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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, 256:271, 274, 275, 277, 27822, 24, 27, 72, 97, 99, 137, 170, 199, 223, 226, 228, 229, 256:271, 274, 275, 277, 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, 5vri, 5vrk, 5vsa, 5w3u, 5w3w, 5w3z (redundant Pocketome entry)

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
[1]5vri.a none . . . . . * . . . . . . . A . M . . . . . . . . . . . . Co,Fe
[1]5vsa.a none . . . . . * . . . . . . . L F - - - - - - . . . . . . . Co,Fe
[1]5w3u.b none . A . W F * . . . V . . . . - - - - - - - - - - . . . . Co,Fe
[1]5w3w.a none . A . W . * . . . . M . . . - - - - - - - - . . . . . . Co,Fe
[1]5w3z.c none . . I . F * . . . . M S . . - - - - - - - - - - . . . . Co,Fe
[2]5vsa.d none . . . . . * . . . . . . . L F A . . . . . . . . . . . . Co,Fe
[3]5w3z.d none . . I . F * . . . . M S . . . L . . . . . . . . . . . . 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
Y
2
5
7
C
2
5
8
C
2
5
9
T
2
6
0
I
2
6
1
D
2
6
2
W
2
6
3
G
2
6
4
T
2
6
5
A
2
6
6
K
2
6
7
P
2
6
8
E
2
6
9
Y
2
7
0
K
2
7
1
L
2
7
4
A
2
7
5
R
2
7
7
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
[1]5vri.a . . . . . . * . . . . . . . . A . . . . M . . . . . . . . . . . . . . . Co,Fe
[1]5vsa.a . . . . . . * . . . . . . . . L . . F - - - - - - - - - . . . . . . . . Co,Fe
[1]5w3u.b . . A . W F * . . . V . . . . . - - - - - - - - - - - - - - - . . . . . Co,Fe
[1]5w3w.a . . A . W . * . . . . M . . . . . - - - - - - - - - - - - . . . . . . * Co,Fe
[1]5w3z.c . . . I . F * . . . . M S . . . . - - - - - - - - - - - - - - . . . . . Co,Fe
[2]5vsa.d . . . . . . * . . . . . . . . L . . F . A . . . * * . . . . . . . . . . Co,Fe
[3]5w3z.d . . . I . F * . . . . M S . . . . . * * L * * * * . . . . . . . . . . . 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

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

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
5vri.a is apo
5vsa.a is apo
5w3u.b is apo
5w3w.a is apo
5w3z.c is apo
5vsa.d is apo
5w3z.d is apo
[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
- - - - - - -
[1] 5vri.a - 0.1 0.1 - - - - 0 - - - 1.0
-
- - - - - -
[1] 5vsa.a - 0.2 0.2 - - - - 0 - - - 0.3 -
-
- - - - -
[1] 5w3u.b - 0 0.1 - - - - 0 - - - 1.1 - -
-
- - - -
[1] 5w3w.a - 0.2 0.2 - - - - 0 - - - 1.0 - - -
-
- - -
[1] 5w3z.c - 0.2 0.2 - - - - 0 - - - 0.3 - - - -
-
- -
[2] 5vsa.d - 7.1 4.8 - - - - 7.0 - - - 7.5 - - - - -
-
-
[3] 5w3z.d - 7.5 8.3 - - - - 6.4 - - - 16 - - - - - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
2vc5.a
2vc7.b
3uf9.c
4g2d.a
4ker.c
4kes.a
4ket.b
4ket.d
4keu.a
4kev.c
4kez.a
4kf1.d
