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BLA2_BACCE_32_257

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

Composition of the binding site

Protein chains monomer
A1 (BLA2_BACCE):64, 69, 89, 116, 118:121, 179, 198, 201, 208:210, 213, 24064, 69, 89, 116, 118:121, 179, 198, 201, 208:210, 213, 240
Metals (Me):Cd/Co/Fe/Zn

Full PDB list

1bc2, 1bmc, 1bvt, 1dxk, 1mqo, 2bc2, 2bfk, 2bfl, 2bfz, 2bg2, 2bg6, 2bg7, 2bg8, 2bga, 2nxa, 2nyp, 2nze, 2nzf, 2uyx, 3bc2, 3fcz, 3i0v, 3i11, 3i13, 3i14, 3i15, 3knr, 3kns, 4c09, 4c1c, 4c1h, 4nq4, 4nq5, 4nq6, 4tyt, 5fqa, 5fqb, 5jmx, 5w8w (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
6
4
V
6
9
W
8
9
H
1
1
6
H
1
1
8
A
1
1
9
D
1
2
0
H
1
7
9
C
1
9
8
K
2
0
1
G
2
0
9
N
2
1
0
D
2
1
3
H
2
4
0
[1]1dxk.a none - - . . . . . . S . . . . . Zn
[1]1mqo.a none . . . . . . . . . . . . . . Cd
[1]2bfl.a none - . . . . . . . . . . . . . Zn
[1]2bfz.a none - . . . . . . . * . . . . . Zn
[1]2bg7.a none - . . . . . . . * . . . . . Zn
[1]2nxa.a none - . . . . . . . D . . . . . Zn
[1]2nze.a none - . . . . . . . S . . . . . Zn
[1]2uyx.a none - . . . . . S . . . . . . . Zn
[1]3i15.a none - - . . . . . . * . . . . . Co
[1]3kns.a none . . . . . . . . D . . . . . Zn
[1]4c1c.a mco14 . . . . . . . . . . . . . . Zn
[1]4c1h.a x8z14 . . . . . . . . . . . . . . Zn
[1]4nq5.a 3c713 - . . . . . . . . . . . . . Zn
[1]4nq6.a 3r913 . . . . . . . . . . . . . . Zn
[1]4tyt.a s3c15 - . . . . . . . . . . . . . Zn
[1]5fqa.a none - . . . . . . . * . . . . . Fe
[1]5fqb.a ok326 . . . . . . . . . . . . . . Zn
[1]5jmx.a dz513 - . . . . . . . . . . . . . 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
F
6
4
V
6
9
W
8
9
H
1
1
6
H
1
1
8
A
1
1
9
D
1
2
0
R
1
2
1
H
1
7
9
C
1
9
8
K
2
0
1
L
2
0
8
G
2
0
9
N
2
1
0
D
2
1
3
H
2
4
0
[1]1dxk.a - - . . . . . . . S . . . * . . Zn
[1]1mqo.a . . . . . . . . . . . . . * . . Cd
[1]2bfl.a - . . . . . . C . . . . . . . . Zn
[1]2bfz.a - . . . . . . C . * . . . . . . Zn
[1]2bg7.a - . . . . . . C . * . . . . . . Zn
[1]2nxa.a - . . . . . . H . D . . . * . . Zn
[1]2nze.a - . . . . . . H . S . . . * . . Zn
[1]2uyx.a - . . . . . S . . . . . . . . . Zn
[1]3i15.a - - . . . . . . . * . . . * . . Co
[1]3kns.a . . . . . . . . . D . . . . . . Zn
