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APHA_ECOLI_26_237

Class B acid phosphatase [Class B bacterial acid phosphatase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (APHA_ECOLI):R: Substrate binding (137, 138)
69, 71, 77, 78, 81, 82, 85, 93, 95, 96, 102, 139, 170, 177, 195, 217:219
69, 71, 77, 78, 81, 82, 85, 93, 95, 96, 102, 137:139, 170, 177, 195, 217:219
Metals (Me):Co/Mg

Full PDB list

1n8n, 1n9k, 1rmq, 1rmt, 1rmy, 1z5g, 1z5u, 2b82, 2b8j, 2g1a, 2heg, 2hf7, 3cz4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
6
9
D
7
1
S
7
7
S
7
8
F
8
1
W
8
2
K
8
5
Y
9
5
L
9
6
W
1
0
2
G
1
3
8
R
1
3
9
D
1
7
0
K
1
7
7
T
2
1
7
Y
2
1
8
[1]1rmq.a os1 . . . . . . . . . . . . . . . . Co
[1]1rmy.b dcz16 . . . . . . . . . . . . . . . . Mg
[1]1z5g.d none . . . . . . . . . . . . . . . . Mg
[1]1z5u.d cmp22 . . . . . . . . . . . . . . . . Mg
[1]2b82.a adn19 . . . . . . . . . . . . . . . . Mg
[1]2b8j.a au,spm15 . . . . . . . . . . . . . . . . Mg
[1]2g1a.b 5hg18 . . . . . . . . . . . . . . . . Mg
[1]2heg.a none * . . . . . . . . . . . . . . . Mg
[1]2hf7.a al1 . . . . . . . . . . . . . . . . Mg
[1]3cz4.a none . . . . . . . . . . . . . . . . Mg

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 Me
D
6
9
D
7
1
S
7
7
S
7
8
F
8
1
W
8
2
K
8
5
E
9
3
Y
9
5
L
9
6
W
1
0
2
T
1
3
7
G
1
3
8
R
1
3
9
D
1
7
0
K
1
7
7
N
1
9
5
T
2
1
7
Y
2
1
8
K
2
1
9
[1]1rmq.a . . . . . . . . . . . . . . . . . . . . Co
[1]1rmy.b . . . . . . . . . . . . . . . . . . . . Mg
[1]1z5g.d . . . . . . . D . . . . . . . . . . . . Mg
[1]1z5u.d . . . . . . . D . . . . . . . . . . . . Mg
[1]2b82.a . . . . . . . . . . . . . . . . . . . . Mg
[1]2b8j.a . . . . . . . . . . . . . . . . . . . . Mg
[1]2g1a.b . . . . . . . . . . . . . . . . . . . . Mg
[1]2heg.a bfd . . . . . . . . . . . . . . . . . . . Mg
[1]2hf7.a . . . . . . . . . . . . . . . . . . . . Mg
[1]3cz4.a . . . . . . . . . . . . . . . . . . . . Mg