5vri.a
5vsa.a
5w3u.b
5w3w.a
5w3z.c
5vsa.d
5w3z.d
[1] 2vc5.a
0
.02 .03 .03 .10 .10 .09 .09 .09 .14 .05 .09 .08 .09 .13 .12 .11 .32 .38
[1] 2vc7.b .02
0
.03 .03 .08 .09 .08 .08 .08 .14 .04 .08 .07 .09 .11 .11 .09 .31 .38
[1] 3uf9.c .03 .03
0
.02 .11 .10 .09 .10 .10 .17 .06 .10 .08 .10 .12 .12 .11 .33 .38
[1] 4g2d.a .03 .03 .02
0
.12 .12 .11 .11 .11 .16 .07 .11 .10 .12 .14 .14 .12 .34 .36
[1] 4ker.c .10 .08 .11 .12
0
.01 .01 .01 .01 .10 .05 .01 .03 .01 .03 .03 .01 .23 .46
[1] 4kes.a .10 .09 .10 .12 .01
0
.01 .01 .02 .11 .05 .01 .03 .01 .03 .03 .01 .23 .46
[1] 4ket.b .09 .08 .09 .11 .01 .01
0
0 .01 .10 .04 0 .02 .01 .03 .03 .01 .24 .46
[1] 4ket.d .09 .08 .10 .11 .01 .01 0
0
.01 .10 .04 0 .02 .01 .04 .03 .02 .23 .46
[1] 4keu.a .09 .08 .10 .11 .01 .02 .01 .01
0
.09 .04 .01 .02 .02 .04 .04 .02 .24 .45
[1] 4kev.c .14 .14 .17 .16 .10 .11 .10 .10 .09
0
.11 .10 .08 .11 .13 .13 .11 .32 .36
[1] 4kez.a .05 .04 .06 .07 .05 .05 .04 .04 .04 .11
0
.04 .03 .05 .08 .07 .06 .27 .42
[1] 4kf1.d .09 .08 .10 .11 .01 .01 0 0 .01 .10 .04
0
.02 .01 .04 .03 .02 .23 .46
[1] 5vri.a .08 .07 .08 .10 .03 .03 .02 .02 .02 .08 .03 .02
0
.02 .05 .05 .03 .25 .44
[1] 5vsa.a .09 .09 .10 .12 .01 .01 .01 .01 .02 .11 .05 .01 .02
0
.03 .03 .01 .23 .47
[1] 5w3u.b .13 .11 .12 .14 .03 .03 .03 .04 .04 .13 .08 .04 .05 .03
0
.03 .03 .26 .48
[1] 5w3w.a .12 .11 .12 .14 .03 .03 .03 .03 .04 .13 .07 .03 .05 .03 .03
0
.03 .25 .49
[1] 5w3z.c .11 .09 .11 .12 .01 .01 .01 .02 .02 .11 .06 .02 .03 .01 .03 .03
0
.23 .46
[2] 5vsa.d .32 .31 .33 .34 .23 .23 .24 .23 .24 .32 .27 .23 .25 .23 .26 .25 .23
0
.64
[3] 5w3z.d .38 .38 .38 .36 .46 .46 .46 .46 .45 .36 .42 .46 .44 .47 .48 .49 .46 .64
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
2vc5.a
2vc7.b
3uf9.c
4g2d.a
4ker.c
4kes.a
4ket.b
4ket.d
4keu.a
4kev.c
4kez.a
4kf1.d
5vri.a
5vsa.a
5w3u.b
5w3w.a
5w3z.c
5vsa.d
5w3z.d
[1] 2vc5.a
0
0.8 0.8 0.5 0.9 0.9 0.9 1.0 0.9 1.5 0.8 1.0 0.7 0.8 0.7 0.7 1.3 1.5 6.0
[1] 2vc7.b 0.8
0
0.6 0.9 0.7 0.5 0.7 0.7 0.6 1.6 0.6 0.8 0.6 0.7 0.6 0.6 1.4 1.5 5.9
[1] 3uf9.c 0.8 0.6
0
0.8 0.5 0.6 0.5 0.6 0.5 1.6 0.5 0.6 0.6 0.7 0.6 0.7 1.5 1.6 5.8
[1] 4g2d.a 0.5 0.9 0.8
0
1.0 0.9 1.1 1.1 1.0 1.6 0.9 1.1 0.9 1.0 0.5 0.4 1.5 1.6 6.1
[1] 4ker.c 0.9 0.7 0.5 1.0
0
0.4 0.3 0.3 0.3 1.6 0.3 0.3 0.4 0.7 0.6 0.7 1.4 1.6 5.9
[1] 4kes.a 0.9 0.5 0.6 0.9 0.4
0
0.4 0.4 0.4 1.7 0.3 0.4 0.5 0.7 0.6 0.6 1.4 1.5 5.9
[1] 4ket.b 0.9 0.7 0.5 1.1 0.3 0.4
0
0.1 0.2 1.7 0.2 0.2 0.4 0.7 0.6 0.7 1.4 1.6 5.9
[1] 4ket.d 1.0 0.7 0.6 1.1 0.3 0.4 0.1
0
0.3 1.7 0.3 0.1 0.5 0.7 0.6 0.7 1.4 1.6 5.9
[1] 4keu.a 0.9 0.6 0.5 1.0 0.3 0.4 0.2 0.3
0
1.6 0.2 0.3 0.4 0.7 0.6 0.6 1.4 1.6 5.9
[1] 4kev.c 1.5 1.6 1.6 1.6 1.6 1.7 1.7 1.7 1.6