[1]4c1c.a . . . . . . . . . . . . . * . . Zn
[1]4c1h.a . . . . . . . . . . . . . . . . Zn
[1]4nq5.a - . . . . . . . . . . . . . . . Zn
[1]4nq6.a . . . . . . . . . . . . . . . . Zn
[1]4tyt.a - . . . . . . . . . . . . . . . Zn
[1]5fqa.a - . . . . . . . . * . . . . . . Fe
[1]5fqb.a . . . . . . . . . . . . . * . . Zn
[1]5jmx.a - . . . . . . . . . . . . . . . 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
1dxk.a is apo
1mqo.a is apo
2bfl.a is apo
2bfz.a is apo
2bg7.a is apo
2nxa.a is apo
2nze.a is apo
2uyx.a is apo
3i15.a is apo
3kns.a is apo
4c1c.a:mco
4c1h.a:x8z
4nq5.a:3c7
4nq6.a:3r9
4tyt.a:s3c
5fqa.a is apo
5fqb.a:ok3
5jmx.a:dz5
[1] 1dxk.a
-
- - - - - - - - - 0 0.1 0.1 0.2 1.1 - 0.1 0.9
[1] 1mqo.a -
-
- - - - - - - - 1.1 1.3 2.0 1.6 2.3 - 1.5 1.6
[1] 2bfl.a - -
-
- - - - - - - 0.3 0.1 0.2 0.2 1.0 - 0.1 0.8
[1] 2bfz.a - - -
-
- - - - - - 0.6 0.3 0.3 0.6 1.6 - 0.4 1.4
[1] 2bg7.a - - - -
-
- - - - - 0.3 0.2 0.1 0.5 0.9 - 0.2 0.8
[1] 2nxa.a - - - - -
-
- - - - 0.4 0.4 0.2 0.6 1.4 - 0.3 1.2
[1] 2nze.a - - - - - -
-
- - - 1.0 0.3 0.6 0.3 1.2 - 0.5 1.3
[1] 2uyx.a - - - - - - -
-
- - 0.1 0.3 0.1 0 0.3 - 0 0.2
[1] 3i15.a - - - - - - - -
-
- 0.4 0.5 0.5 0.7 1.6 - 0.3 1.6
[1] 3kns.a - - - - - - - - -
-
0.5 0.4 0.2 0.7 0.9 - 0.4 0.9
[1] 4c1c.a - - - - - - - - - -
0
0 0.1 0.2 1.3 - 0 0.8
[1] 4c1h.a - - - - - - - - - - 0
0
0 0.2 0.1 - 0 0
[1] 4nq5.a - - - - - - - - - - 0 0.1
0
0.2 0.3 - 0 0.1
[1] 4nq6.a - - - - - - - - - - 0.1 0.2 0.8
0.1
0 - 0 0
[1] 4tyt.a - - - - - - - - - - 0.1 0.1 0 0.3
0
- 0.1 0
[1] 5fqa.a - - - - - - - - - - 0.3 0.4 0.3 0.6 0.7
-
0.1 0.4
[1] 5fqb.a - - - - - - - - - - 0.2 0.7 1.4 0.4 1.1 -
0
0.9
[1] 5jmx.a - - - - - - - - - - 0 0.1 0 0.3 0 - 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
1dxk.a
1mqo.a
2bfl.a
2bfz.a
2bg7.a
2nxa.a
2nze.a
2uyx.a
3i15.a
3kns.a
4c1c.a
4c1h.a
4nq5.a
4nq6.a
4tyt.a
5fqa.a
5fqb.a
5jmx.a
[1] 1dxk.a
0
.21 .06 .08 .09 .07 .09 .08 .07 .13 .03 .08 .07 .12 .08 .07 .08 .08
[1] 1mqo.a .21
0
.22 .23 .24 .17 .21 .25 .23 .28 .21 .27 .26 .22 .26 .23 .16 .25
[1] 2bfl.a .06 .22
0
.04 .07 .08 .07 .08 .09 .12 .04 .08 .07 .14 .09 .07 .12 .09
[1] 2bfz.a .08 .23 .04
0
.06 .07 .08 .12 .05 .10 .06 .13 .11 .19 .13 .08 .13 .12
[1] 2bg7.a .09 .24 .07 .06
0
.09 .11 .07 .08 .06 .09 .08 .06 .14 .08 .02 .14 .07