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
1rmq.a:os
1rmy.b:dcz
1z5g.d is apo
1z5u.d:cmp
2b82.a:adn
2b8j.a:au,spm
2g1a.b:5hg
2heg.a is apo
2hf7.a:al
3cz4.a is apo
[1] 1rmq.a
0.1
0 - 0.2 0 0 0.1 - 0.1 -
[1] 1rmy.b 0.1
0
- 0.3 0 0.1 0.2 - 0.1 -
[1] 1z5g.d 0.1 0
-
0.3 0 0.1 0.1 - 0.1 -
[1] 1z5u.d 0.1 0 -
0
0 0.1 0.1 - 0.1 -
[1] 2b82.a 0.1 0 - 0.3
0
0.1 0.1 - 0.1 -
[1] 2b8j.a 0.1 0 - 0.3 0
0
0 - 0.1 -
[1] 2g1a.b 0.1 0 - 0.3 0 0.1
0.1
- 0.1 -
[1] 2heg.a 1.5 0 - 0.9 0 0 1.2
-
1.9 -
[1] 2hf7.a 0.1 0 - 0.2 0 0.1 0.1 -
0.1
-
[1] 3cz4.a 0.1 0 - 0 0 0 0.1 - 0.1
-
[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
1rmq.a
1rmy.b
1z5g.d
1z5u.d
2b82.a
2b8j.a
2g1a.b
2heg.a
2hf7.a
3cz4.a
[1] 1rmq.a
0
.01 .01 .01 .01 .01 .01 .09 0 .01
[1] 1rmy.b .01
0
0 .02 0 .01 0 .09 .01 .02
[1] 1z5g.d .01 0
0
.02 0 .01 0 .09 .01 .02
[1] 1z5u.d .01 .02 .02
0
.02 .02 .02 .10 .01 0
[1] 2b82.a .01 0 0 .02
0
.01 0 .09 .01 .02
[1] 2b8j.a .01 .01 .01 .02 .01
0
.01 .09 .01 .02
[1] 2g1a.b .01 0 0 .02 0 .01
0
.09 .01 .02
[1] 2heg.a .09 .09 .09 .10 .09 .09 .09
0
.09 .10
[1] 2hf7.a 0 .01 .01 .01 .01 .01 .01 .09
0
.01
[1] 3cz4.a .01 .02 .02 0 .02 .02 .02 .10 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1rmq.a
1rmy.b
1z5g.d
1z5u.d
2b82.a
2b8j.a
2g1a.b
2heg.a
2hf7.a
3cz4.a
[1] 1rmq.a
0
0.2 0.3 0.3 0.3 0.2 0.2 0.2 0.2 1.3
[1] 1rmy.b 0.2
0
0.2 0.3 0.3 0.2 0.2 0.1 0.1 1.4
[1] 1z5g.d 0.3 0.2
0
0.2 0.3 0.2 0.2 0.2 0.2 1.3
[1] 1z5u.d 0.3 0.3 0.2
0
0.5 0.3 0.3 0.4 0.3 1.2
[1] 2b82.a 0.3 0.3 0.3 0.5
0
0.3 0.3 0.3 0.3 1.5
[1] 2b8j.a 0.2 0.2 0.2 0.3 0.3
0
0.2 0.2 0.2 1.4
[1] 2g1a.b 0.2 0.2 0.2 0.3 0.3 0.2
0
0.2 0.2 1.3
[1] 2heg.a 0.2 0.1 0.2 0.4 0.3 0.2 0.2
0
0.2 1.4
[1] 2hf7.a 0.2 0.1 0.2 0.3 0.3 0.2 0.2 0.2
0
1.3
[1] 3cz4.a 1.3 1.4 1.3 1.2 1.5 1.4 1.3 1.4 1.3
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
1rmq.a
1rmy.b
1z5g.d
1z5u.d
2b82.a
2b8j.a
2g1a.b
2heg.a
2hf7.a
3cz4.a
[1] 1rmq.a
0
0.6 0.7 0.7 0.7 0.5 0.5 0.4 0.5 1.3
[1] 1rmy.b 0.6
0
0.8 0.8 0.5 0.6 0.6 0.5 0.6 1.5
[1] 1z5g.d 0.7 0.8
0
0.3 0.8 0.6 0.6 0.6 0.7 1.4
[1] 1z5u.d 0.7 0.8 0.3
0
0.9 0.7 0.7 0.7 0.7 1.4
[1] 2b82.a 0.7 0.5 0.8 0.9
0
0.6 0.7 0.6 0.7 1.6
[1] 2b8j.a 0.5 0.6 0.6 0.7 0.6
0
0.4 0.3 0.5 1.4
[1] 2g1a.b 0.5 0.6 0.6 0.7 0.7 0.4
0
0.4 0.4 1.4
[1] 2heg.a 0.4 0.5 0.6 0.7 0.6 0.3 0.4
0
0.3 1.4
[1] 2hf7.a 0.5 0.6 0.7 0.7 0.7 0.5 0.4 0.3
0
1.4
[1] 3cz4.a 1.3 1.5 1.4 1.4 1.6 1.4 1.4 1.4 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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