0
1.6 1.7 1.5 1.0 0.8 0.9 1.4 2.0 6.2
[1] 4kez.a 0.8 0.6 0.5 0.9 0.3 0.3 0.2 0.3 0.2 1.6
0
0.3 0.4 0.7 0.6 0.7 1.4 1.6 5.8
[1] 4kf1.d 1.0 0.8 0.6 1.1 0.3 0.4 0.2 0.1 0.3 1.7 0.3
0
0.5 0.7 0.7 0.8 1.5 1.6 6.0
[1] 5vri.a 0.7 0.6 0.6 0.9 0.4 0.5 0.4 0.5 0.4 1.5 0.4 0.5
0
0.7 0.6 0.7 1.5 1.5 6.1
[1] 5vsa.a 0.8 0.7 0.7 1.0 0.7 0.7 0.7 0.7 0.7 1.0 0.7 0.7 0.7
0
0.7 0.8 1.4 0.9 3.6
[1] 5w3u.b 0.7 0.6 0.6 0.5 0.6 0.6 0.6 0.6 0.6 0.8 0.6 0.7 0.6 0.7
0
0.5 1.2 0.6 0.9
[1] 5w3w.a 0.7 0.6 0.7 0.4 0.7 0.6 0.7 0.7 0.6 0.9 0.7 0.8 0.7 0.8 0.5
0
1.5 0.7 2.0
[1] 5w3z.c 1.3 1.4 1.5 1.5 1.4 1.4 1.4 1.4 1.4 1.4 1.4 1.5 1.5 1.4 1.2 1.5
0
1.5 1.6
[2] 5vsa.d 1.5 1.5 1.6 1.6 1.6 1.5 1.6 1.6 1.6 2.0 1.6 1.6 1.5 0.9 0.6 0.7 1.5
0
5.8
[3] 5w3z.d 6.0 5.9 5.8 6.1 5.9 5.9 5.9 5.9 5.9 6.2 5.8 6.0 6.1 3.6 0.9 2.0 1.6 5.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
5vri.a
5vsa.a
5w3u.b
5w3w.a
5w3z.c
5vsa.d
5w3z.d
[1] 2vc5.a
0
1.0 1.1 0.9 1.3 1.2 1.3 1.4 1.5 1.9 1.2 1.3 1.0 1.4 1.5 1.5 2.0 2.8 6.5
[1] 2vc7.b 1.0
0
0.8 1.1 1.1 0.9 1.0 1.1 1.2 2.0 0.9 1.0 0.8 1.2 1.4 1.4 2.0 2.7 6.4
[1] 3uf9.c 1.1 0.8
0
1.1 0.9 0.9 0.9 1.0 1.2 2.0 0.8 0.9 0.8 1.2 1.4 1.4 2.0 2.8 6.4
[1] 4g2d.a 0.9 1.1 1.1
0
1.3 1.1 1.2 1.3 1.1 1.8 1.0 1.2 1.0 1.0 0.8 0.9 2.1 2.2 6.2
[1] 4ker.c 1.3 1.1 0.9 1.3
0
0.6 0.6 0.6 1.1 2.0 0.7 0.6 0.8 1.2 1.4 1.4 1.9 2.7 6.3
[1] 4kes.a 1.2 0.9 0.9 1.1 0.6
0
0.5 0.7 0.9 1.9 0.5 0.6 0.6 1.1 1.3 1.4 1.9 2.7 6.4
[1] 4ket.b 1.3 1.0 0.9 1.2 0.6 0.5
0
0.5 0.9 2.0 0.5 0.5 0.6 1.1 1.3 1.4 1.9 2.8 6.4
[1] 4ket.d 1.4 1.1 1.0 1.3 0.6 0.7 0.5
0
1.1 2.0 0.7 0.6 0.8 1.2 1.5 1.4 1.9 2.8 6.4
[1] 4keu.a 1.5 1.2 1.2 1.1 1.1 0.9 0.9 1.1
0
1.8 0.9 1.0 1.0 1.0 0.9 1.2 2.3 2.7 6.3
[1] 4kev.c 1.9 2.0 2.0 1.8 2.0 1.9 2.0 2.0 1.8
0
1.9 2.0 1.8 1.1 1.1 1.2 2.2 2.6 6.6
[1] 4kez.a 1.2 0.9 0.8 1.0 0.7 0.5 0.5 0.7 0.9 1.9
0
0.5 0.5 1.1 1.3 1.3 2.0 2.8 6.3
[1] 4kf1.d 1.3 1.0 0.9 1.2 0.6 0.6 0.5 0.6 1.0 2.0 0.5
0
0.6 1.1 1.3 1.4 1.9 2.8 6.4
[1] 5vri.a 1.0 0.8 0.8 1.0 0.8 0.6 0.6 0.8 1.0 1.8 0.5 0.6
0
1.1 1.3 1.4 1.9 2.8 6.6
[1] 5vsa.a 1.4 1.2 1.2 1.0 1.2 1.1 1.1 1.2 1.0 1.1 1.1 1.1 1.1
0
1.1 1.1 2.2 1.6 4.5
[1] 5w3u.b 1.5 1.4 1.4 0.8 1.4 1.3 1.3 1.5 0.9 1.1 1.3 1.3 1.3 1.1
0
0.8 2.2 1.1 3.1
[1] 5w3w.a 1.5 1.4 1.4 0.9 1.4 1.4 1.4 1.4 1.2 1.2 1.3 1.4 1.4 1.1 0.8
0
2.2 1.1 3.5
[1] 5w3z.c 2.0 2.0 2.0 2.1 1.9 1.9 1.9 1.9 2.3 2.2 2.0 1.9 1.9 2.2 2.2 2.2
0
2.1 3.3
[2] 5vsa.d 2.8 2.7 2.8 2.2 2.7 2.7 2.8 2.8 2.7 2.6 2.8 2.8 2.8 1.6 1.1 1.1 2.1
0
6.3
[3] 5w3z.d 6.5 6.4 6.4 6.2 6.3 6.4 6.4 6.4 6.3 6.6 6.3 6.4 6.6 4.5 3.1 3.5 3.3 6.3
0
[Binding site full-atom RMSD matrix]







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