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ALLC_ECOLI_1_411

Allantoate amidohydrolase [Peptidase M20 family]

Composition of the binding site

Protein chains monomer
A1 (ALLC_ECOLI):215, 286, 288, 382215, 286, 288, 382
Metals (Me):Mn/Zn

Full PDB list

1z2l, 2imo, 4pxd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
2
1
5
R
2
8
8
H
3
8
2
[1]1z2l.a 1al12 . . . Zn
[2]4pxd.a none . . . Mn

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
R
2
1
5
D
2
8
6
R
2
8
8
H
3
8
2
[1]1z2l.a . . . . Zn
[2]4pxd.a . . * . Mn

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
1z2l.a:1al
4pxd.a is apo
[1] 1z2l.a
0.1
-
[2] 4pxd.a 1.5
-
[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
1z2l.a
4pxd.a
[1] 1z2l.a
0
.35
[2] 4pxd.a .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.7 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
1z2l.a
4pxd.a
[1] 1z2l.a
0
5.9
[2] 4pxd.a 5.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.9 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
1z2l.a
4pxd.a
[1] 1z2l.a
0
5.4
[2] 4pxd.a 5.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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