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AMPC_PSEAE_28_392

Beta-lactamase [Class-C beta-lactamase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPC_PSEAE):R: Substrate binding (342:344)
89, 90, 93, 145, 146, 177, 179, 239:242, 249, 319, 345:347, 373
89, 90, 93, 145, 146, 177, 179, 239:242, 249, 319, 342:347, 373

Full PDB list

2wzx, 2wzz, 3s1y, 3s22, 4gzb, 4hef, 4nk3, 4ooy, 4wyy, 4wz4, 4x68 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
8
9
S
9
0
L
1
4
5
Q
1
4
6
Y
1
7
7
N
1
7
9
V
2
3
9
G
2
4
0
P
2
4
1
G
2
4
2
Y
2
4
9
A
3
1
9
K
3
4
2
T
3
4
3
G
3
4
4
S
3
4
5
T
3
4
6
N
3
4
7
N
3
7
3
[1]2wzx.a zx022 . * . . . . . . . . . . . . . . . . .
[1]2wzz.a zx122 . * . . . . . . . . . . . . . . . . .
[1]3s1y.a s1y25 . * . . . . . . . . . . . . . . . . .
[1]3s22.a 3s221 . * . . . . . . . . . . . . . . . . .
[1]4gzb.a none . . . . . . . . . . . . . . . . . . .
[1]4nk3.a mk723 . * . . . . . . . . . . . . . . . . .
[1]4ooy.a nxl17 . * . . . . . . . . . . . . . . . . .
[1]4wyy.a 3vt23 . * . . . . . . . . . . . . . . . . .
[1]4wz4.a 3vu23 . * . . . . . . . . . . . . . . . . .
[1]4x68.a op021 . * . . . . . . . . . . . . . . . . .

