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AMPC_ENTCL_21_381

Beta-lactamase [Class-C beta-lactamase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPC_ENTCL):R: Substrate binding (335:337)
83, 84, 87, 139, 140, 170, 172, 224, 231, 239:242, 307, 309, 312, 313, 338:340, 366
83, 84, 87, 139, 140, 170, 172, 224, 231, 239:242, 307, 309, 312, 313, 335:340, 366

Full PDB list

1bls, 1ga0, 1gce, 1onh, 1q2q, 1rgz, 1s6r, 1xx2, 1y54, 2q9m, 2q9n, 3s4x, 4xux, 5hai, 5xhr (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
8
3
S
8
4
L
1
3
9
Q
1
4
0
Y
1
7
0
N
1
7
2
R
2
2
4
V
2
3
1
Q
2
3
9
A
2
4
0
Y
2
4
1
G
2
4
2
S
3
0
7
S
3
0
9
A
3
1
2
L
3
1
3
K
3
3
5
T
3
3
6
G
3
3
7
S
3
3
8
T
3
3
9
G
3
4
0
N
3
6
6
[1]1bls.a ipp15 . * . . . . . . . . . . . . . . . . . . . . .
[1]1ga0.a dvr26 . * . . . . . . . . . . . . . . . . . . . . .
[1]1onh.a wy421 . * . . . . . . . . . . . . . . . . . . . . .
[1]1q2q.a wy223 . . . . . . . A . . . . . . . . . . . . . . .
[1]1rgz.a ptx17 . * . . . . . . . . . . . . . . . . . . . . .
[1]1s6r.a iap14 . * . . . . . . . . . . . . . . . . . . . . .
[1]1xx2.a none . . . . . . . . . . . . . . . . . . . . . . .
[1]1y54.a fdt18 . * . . . . . . . . . . . . . . . . . . . . .
[1]2q9m.a lk719 . * . . . . . . . . . . . . . . . . . . . . .
[1]2q9n.a lk518 . * . . . . . . . . . . . . . . . . . . . . .
[1]3s4x.a none . . . . . G . . . . . . . . . . . . . . . . .
[1]4xux.a 4d620 . * . . . . . . . . . . . . . . . . . . . . .
[1]5hai.a none . G . . . . . . . . . . . . . . . . . . . . .
[1]5xhr.a pxh22 . * . . . . . . . . . . . . . . . . . . . . .

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
G
8
3
S
8
4
K
8
7
L
1
3
9
Q
1
4
0
Y
1
7
0
N
1
7
2
R
2
2
4
V
2
3
1
Q
2
3
9
A
2
4
0
Y
2
4
1
G
2
4
2
S
3
0
7
S
3
0
9
A
3
1
2
L
3
1
3
K
3
3
5
T
3
3
6
G
3
3
7
S
3
3
8
T
3
3
9
G
3
4
0
N
3
6
6
[1]1bls.a . * . . * . . . . . . * . . . . . . . . . . . .
[1]1ga0.a . * . . . . . . . . . . . . . . . . . . . . . .
[1]1onh.a . * . . . . . . . . . . . . . . . . . . . . . .
[1]1q2q.a . * . . * . . . A . . * . . . . . . . . . . . .
[1]1rgz.a . * . . * . . . . . . . . . . . . . . . . . . .
[1]1s6r.a . * . . . . . . . . . * . . . . . . . . . . . .
[1]1xx2.a . * . . * . . . . . . * . . . . . . . . . . . .
[1]1y54.a . * . . . . . . . . . * . . . . . . . . . . . .
[1]2q9m.a . * . . . . . . . . . * . . . . . . . . . . . .
[1]2q9n.a . * . . . . . . . . . * . . . . . . . . . . . .
[1]3s4x.a . * . . . . G . . . . * . . . . . . . . . . . .
[1]4xux.a . * . . * . . . . . . * . . . . . . . . . . . .
[1]5hai.a . G . . * . . . . . . * . . * . . . . . . . . .