[1] 2nxa.a .07 .17 .08 .07 .09
0
.06 .11 .06 .11 .06 .11 .11 .16 .10 .08 .09 .09
[1] 2nze.a .09 .21 .07 .08 .11 .06
0
.14 .11 .16 .07 .12 .12 .18 .12 .12 .11 .11
[1] 2uyx.a .08 .25 .08 .12 .07 .11 .14
0
.12 .07 .09 .04 .03 .07 .04 .06 .14 .04
[1] 3i15.a .07 .23 .09 .05 .08 .06 .11 .12
0
.06 .08 .11 .11 .16 .10 .06 .10 .09
[1] 3kns.a .13 .28 .12 .10 .06 .11 .16 .07 .06
0
.14 .08 .08 .13 .06 .06 .16 .06
[1] 4c1c.a .03 .21 .04 .06 .09 .06 .07 .09 .08 .14
0
.08 .06 .14 .09 .08 .08 .08
[1] 4c1h.a .08 .27 .08 .13 .08 .11 .12 .04 .11 .08 .08
0
.01 .08 .03 .06 .13 .02
[1] 4nq5.a .07 .26 .07 .11 .06 .11 .12 .03 .11 .08 .06 .01
0
.08 .03 .05 .13 .02
[1] 4nq6.a .12 .22 .14 .19 .14 .16 .18 .07 .16 .13 .14 .08 .08
0
.08 .11 .09 .07
[1] 4tyt.a .08 .26 .09 .13 .08 .10 .12 .04 .10 .06 .09 .03 .03 .08
0
.05 .11 .01
[1] 5fqa.a .07 .23 .07 .08 .02 .08 .12 .06 .06 .06 .08 .06 .05 .11 .05
0
.11 .04
[1] 5fqb.a .08 .16 .12 .13 .14 .09 .11 .14 .10 .16 .08 .13 .13 .09 .11 .11
0
.11
[1] 5jmx.a .08 .25 .09 .12 .07 .09 .11 .04 .09 .06 .08 .02 .02 .07 .01 .04 .11
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
1dxk.a
1mqo.a
2bfl.a
2bfz.a
2bg7.a
2nxa.a
2nze.a
2uyx.a
3i15.a
3kns.a
4c1c.a
4c1h.a
4nq5.a
4nq6.a
4tyt.a
5fqa.a
5fqb.a
5jmx.a
[1] 1dxk.a
0
0.8 0.5 0.5 0.5 0.5 0.9 0.3 0.5 0.6 0.3 0.4 0.3 0.4 0.3 0.3 0.3 0.3
[1] 1mqo.a 0.8
0
1.1 1.0 1.0 0.4 0.5 0.9 0.4 1.6 1.1 1.5 0.9 0.8 0.9 1.0 1.0 1.0
[1] 2bfl.a 0.5 1.1
0
0.2 0.1 0.9 1.0 0.4 0.8 0.4 0.6 0.6 0.5 0.7 0.6 0.5 0.5 0.5
[1] 2bfz.a 0.5 1.0 0.2
0
0.2 0.8 1.0 0.4 0.8 0.4 0.6 0.6 0.5 0.7 0.5 0.5 0.5 0.5
[1] 2bg7.a 0.5 1.0 0.1 0.2
0
0.8 1.0 0.4 0.8 0.4 0.6 0.6 0.5 0.6 0.5 0.5 0.5 0.5
[1] 2nxa.a 0.5 0.4 0.9 0.8 0.8
0
0.5 0.7 0.3 0.9 0.8 0.8 0.7 0.4 0.7 0.8 0.7 0.8
[1] 2nze.a 0.9 0.5 1.0 1.0 1.0 0.5
0
1.0 0.6 1.1 1.1 1.1 1.0 0.7 1.1 1.1 1.0 1.1
[1] 2uyx.a 0.3 0.9 0.4 0.4 0.4 0.7 1.0
0
0.7 0.5 0.4 0.4 0.3 0.5 0.4 0.3 0.3 0.3
[1] 3i15.a 0.5 0.4 0.8 0.8 0.8 0.3 0.6 0.7
0
0.8 0.7 0.7 0.6 0.3 0.6 0.7 0.7 0.7
[1] 3kns.a 0.6 1.6 0.4 0.4 0.4 0.9 1.1 0.5 0.8
0
0.7 0.6 0.6 1.0 0.6 0.5 1.2 0.5
[1] 4c1c.a 0.3 1.1 0.6 0.6 0.6 0.8 1.1 0.4 0.7 0.7
0
0.3 0.3 0.6 0.3 0.2 0.5 0.3
[1] 4c1h.a 0.4 1.5 0.6 0.6 0.6 0.8 1.1 0.4 0.7 0.6 0.3
0
0.3 0.8 0.2 0.2 1.0 0.2
