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AHLLA_BACTK_1_250

N-acyl homoserine lactonase AiiA [Metallo-beta-lactamase superfamily]

Composition of the binding site

Protein chains monomer
A1 (AHLLA_BACTK):14, 16, 20, 33, 64, 67:69, 72, 73, 104, 106:109, 135:138, 169, 191, 194, 206:208, 23514, 16, 20, 33, 64, 67:69, 72, 73, 104, 106:109, 135:138, 169, 191, 194, 206:208, 235
Metals (Me):Zn

Full PDB list

2a7m, 2br6, 2btn, 3dha, 3dhb, 3dhc, 4j5f, 4j5h, 5eh9, 5eht (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
C
1
4
L
1
6
S
2
0
L
3
3
F
6
4
T
6
7
F
6
8
V
6
9
Q
7
2
I
7
3
H
1
0
6
F
1
0
7
D
1
0
8
H
1
0
9
E
1
3
5
E
1
3
6
M
1
3
8
H
1
6
9
D
1
9
1
Y
1
9
4
A
2
0
6
G
2
0
7
H
2
3
5
[1]2a7m.a none . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2br6.a hsl7 . . . . - - - - - . . . . . . . . . . . . . . Zn
[1]3dha.a c6l15 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3dhc.a cyk15 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4j5f.a none . . . . . . . . . . . W . . . . . . . . . . . Zn
[1]4j5h.a 1k419 . . . . . . . . . . . W . . . . . . . . . . . Zn
[1]5eh9.a hed8 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5eht.a none . . F V * . . G . . . . . . . . . . . . . . . Zn

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 Me
C
1
4
L
1
6
S
2
0
L
3
3
F
6
4
T
6
7
F
6
8
V
6
9
Q
7
2
I
7
3
H
1
0
4
H
1
0
6
F
1
0
7
D
1
0
8
H
1
0
9
E
1
3
5
E
1
3
6
Y
1
3
7
M
1
3
8
H
1
6
9
D
1
9
1
Y
1
9
4
A
2
0
6
G
2
0
7
F
2
0
8
H
2
3
5
[1]2a7m.a . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2br6.a . . . . - - - - - . . . . . . . . . . . . . . . . . Zn
[1]3dha.a . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3dhc.a . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4j5f.a . . . . . . . . . . . . W . . . . . . . . . . . . . Zn
[1]4j5h.a . . . . . . . . . . . . W . . . . . . . . . . . . . Zn
[1]5eh9.a . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5eht.a . . F V * . . G . . . . . . . . . . . . . . . . . . Zn

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
2a7m.a is apo
2br6.a:hsl
3dha.a:c6l
3dhc.a:cyk
4j5f.a is apo
4j5h.a:1k4
5eh9.a:hed
5eht.a is apo
[1] 2a7m.a
-
0.1 0.2 0.6 - 0.9 0.1 -
[1] 2br6.a -
0.1
0.1 0.1 - 0.4 0 -
[1] 3dha.a - 0.1
0
0.4 - 0.6 0.1 -
[1] 3dhc.a - 0.1 0.6
0
- 0 0 -
[1] 4j5f.a - 0.3 0.6 0.7
-
0.5 0 -
[1] 4j5h.a - 0.1 0.5 0.3 -
0
0 -
[1] 5eh9.a - 0.1 0.5 0.3 - 0.6
0
-
[1] 5eht.a - 0.1 2.6 0.4 - 1.0 0.3
-
[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
2a7m.a
2br6.a
3dha.a
3dhc.a
4j5f.a
4j5h.a
5eh9.a
5eht.a
[1] 2a7m.a
0
.03 .02 .05 .04 .05 .02 .13
[1] 2br6.a .03
0
.03 .04 .05 .03 .06 .15
[1] 3dha.a .02 .03
0
.05 .05 .06 .03 .12
[1] 3dhc.a .05 .04 .05
0
.04 .02 .04 .12
[1] 4j5f.a .04 .05 .05 .04
0
.03 .03 .12
[1] 4j5h.a .05 .03 .06 .02 .03
0
.05 .14
[1] 5eh9.a .02 .06 .03 .04 .03 .05
0
.10
[1] 5eht.a .13 .15 .12 .12 .12 .14 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2a7m.a
2br6.a
3dha.a
3dhc.a
4j5f.a
4j5h.a
5eh9.a
5eht.a
[1] 2a7m.a
0
0.5 0.6 0.4 0.3 0.5 0.3 0.8
[1] 2br6.a 0.5
0
0.6 0.6 0.5 0.6 0.5 0.7
[1] 3dha.a 0.6 0.6
0
0.7 0.8 0.8 0.7 1.0
[1] 3dhc.a 0.4 0.6 0.7
0
0.4 0.2 0.2 0.5
[1] 4j5f.a 0.3 0.5 0.8 0.4
0
0.5 0.4 0.9
[1] 4j5h.a 0.5 0.6 0.8 0.2 0.5
0
0.3 0.5
[1] 5eh9.a 0.3 0.5 0.7 0.2 0.4 0.3
0
0.6
[1] 5eht.a 0.8 0.7 1.0 0.5 0.9 0.5 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2a7m.a
2br6.a
3dha.a
3dhc.a
4j5f.a
4j5h.a
5eh9.a
5eht.a
[1] 2a7m.a
0
0.9 1.2 0.6 0.7 0.9 0.8 1.0
[1] 2br6.a 0.9
0
1.1 1.0 1.0 1.0 0.9 1.0
[1] 3dha.a 1.2 1.1
0
1.4 1.5 1.5 1.4 1.7
[1] 3dhc.a 0.6 1.0 1.4
0
0.8 0.7 0.8 1.0
[1] 4j5f.a 0.7 1.0 1.5 0.8
0
0.8 0.7 1.1
[1] 4j5h.a 0.9 1.0 1.5 0.7 0.8
0
0.6 0.9
[1] 5eh9.a 0.8 0.9 1.4 0.8 0.7 0.6
0
0.8
[1] 5eht.a 1.0 1.0 1.7 1.0 1.1 0.9 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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