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BLAB_AERHY_28_254

Metallo-beta-lactamase type 2 [Metallo-beta-lactamase superfamily. Class-B beta-lactamase family]

Composition of the binding site

Protein chains monomer
A1 (BLAB_AERHY):48, 68, 97:99, 131, 134, 135, 138, 139, 174, 193, 196, 200, 201, 204, 23148, 68, 97:99, 131, 134, 135, 138, 139, 174, 193, 196, 200, 201, 204, 231
Metals (Me):Zn

Full PDB list

1x8g, 1x8h, 1x8i, 2gkl, 2qds, 3f9o, 3fai, 3iof, 3iog, 3sw3, 3t9m (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
4
8
W
6
8
H
9
7
T
9
8
D
9
9
I
1
3
1
F
1
3
4
T
1
3
5
G
1
3
8
L
1
3
9
H
1
7
4
C
1
9
3
K
1
9
6
G
2
0
0
N
2
0
1
F
2
0
4
H
2
3
1
[1]1x8i.a bmh25 . . . . . . . . . . . . . . . . . Zn
[1]2gkl.a pd212 . . . . . . . . . . . . . . . . . Zn
[1]2qds.a mco14 . . . . . . . . . . . . . . . . . Zn
[1]3fai.a none . . . . . . . . . . . . . . . . . Zn
[1]3iof.a ifs18 . . . . . . . . . . . . . . . . . Zn
[1]3iog.a sdf14 . . . . . . . . . . . . . . . . . Zn
[1]3t9m.a none . . . . . . . . . . . D . . . . .

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
V
4
8
W
6
8
H
9
7
T
9
8
D
9
9
I
1
3
1
F
1
3
4
T
1
3
5
G
1
3
8
L
1
3
9
H
1
7
4
C
1
9
3
K
1
9
6
G
2
0
0
N
2
0
1
F
2
0
4
H
2
3
1
[1]1x8i.a . . . . . . . . . . . . . . . . . Zn
[1]2gkl.a . . . . . . . . . . . . . . . . . Zn
[1]2qds.a . . . . . . . . . . . . . . * . . Zn
[1]3fai.a . . . . . . . . . . . . . . . . . Zn
[1]3iof.a . . . . . . . . . . . . . . * . . Zn
[1]3iog.a . . . . . . . . . . . . . . . . . Zn
[1]3t9m.a . . . . . . . . . . . D . . . . .

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
1x8i.a:bmh
2gkl.a:pd2
2qds.a:mco
3fai.a is apo
3iof.a:ifs
3iog.a:sdf
3t9m.a is apo
[1] 1x8i.a
0
0 0.5 - 0.3 0.2 -
[1] 2gkl.a 0
0
0.4 - 0.4 0.2 -
[1] 2qds.a 0.8 0
0
- 0.4 0.2 -
[1] 3fai.a 0 0.1 0
-
0.2 0.2 -
[1] 3iof.a 0.9 0 0 -
0.1
0.4 -
[1] 3iog.a 0.1 0 0.1 - 0.3
0
-
[1] 3t9m.a 0.1 0 0 - 0.3 0.1
-
[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
1x8i.a
2gkl.a
2qds.a
3fai.a
3iof.a
3iog.a
3t9m.a
[1] 1x8i.a
0
.02 .05 .04 .06 .04 .04
[1] 2gkl.a .02
0
.04 .05 .07 .02 .04
[1] 2qds.a .05 .04
0
.06 .03 .05 .05
[1] 3fai.a .04 .05 .06
0
.07 .03 .02
[1] 3iof.a .06 .07 .03 .07
0
.06 .07
[1] 3iog.a .04 .02 .05 .03 .06
0
.03
[1] 3t9m.a .04 .04 .05 .02 .07 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1x8i.a
2gkl.a
2qds.a
3fai.a
3iof.a
3iog.a
3t9m.a
[1] 1x8i.a
0
0.2 0.2 0.4 0.2 0.3 8.8
[1] 2gkl.a 0.2
0
0.2 0.4 0.2 0.3 8.8
[1] 2qds.a 0.2 0.2
0
0.4 0.2 0.3 8.8
[1] 3fai.a 0.4 0.4 0.4
0
0.4 0.4 8.8
[1] 3iof.a 0.2 0.2 0.2 0.4
0
0.3 8.8
[1] 3iog.a 0.3 0.3 0.3 0.4 0.3
0
8.8
[1] 3t9m.a 8.8 8.8 8.8 8.8 8.8 8.8
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1x8i.a
2gkl.a
2qds.a
3fai.a
3iof.a
3iog.a
3t9m.a
[1] 1x8i.a
0
0.5 0.6 0.5 0.5 0.4 8.9
[1] 2gkl.a 0.5
0
0.4 0.7 0.5 0.6 8.8
[1] 2qds.a 0.6 0.4
0
0.7 0.5 0.6 8.8
[1] 3fai.a 0.5 0.7 0.7
0
0.6 0.5 8.9
[1] 3iof.a 0.5 0.5 0.5 0.6
0
0.4 8.8
[1] 3iog.a 0.4 0.6 0.6 0.5 0.4
0
8.8
[1] 3t9m.a 8.9 8.8 8.8 8.9 8.8 8.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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