[1]5xhr.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
1bls.a:ipp
1ga0.a:dvr
1onh.a:wy4
1q2q.a:wy2
1rgz.a:ptx
1s6r.a:iap
1xx2.a is apo
1y54.a:fdt
2q9m.a:lk7
2q9n.a:lk5
3s4x.a is apo
4xux.a:4d6
5hai.a is apo
5xhr.a:pxh
[1] 1bls.a
0.6
2.0 1.7 1.4 4.4 1.0 - 0.8 1.0 1.1 - 0.6 - 1.0
[1] 1ga0.a 0.7
0.6
0.8 0.8 0.8 0.7 - 0.8 0.8 0.4 - 0.6 - 0.8
[1] 1onh.a 0.6 0.9
0.8
0.8 0.8 0.6 - 0.8 0.8 0.5 - 0.7 - 1.0
[1] 1q2q.a 0.5 1.3 1.8
0.8
4.3 0.8 - 0.8 0.8 0.7 - 0.6 - 0.9
[1] 1rgz.a 0.4 1.1 1.3 0.4
0.8
0.5 - 0.5 0.8 0.9 - 0.5 - 0.6
[1] 1s6r.a 0.4 1.8 1.4 0.8 4.2
0.7
- 0.5 0.9 1.3 - 0.6 - 0.7
[1] 1xx2.a 0.5 1.7 1.9 1.5 4.4 1.2
-
0.9 1.0 0.9 - 0.6 - 1.0
[1] 1y54.a 0.8 1.3 1.0 1.1 4.8 0.9 -
0.9
1.0 0.7 - 1.1 - 1.3
[1] 2q9m.a 0.8 1.2 1.4 0.8 4.1 0.9 - 0.5
0.8
0.9 - 0.5 - 0.6
[1] 2q9n.a 0.6 1.5 1.8 1.2 4.3 1.5 - 1.0 1.6
0.9
- 0.9 - 1.4
[1] 3s4x.a 0.4 1.6 1.5 1.0 3.6 1.0 - 0.6 1.0 0.9
-
0.4 - 1.0
[1] 4xux.a 0.5 1.5 1.7 0.9 3.9 1.1 - 0.7 0.9 1.0 -
0.6
- 0.9
[1] 5hai.a 0.2 2.2 0.7 0.5 3.2 0.5 - 0.1 0.2 0.7 - 0.2
-
0.4
[1] 5xhr.a 0.6 1.8 1.9 0.9 4.4 1.1 - 0.9 0.9 0.9 - 0.6 -
0.6
[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
1bls.a
1ga0.a
1onh.a
1q2q.a
1rgz.a
1s6r.a
1xx2.a
1y54.a
2q9m.a
2q9n.a
3s4x.a
4xux.a
5hai.a
5xhr.a
[1] 1bls.a
0
.22 .22 .05 .18 .04 .03 .10 .08 .07 .07 .04 .18 .06
[1] 1ga0.a .22
0
.03 .20 .04 .23 .22 .22 .22 .22 .20 .21 .30 .23
[1] 1onh.a .22 .03
0
.21 .05 .22 .22 .22 .23 .24 .20 .22 .30 .24
[1] 1q2q.a .05 .20 .21
0
.16 .05 .03 .10 .06 .07 .08 .04 .17 .05
[1] 1rgz.a .18 .04 .05 .16
0
.19 .18 .24 .18 .19 .17 .17 .28 .19
[1] 1s6r.a .04 .23 .22 .05 .19
0
.04 .09 .08 .10 .08 .05 .15 .06
[1] 1xx2.a .03 .22 .22 .03 .18 .04
0
.09 .07 .07 .07 .04 .16 .04
[1] 1y54.a .10 .22 .22 .10 .24 .09 .09
0
.10 .13 .15 .12 .18 .11
[1] 2q9m.a .08 .22 .23 .06 .18 .08 .07 .10
0
.08 .11 .08 .14 .08
[1] 2q9n.a .07 .22 .24 .07 .19 .10 .07 .13 .08
0
.08 .08 .20 .07
[1] 3s4x.a .07 .20 .20 .08 .17 .08 .07 .15 .11 .08
0
.05 .17 .08
[1] 4xux.a .04 .21 .22 .04 .17 .05 .04 .12 .08 .08 .05
0
.15 .05
[1] 5hai.a .18 .30 .30 .17 .28 .15 .16 .18 .14 .20 .17 .15
0
.17
[1] 5xhr.a .06 .23 .24 .05 .19 .06 .04 .11 .08 .07 .08 .05 .17
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