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
G
8
9
S
9
0
K
9
3
L
1
4
5
Q
1
4
6
Y
1
7
7
N
1
7
9
V
2
3
9
G
2
4
0
P
2
4
1
G
2
4
2
Y
2
4
9
A
3
1
9
K
3
4
2
T
3
4
3
G
3
4
4
S
3
4
5
T
3
4
6
N
3
4
7
N
3
7
3
[1]2wzx.a . * . . . . . . . . . . . . . . . . . .
[1]2wzz.a . * . . . . . . . . . . . . . . . . . .
[1]3s1y.a . * . . . . . . . . . . . . . . . . . .
[1]3s22.a . * . . . . . . . . . . . . . . . . . .
[1]4gzb.a . * . . . * . . . . . . . . . . . . . .
[1]4nk3.a . * . . . . . . . . . . . . . . . . . .
[1]4ooy.a . * . . . . . . . . . . . . . . . . . .
[1]4wyy.a . * . . . . . . . . . . . . . . . . . .
[1]4wz4.a . * . . . . . . . . . . . . . . . . . .
[1]4x68.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
2wzx.a:zx0
2wzz.a:zx1
3s1y.a:s1y
3s22.a:3s2
4gzb.a is apo
4nk3.a:mk7
4ooy.a:nxl
4wyy.a:3vt
4wz4.a:3vu
4x68.a:op0
[1] 2wzx.a
0.4
0.4 0.8 0.6 - 0.5 0.8 0.9 0.8 0.6
[1] 2wzz.a 0.4
0.4
0.8 0.6 - 0.5 0.8 0.9 0.6 0.5
[1] 3s1y.a 0.7 0.8
0.9
0.9 - 1.0 1.3 1.4 1.5 0.9
[1] 3s22.a 0.6 0.6 0.8
0.6
- 0.6 1.0 0.7 0.6 0.4
[1] 4gzb.a 0.6 0.8 1.1 0.7
-
0.8 1.4 1.1 1.1 0.7
[1] 4nk3.a 0.6 0.7 0.8 0.8 -
0.6
0.9 1.1 1.1 0.6
[1] 4ooy.a 0.6 0.6 1.0 0.7 - 0.6
0.6
1.1 1.1 0.7
[1] 4wyy.a 0.4 0.4 0.7 0.6 - 0.5 0.9
0.4
0.4 0.7
[1] 4wz4.a 0.4 0.4 0.7 0.6 - 0.5 0.9 0.4
0.4
0.7
[1] 4x68.a 0.8 0.9 1.1 0.8 - 0.8 0.9 1.2 1.3
0.8
[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
2wzx.a
2wzz.a
3s1y.a
3s22.a
4gzb.a
4nk3.a
4ooy.a
4wyy.a
4wz4.a
4x68.a
[1] 2wzx.a
0
.01 .04 .03 .03 .03 .04 .04 .04 .04
[1] 2wzz.a .01
0
.04 .03 .03 .02 .03 .04 .04 .03
[1] 3s1y.a .04 .04
0
.07 .07 .06 .06 .08 .08 .06
[1] 3s22.a .03 .03 .07
0
.05 .04 .06 .03 .03 .05
[1] 4gzb.a .03 .03 .07 .05
0
.05 .05 .05 .05 .05
[1] 4nk3.a .03 .02 .06 .04 .05
0
.02 .06 .06 .01
[1] 4ooy.a .04 .03 .06 .06 .05 .02
0
.06 .06 .02
[1] 4wyy.a .04 .04 .08 .03 .05 .06 .06
0
0 .07
[1] 4wz4.a .04 .04 .08 .03 .05 .06 .06 0
0
.07
[1] 4x68.a .04 .03 .06 .05 .05 .01 .02 .07 .07
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
2wzx.a
2wzz.a
3s1y.a
3s22.a
4gzb.a
4nk3.a
4ooy.a
4wyy.a
4wz4.a
4x68.a
[1] 2wzx.a
0
0.1 0.4 0.2 0.3 0.3 0.3 0.4 0.4 0.3
[1] 2wzz.a 0.1
0
0.4 0.1 0.3 0.3 0.3 0.4 0.4 0.3
[1] 3s1y.a 0.4 0.4
0
0.3 0.5 0.5 0.5 0.6 0.6 0.5
[1] 3s22.a 0.2 0.1 0.3
0
0.3 0.3 0.3 0.4 0.3 0.3
[1] 4gzb.a 0.3 0.3 0.5 0.3
0
0.3 0.2 0.3 0.3 0.3
[1] 4nk3.a 0.3 0.3 0.5 0.3 0.3
0
0.2 0.2 0.2 0.2
[1] 4ooy.a 0.3 0.3 0.5 0.3 0.2 0.2
0
0.2 0.1 0.2
[1] 4wyy.a 0.4 0.4 0.6 0.4 0.3 0.2 0.2
0
0.1 0.3
[1] 4wz4.a 0.4 0.4 0.6 0.3 0.3 0.2 0.1 0.1
0
0.3
[1] 4x68.a 0.3 0.3 0.5 0.3 0.3 0.2 0.2 0.3 0.3
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
2wzx.a
2wzz.a
3s1y.a
3s22.a
4gzb.a
4nk3.a
4ooy.a
4wyy.a
4wz4.a
4x68.a
[1] 2wzx.a
0
0.1 0.5 0.3 0.7 0.6 0.7 0.6 0.5 0.5
[1] 2wzz.a 0.1
0
0.5 0.3 0.8 0.6 0.7 0.6 0.5 0.6
[1] 3s1y.a 0.5 0.5
0
0.4 0.8 0.6 0.8 0.7 0.7 0.7
[1] 3s22.a 0.3 0.3 0.4
0
0.8 0.6 0.8 0.6 0.5 0.6
[1] 4gzb.a 0.7 0.8 0.8 0.8
0
0.6 0.8 0.7 0.8 0.6
[1] 4nk3.a 0.6 0.6 0.6 0.6 0.6
0
0.6 0.6 0.6 0.2
[1] 4ooy.a 0.7 0.7 0.8 0.8 0.8 0.6
0
0.7 0.7 0.6
[1] 4wyy.a 0.6 0.6 0.7 0.6 0.7 0.6 0.7
0
0.3 0.6
[1] 4wz4.a 0.5 0.5 0.7 0.5 0.8 0.6 0.7 0.3
0
0.6
[1] 4x68.a 0.5 0.6 0.7 0.6 0.6 0.2 0.6 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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