - - 0.1 - - - 3.7
[1] 2vc7.b -
0.1
0.2 - - - - 0 - - - 3.4
[1] 3uf9.c - 0
0.2
- - - - 0 - - - 4.2
[1] 4g2d.a - 0.3 0.4
-
- - - 0.3 - - - 4.3
[1] 4ker.c - 0.1 0.2 -
-
- - 0.1 - - - 0.2
[1] 4kes.a - 0.1 0.2 - -
-
- 0 - - - 0.3
[1] 4ket.b - 0.1 0.5 - - -
-
0 - - - 0.3
[1] 4ket.d - 0.1 0.5 - - - -
0
- - - 0.2
[1] 4keu.a - 0 0.2 - - - - 0
-
- - 0.5
[1] 4kev.c - 3.1 2.4 - - - - 3.1 -
-
- 3.1
[1] 4kez.a - 0.1 0.2 - - - - 0 - -
-
2.0
[1] 4kf1.d - 0.1 0.5 - - - - 0 - - -
0.2
[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
2vc5.a
2vc7.b
3uf9.c
4g2d.a
4ker.c
4kes.a
4ket.b
4ket.d
4keu.a
4kev.c
4kez.a
4kf1.d
[1] 2vc5.a
0
.02 .04 .03 .13 .13 .12 .11 .12 .18 .06 .11
[1] 2vc7.b .02
0
.03 .04 .10 .11 .10 .10 .10 .18 .05 .10
[1] 3uf9.c .04 .03
0
.03 .14 .13 .12 .12 .13 .21 .07 .12
[1] 4g2d.a .03 .04 .03
0
.15 .15 .14 .14 .14 .20 .09 .14
[1] 4ker.c .13 .10 .14 .15
0
.01 .02 .01 .01 .13 .06 .01
[1] 4kes.a .13 .11 .13 .15 .01
0
.01 .01 .02 .14 .06 .01
[1] 4ket.b .12 .10 .12 .14 .02 .01
0
0 .01 .13 .05 0
[1] 4ket.d .11 .10 .12 .14 .01 .01 0
0
.01 .12 .05 0
[1] 4keu.a .12 .10 .13 .14 .01 .02 .01 .01
0
.12 .06 .01
[1] 4kev.c .18 .18 .21 .20 .13 .14 .13 .12 .12
0
.14 .12
[1] 4kez.a .06 .05 .07 .09 .06 .06 .05 .05 .06 .14
0
.05
[1] 4kf1.d .11 .10 .12 .14 .01 .01 0 0 .01 .12 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2vc5.a
2vc7.b
3uf9.c
4g2d.a
4ker.c
4kes.a
4ket.b
4ket.d
4keu.a
4kev.c
4kez.a
4kf1.d
[1] 2vc5.a
0
0.8 0.8 0.4 0.9 0.8 0.9 1.0 0.8 1.4 0.8 1.0
[1] 2vc7.b 0.8
0
0.6 0.8 0.7 0.6 0.8 0.8 0.7 1.5 0.7 0.8
[1] 3uf9.c 0.8 0.6
0
0.7 0.5 0.6 0.5 0.6 0.5 1.4 0.4 0.6
[1] 4g2d.a 0.4 0.8 0.7
0
0.9 0.9 1.0 1.0 0.9 1.5 0.8 1.1
[1] 4ker.c 0.9 0.7 0.5 0.9
0
0.4 0.3 0.3 0.3 1.5 0.3 0.3
[1] 4kes.a 0.8 0.6 0.6 0.9 0.4
0
0.4 0.4 0.4 1.5 0.4 0.5
[1] 4ket.b 0.9 0.8 0.5 1.0 0.3 0.4
0
0.1 0.2 1.6 0.2 0.2
[1] 4ket.d 1.0 0.8 0.6 1.0 0.3 0.4 0.1
0
0.3 1.6 0.3 0.1
[1] 4keu.a 0.8 0.7 0.5 0.9 0.3 0.4 0.2 0.3
0
1.5 0.2 0.3
[1] 4kev.c 1.4 1.5 1.4 1.5 1.5 1.5 1.6 1.6 1.5
0
1.5 1.6
[1] 4kez.a 0.8 0.7 0.4 0.8 0.3 0.4 0.2 0.3 0.2 1.5
0
0.4
[1] 4kf1.d 1.0 0.8 0.6 1.1 0.3 0.5 0.2 0.1 0.3 1.6 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2vc5.a
2vc7.b
3uf9.c
4g2d.a
4ker.c
4kes.a
4ket.b
4ket.d
4keu.a
4kev.c
4kez.a
4kf1.d
[1] 2vc5.a
0
1.1 1.1 0.8 1.3 1.2 1.2 1.2 1.4 2.0 1.2 1.3
[1] 2vc7.b 1.1
0
0.8 1.0 1.0 0.9 1.0 1.1 1.2 2.0 0.9 1.0
[1] 3uf9.c 1.1 0.8
0
0.9 0.9 0.8 0.9 0.9 1.2 2.0 0.8 0.9
[1] 4g2d.a 0.8 1.0 0.9
0
1.1 1.0 1.1 1.1 1.0 1.8 0.9 1.1
[1] 4ker.c 1.3 1.0 0.9 1.1
0
0.6 0.5 0.6 1.0 1.9 0.5 0.5
[1] 4kes.a 1.2 0.9 0.8 1.0 0.6
0
0.5 0.6 0.9 1.9 0.5 0.6
[1] 4ket.b 1.2 1.0 0.9 1.1 0.5 0.5
0
0.4 0.9 1.9 0.4 0.4
[1] 4ket.d 1.2 1.1 0.9 1.1 0.6 0.6 0.4
0
0.9 1.9 0.6 0.5
[1] 4keu.a 1.4 1.2 1.2 1.0 1.0 0.9 0.9 0.9
0
1.7 0.9 0.9
[1] 4kev.c 2.0 2.0 2.0 1.8 1.9 1.9 1.9 1.9 1.7
0
1.9 2.0
[1] 4kez.a 1.2 0.9 0.8 0.9 0.5 0.5 0.4 0.6 0.9 1.9
0
0.5
[1] 4kf1.d 1.3 1.0 0.9 1.1 0.5 0.6 0.4 0.5 0.9 2.0 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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