1bls.a
1ga0.a
1onh.a
1q2q.a
1rgz.a
1s6r.a
1xx2.a
1y54.a
2q9m.a
2q9n.a
3s4x.a
4xux.a
5hai.a
5xhr.a
[1] 1bls.a
0
2.5 2.5 0.5 2.4 0.3 0.3 0.3 0.4 0.5 0.5 0.4 0.5 0.4
[1] 1ga0.a 2.5
0
0.2 2.7 0.2 2.5 2.5 2.6 2.6 2.6 2.6 2.6 2.5 2.6
[1] 1onh.a 2.5 0.2
0
2.6 0.3 2.5 2.5 2.6 2.5 2.5 2.6 2.5 2.5 2.6
[1] 1q2q.a 0.5 2.7 2.6
0
2.5 0.5 0.4 0.5 0.6 0.5 0.6 0.3 0.5 0.3
[1] 1rgz.a 2.4 0.2 0.3 2.5
0
2.4 2.4 2.5 2.5 2.5 2.5 2.5 2.4 2.5
[1] 1s6r.a 0.3 2.5 2.5 0.5 2.4
0
0.4 0.4 0.5 0.5 0.5 0.4 0.6 0.5
[1] 1xx2.a 0.3 2.5 2.5 0.4 2.4 0.4
0
0.5 0.6 0.5 0.3 0.3 0.4 0.3
[1] 1y54.a 0.3 2.6 2.6 0.5 2.5 0.4 0.5
0
0.5 0.5 0.5 0.4 0.5 0.5
[1] 2q9m.a 0.4 2.6 2.5 0.6 2.5 0.5 0.6 0.5
0
0.5 0.7 0.5 0.5 0.5
[1] 2q9n.a 0.5 2.6 2.5 0.5 2.5 0.5 0.5 0.5 0.5
0
0.6 0.4 0.6 0.4
[1] 3s4x.a 0.5 2.6 2.6 0.6 2.5 0.5 0.3 0.5 0.7 0.6
0
0.3 0.5 0.5
[1] 4xux.a 0.4 2.6 2.5 0.3 2.5 0.4 0.3 0.4 0.5 0.4 0.3
0
0.4 0.3
[1] 5hai.a 0.5 2.5 2.5 0.5 2.4 0.6 0.4 0.5 0.5 0.6 0.5 0.4
0
0.4
[1] 5xhr.a 0.4 2.6 2.6 0.3 2.5 0.5 0.3 0.5 0.5 0.4 0.5 0.3 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
1bls.a
1ga0.a
1onh.a
1q2q.a
1rgz.a
1s6r.a
1xx2.a
1y54.a
2q9m.a
2q9n.a
3s4x.a
4xux.a
5hai.a
5xhr.a
[1] 1bls.a
0
3.1 3.0 0.7 3.0 0.9 0.5 0.9 0.8 0.9 0.7 0.5 1.0 0.6
[1] 1ga0.a 3.1
0
0.5 3.0 0.4 3.0 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1
[1] 1onh.a 3.0 0.5
0
3.0 0.6 3.0 3.0 3.1 3.1 3.1 3.1 3.1 3.1 3.1
[1] 1q2q.a 0.7 3.0 3.0
0
2.9 0.7 0.7 0.7 0.8 0.8 0.9 0.5 0.8 0.6
[1] 1rgz.a 3.0 0.4 0.6 2.9
0
2.9 2.9 3.0 3.0 3.0 3.0 2.9 3.0 3.0
[1] 1s6r.a 0.9 3.0 3.0 0.7 2.9
0
0.9 0.5 0.8 0.9 1.0 0.8 0.7 0.9
[1] 1xx2.a 0.5 3.1 3.0 0.7 2.9 0.9
0
0.9 0.8 0.8 0.6 0.5 1.0 0.4
[1] 1y54.a 0.9 3.1 3.1 0.7 3.0 0.5 0.9
0
0.8 0.9 1.1 0.8 0.6 0.9
[1] 2q9m.a 0.8 3.1 3.1 0.8 3.0 0.8 0.8 0.8
0
0.7 1.0 0.8 0.8 0.7
[1] 2q9n.a 0.9 3.1 3.1 0.8 3.0 0.9 0.8 0.9 0.7
0
1.0 0.8 0.9 0.8
[1] 3s4x.a 0.7 3.1 3.1 0.9 3.0 1.0 0.6 1.1 1.0 1.0
0
0.7 1.2 0.7
[1] 4xux.a 0.5 3.1 3.1 0.5 2.9 0.8 0.5 0.8 0.8 0.8 0.7
0
0.9 0.5
[1] 5hai.a 1.0 3.1 3.1 0.8 3.0 0.7 1.0 0.6 0.8 0.9 1.2 0.9
0
0.9
[1] 5xhr.a 0.6 3.1 3.1 0.6 3.0 0.9 0.4 0.9 0.7 0.8 0.7 0.5 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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