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AAAA_PENCH_1_357

Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form [Peptidase C45 family]

Composition of the binding site

Protein chains monomer
A1 (AAAA_PENCH):100:103, 121:123, 262, 302, 310, 311100:103, 121:123, 262, 302, 310, 311

Full PDB list

2x1c, 2x1d, 2x1e

Pocket contact map

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PDB.ch
   
ligand
A1
C
1
0
3
D
1
2
1
F
1
2
2
F
1
2
3
L
2
6
2
R
3
0
2
R
3
1
0
G
3
1
1
[1]2x1c.b none A . . . . . . .
[1]2x1d.b none * . . . . . . .
[1]2x1e.a x1e14 * . . . . . . .

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

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PDB.ch
A1
R
1
0
0
D
1
0
1
G
1
0
2
C
1
0
3
D
1
2
1
F
1
2
2
F
1
2
3
L
2
6
2
R
3
0
2
R
3
1
0
G
3
1
1
[1]2x1c.b . . * A . . . . . . .
[1]2x1d.b - - - * . . . . . . .
[1]2x1e.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
2x1c.b is apo
2x1d.b is apo
2x1e.a:x1e
[1] 2x1c.b
-
- 2.3
[1] 2x1d.b -
-
0.1
[1] 2x1e.a - -
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
2x1c.b
2x1d.b
2x1e.a
[1] 2x1c.b
0
.20 .21
[1] 2x1d.b .20
0
.01
[1] 2x1e.a .21 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2x1c.b
2x1d.b
2x1e.a
[1] 2x1c.b
0
0.6 8.6
[1] 2x1d.b 0.6
0
0.1
[1] 2x1e.a 8.6 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2x1c.b
2x1d.b
2x1e.a
[1] 2x1c.b
0
1.0 8.1
[1] 2x1d.b 1.0
0
0.8
[1] 2x1e.a 8.1 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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