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BLAB_BACFG_18_249

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

Composition of the binding site

Protein chains monomer
A1 (BLAB_BACFG):46, 49, 52, 53, 162, 181, 184, 185, 188, 190, 192, 193, 223:22546, 49, 52, 53, 162, 181, 184, 185, 188, 190, 192, 193, 223:225
Metals (Me):Na/Zn

Full PDB list

1a7t, 1a8t, 1hlk, 1kr3, 1znb, 2bmi, 2znb, 3znb, 4znb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
4
6
W
4
9
V
5
2
P
5
3
H
1
6
2
C
1
8
1
K
1
8
4
D
1
8
5
G
1
9
2
N
1
9
3
H
2
2
3
G
2
2
4
D
2
2
5
[1]1a7t.a none . . . . . . . . . . . . N Na,Zn
[1]1a8t.a 06134 . . . . . . . . . . . . N Zn
[1]1hlk.a 11323 . . . . . . . . . . . . . Zn
[1]1znb.a none . - . . . . . . . . . . . Na,Zn
[1]4znb.a none . - . . . S . . . . . . . Na,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

[download in TSV format]
   
PDB.ch
A1 Me
I
4
6
W
4
9
V
5
2
P
5
3
H
1
6
2
C
1
8
1
K
1
8
4
D
1
8
5
A
1
8
8
S
1
9
0
G
1
9
2
N
1
9
3
H
2
2
3
G
2
2
4
D
2
2
5
[1]1a7t.a . . . . . . . . T . . . . . N Na,Zn
[1]1a8t.a . . . . . . . . T . . . . . N Zn
[1]1hlk.a . . . . . . . . . . . . . . . Zn
[1]1znb.a . - . . . . . . . . . . . . . Na,Zn
[1]4znb.a . - . . . S . . . . . . . . . Na,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
1a7t.a is apo
1a8t.a:061
1hlk.a:113
1znb.a is apo
4znb.a is apo
[1] 1a7t.a
-
0.5 0.1 - -
[1] 1a8t.a -
0.2
0.2 - -
[1] 1hlk.a - 0.4
0
- -
[1] 1znb.a - 0 0
-
-
[1] 4znb.a - 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
1a7t.a
1a8t.a
1hlk.a
1znb.a
4znb.a
[1] 1a7t.a
0
.06 .01 .03 .03
[1] 1a8t.a .06
0
.04 .02 .02
[1] 1hlk.a .01 .04
0
.02 .02
[1] 1znb.a .03 .02 .02
0
0
[1] 4znb.a .03 .02 .02 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1a7t.a
1a8t.a
1hlk.a
1znb.a
4znb.a
[1] 1a7t.a
0
1.4 0.8 0.8 0.8
[1] 1a8t.a 1.4
0
1.1 1.6 1.6
[1] 1hlk.a 0.8 1.1
0
1.0 1.1
[1] 1znb.a 0.8 1.6 1.0
0
0.2
[1] 4znb.a 0.8 1.6 1.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1a7t.a
1a8t.a
1hlk.a
1znb.a
4znb.a
[1] 1a7t.a
0
1.8 1.2 1.2 0.8
[1] 1a8t.a 1.8
0
1.5 1.8 1.4
[1] 1hlk.a 1.2 1.5
0
1.2 1.1
[1] 1znb.a 1.2 1.8 1.2
0
0.7
[1] 4znb.a 0.8 1.4 1.1 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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