[1] 4nq5.a 0.3 0.9 0.5 0.5 0.5 0.7 1.0 0.3 0.6 0.6 0.3 0.3
0
0.4 0.2 0.2 0.4 0.2
[1] 4nq6.a 0.4 0.8 0.7 0.7 0.6 0.4 0.7 0.5 0.3 1.0 0.6 0.8 0.4
0
0.4 0.5 0.6 0.5
[1] 4tyt.a 0.3 0.9 0.6 0.5 0.5 0.7 1.1 0.4 0.6 0.6 0.3 0.2 0.2 0.4
0
0.2 0.4 0.2
[1] 5fqa.a 0.3 1.0 0.5 0.5 0.5 0.8 1.1 0.3 0.7 0.5 0.2 0.2 0.2 0.5 0.2
0
0.4 0.2
[1] 5fqb.a 0.3 1.0 0.5 0.5 0.5 0.7 1.0 0.3 0.7 1.2 0.5 1.0 0.4 0.6 0.4 0.4
0
0.4
[1] 5jmx.a 0.3 1.0 0.5 0.5 0.5 0.8 1.1 0.3 0.7 0.5 0.3 0.2 0.2 0.5 0.2 0.2 0.4
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
1dxk.a
1mqo.a
2bfl.a
2bfz.a
2bg7.a
2nxa.a
2nze.a
2uyx.a
3i15.a
3kns.a
4c1c.a
4c1h.a
4nq5.a
4nq6.a
4tyt.a
5fqa.a
5fqb.a
5jmx.a
[1] 1dxk.a
0
1.2 0.9 0.9 0.7 1.0 1.2 0.9 1.1 1.1 0.9 1.0 0.9 1.0 1.0 0.9 0.8 0.9
[1] 1mqo.a 1.2
0
1.1 1.1 1.3 0.7 0.7 0.9 0.6 2.0 1.1 1.9 1.1 1.1 1.0 1.0 1.1 1.0
[1] 2bfl.a 0.9 1.1
0
0.2 0.7 0.9 1.0 0.5 0.8 0.7 0.7 0.7 0.7 0.8 0.7 0.5 0.6 0.5
[1] 2bfz.a 0.9 1.1 0.2
0
0.8 0.9 1.0 0.6 0.8 0.8 0.7 0.7 0.7 0.8 0.7 0.5 0.6 0.6
[1] 2bg7.a 0.7 1.3 0.7 0.8
0
1.2 1.2 0.9 1.1 1.0 1.1 1.1 1.1 1.1 1.1 0.9 1.0 1.0
[1] 2nxa.a 1.0 0.7 0.9 0.9 1.2
0
0.6 0.8 0.6 1.0 0.8 0.9 0.8 0.8 0.9 0.8 0.7 0.8
[1] 2nze.a 1.2 0.7 1.0 1.0 1.2 0.6
0
1.0 0.8 1.1 1.1 1.2 1.1 1.0 1.1 1.1 1.0 1.1
[1] 2uyx.a 0.9 0.9 0.5 0.6 0.9 0.8 1.0
0
0.7 0.7 0.6 0.5 0.7 0.6 0.5 0.4 0.6 0.4
[1] 3i15.a 1.1 0.6 0.8 0.8 1.1 0.6 0.8 0.7
0
0.9 0.8 0.9 0.8 0.7 0.7 0.7 0.7 0.8
[1] 3kns.a 1.1 2.0 0.7 0.8 1.0 1.0 1.1 0.7 0.9
0
0.8 0.7 0.9 1.5 0.8 0.7 1.6 0.7
[1] 4c1c.a 0.9 1.1 0.7 0.7 1.1 0.8 1.1 0.6 0.8 0.8
0
0.5 0.6 0.8 0.6 0.3 0.5 0.5
[1] 4c1h.a 1.0 1.9 0.7 0.7 1.1 0.9 1.2 0.5 0.9 0.7 0.5
0
0.6 1.4 0.4 0.3 1.5 0.3
[1] 4nq5.a 0.9 1.1 0.7 0.7 1.1 0.8 1.1 0.7 0.8 0.9 0.6 0.6
0
0.7 0.6 0.5 0.7 0.6
[1] 4nq6.a 1.0 1.1 0.8 0.8 1.1 0.8 1.0 0.6 0.7 1.5 0.8 1.4 0.7
0
0.7 0.6 0.9 0.6
[1] 4tyt.a 1.0 1.0 0.7 0.7 1.1 0.9 1.1 0.5 0.7 0.8 0.6 0.4 0.6 0.7
0
0.4 0.6 0.4
[1] 5fqa.a 0.9 1.0 0.5 0.5 0.9 0.8 1.1 0.4 0.7 0.7 0.3 0.3 0.5 0.6 0.4
0
0.4 0.2
[1] 5fqb.a 0.8 1.1 0.6 0.6 1.0 0.7 1.0 0.6 0.7 1.6 0.5 1.5 0.7 0.9 0.6 0.4
0
0.5
[1] 5jmx.a 0.9 1.0 0.5 0.6 1.0 0.8 1.1 0.4 0.8 0.7 0.5 0.3 0.6 0.6 0.4 0.2 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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