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ALYS_STRPN_224_318

Autolysin [N-acetylmuramoyl-L-alanine amidase 2 family]

Composition of the binding site

Protein chains monomer
A1 (ALYS_STRPN):219:222, 228, 249, 257, 274, 275219:222, 228, 249, 257, 274, 275

Full PDB list

1gvm, 1h8g, 1hcx, 2bml, 4iwt, 4x36 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
W
2
2
0
R
2
2
1
K
2
2
2
W
2
2
8
Y
2
4
9
M
2
5
7
K
2
7
4
E
2
7
5
[1]1hcx.a cht7 . . . . . . . .
[1]1hcx.b ddq14 . . . . . . . .
[1]2bml.a none . . . . . . . .
[1]2bml.b xed26 . . . . . . . .
[1]4iwt.a cht7 . K . . . . . .
[1]4x36.a cht7 . . . . . * . .

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
R
2
1
9
W
2
2
0
R
2
2
1
K
2
2
2
W
2
2
8
Y
2
4
9
M
2
5
7
K
2
7
4
E
2
7
5
[1]1hcx.a . . . . . . . . .
[1]1hcx.b . . . . . . . . .
[1]2bml.a . . . . . . . . .
[1]2bml.b . . . . . . . . .
[1]4iwt.a . . K . . . . . .
[1]4x36.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
1hcx.a:cht
1hcx.b:ddq
2bml.a is apo
2bml.b:xed
4iwt.a:cht
4x36.a:cht
[1] 1hcx.a
0
0 - 0 0 0
[1] 1hcx.b 0
0
- 0.1 0 0
[1] 2bml.a 0.1 0.1
-
0 0 0
[1] 2bml.b 0 0 -
0
0 0
[1] 4iwt.a 0 0 - 0
0
0
[1] 4x36.a 0.1 0 - 0 0
0
[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
1hcx.a
1hcx.b
2bml.a
2bml.b
4iwt.a
4x36.a
[1] 1hcx.a
0
.01 .02 0 0 .01
[1] 1hcx.b .01
0
.01 .01 .01 0
[1] 2bml.a .02 .01
0
.02 .02 .01
[1] 2bml.b 0 .01 .02
0
0 .01
[1] 4iwt.a 0 .01 .02 0
0
.01
[1] 4x36.a .01 0 .01 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1hcx.a
1hcx.b
2bml.a
2bml.b
4iwt.a
4x36.a
[1] 1hcx.a
0
0.4 0.5 0.4 0.3 0.4
[1] 1hcx.b 0.4
0
0.4 0.4 0.3 0.3
[1] 2bml.a 0.5 0.4
0
0.4 0.4 0.4
[1] 2bml.b 0.4 0.4 0.4
0
0.5 0.6
[1] 4iwt.a 0.3 0.3 0.4 0.5
0
0.3
[1] 4x36.a 0.4 0.3 0.4 0.6 0.3
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
1hcx.a
1hcx.b
2bml.a
2bml.b
4iwt.a
4x36.a
[1] 1hcx.a
0
1.3 1.4 1.4 1.3 1.5
[1] 1hcx.b 1.3
0
1.6 1.6 1.3 1.3
[1] 2bml.a 1.4 1.6
0
1.5 1.4 1.3
[1] 2bml.b 1.4 1.6 1.5
0
1.1 1.7
[1] 4iwt.a 1.3 1.3 1.4 1.1
0
1.1
[1] 4x36.a 1.5 1.3 1.3 1.7 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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