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BXB_CLOBO_438_856

Botulinum neurotoxin type B [Peptidase M27 family]

Composition of the binding site

Protein chains monomer
A1 (BXB_CLOBO):204, 218, 376:378, 447:449, 453, 537, 538, 541, 542, 714, 717, 721, 725204, 218, 376:378, 447:449, 453, 537, 538, 541, 542, 714, 717, 721, 725
Metals (Me):Zn

Full PDB list

1epw, 1f31, 1g9a, 1g9b, 1g9c, 1g9d, 1i1e, 1s0b, 1s0c, 1s0d, 1s0e, 1s0f, 1s0g, 2np0, 2xhl, 3zuq (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
2
0
4
R
2
1
8
D
3
7
6
L
3
7
8
D
4
4
8
V
4
4
9
D
4
5
3
F
5
3
8
L
5
4
1
E
7
1
7
K
7
2
1
[1]1g9d.a bab25 . . . . . . . . . . . Zn
[1]2np0.a none . . . . . . . . . . . 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

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PDB.ch
A1 Me
N
2
0
4
R
2
1
8
D
3
7
6
S
3
7
7
L
3
7
8
I
4
4
7
D
4
4
8
V
4
4
9
D
4
5
3
I
5
3
7
F
5
3
8
L
5
4
1
Y
5
4
2
T
7
1
4
E
7
1
7
K
7
2
1
Y
7
2
5
[1]1g9d.a . . . . . . . . . . . . . . . . . Zn
[1]2np0.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
1g9d.a:bab
2np0.a is apo
[1] 1g9d.a
0.2
-
[1] 2np0.a 1.7
-
[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
1g9d.a
2np0.a
[1] 1g9d.a
0
.08
[1] 2np0.a .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1g9d.a
2np0.a
[1] 1g9d.a
0
1.0
[1] 2np0.a 1.0
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
1g9d.a
2np0.a
[1] 1g9d.a
0
2.1
[1] 2np0.a 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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