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AMPC_CITFR_21_381

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPC_CITFR):R: Substrate binding (335:337)
83, 84, 87, 139, 140, 170, 172, 231, 241, 338:340, 366
83, 84, 87, 139, 140, 170, 172, 231, 241, 335:340, 366

Full PDB list

1fr1, 1fr6, 1rgy, 1zc2 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
8
4
L
1
3
9
Q
1
4
0
Y
1
7
0
N
1
7
2
V
2
3
1
Y
2
4
1
K
3
3
5
T
3
3
6
G
3
3
7
S
3
3
8
T
3
3
9
G
3
4
0
[1]1fr6.a azr28 * . . . . . . . . . . . .
[1]1rgy.a ptx17 * . . . . . . . . . . . .
[1]1zc2.a none . . . . . . . . . . . . .

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
V
2
3
1
Y
2
4
1
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]1fr6.a . * . . . . . . . . . . . . . .
[1]1rgy.a . * . . . . . . . . . . . . . .
[1]1zc2.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
1fr6.a:azr
1rgy.a:ptx
1zc2.a is apo
[1] 1fr6.a
0.8
0.8 -
[1] 1rgy.a 0.7
0.6
-
[1] 1zc2.a 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
1fr6.a
1rgy.a
1zc2.a
[1] 1fr6.a
0
.01 .02
[1] 1rgy.a .01
0
.01
[1] 1zc2.a .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1fr6.a
1rgy.a
1zc2.a
[1] 1fr6.a
0
0.3 0.4
[1] 1rgy.a 0.3
0
0.3
[1] 1zc2.a 0.4 0.3
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
1fr6.a
1rgy.a
1zc2.a
[1] 1fr6.a
0
0.4 0.8
[1] 1rgy.a 0.4
0
0.8
[1] 1zc2.a 0.8 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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