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BXB_CLOBO_2_438

Botulinum neurotoxin type B [Peptidase M27 family]

Composition of the binding site

Protein chains monomer
A1 (BXB_CLOBO):69, 259, 370, 373:377, 452, 454:456, 710, 711, 713, 71469, 259, 370, 373:377, 452, 454:456, 710, 711, 713, 714
Metals (Me):Zn

Full PDB list

1epw, 1f31, 1f82, 1g9a, 1g9b, 1g9c, 1g9d, 1i1e, 1s0b, 1s0c, 1s0d, 1s0e, 1s0f, 1s0g, 2etf, 2np0, 2xhl, 3zuq (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
6
9
Q
2
5
9
R
3
7
0
Y
3
7
3
F
3
7
4
S
3
7
5
D
3
7
6
S
3
7
7
E
4
5
2
L
4
5
4
F
4
5
5
F
4
5
6
T
7
1
0
Q
7
1
1
Y
7
1
3
T
7
1
4
[1]1epw.a none . . . . . . . . . . . . . . . . Zn
[1]1g9a.a bab25 . . . . . . . . . . . . . . . . Zn
[1]1g9b.a bab,zn26 . . . . . . . . . . . . . . . . Zn
[1]2np0.a ca1 . . . . . . . . . . . . . . . . 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
D
6
9
Q
2
5
9
R
3
7
0
Y
3
7
3
F
3
7
4
S
3
7
5
D
3
7
6
S
3
7
7
E
4
5
2
L
4
5
4
F
4
5
5
F
4
5
6
T
7
1
0
Q
7
1
1
Y
7
1
3
T
7
1
4
[1]1epw.a . . . . . . . . . . . . . . . . Zn
[1]1g9a.a . . . . . . . . . . . . . . . . Zn
[1]1g9b.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
1epw.a is apo
1g9a.a:bab
1g9b.a:bab,zn
2np0.a:ca
[1] 1epw.a
-
1.3 1.3 0
[1] 1g9a.a -
0.5
0.8 0.1
[1] 1g9b.a - 0.8
0.8
0
[1] 2np0.a - 1.7 1.8
0.2
[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
1epw.a
1g9a.a
1g9b.a
2np0.a
[1] 1epw.a
0
.05 .05 .08
[1] 1g9a.a .05
0
.01 .08
[1] 1g9b.a .05 .01
0
.07
[1] 2np0.a .08 .08 .07
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
1epw.a
1g9a.a
1g9b.a
2np0.a
[1] 1epw.a
0
0.3 0.3 0.7
[1] 1g9a.a 0.3
0
0.1 0.6
[1] 1g9b.a 0.3 0.1
0
0.7
[1] 2np0.a 0.7 0.6 0.7
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

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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
1epw.a
1g9a.a
1g9b.a
2np0.a
[1] 1epw.a
0
0.4 0.4 1.1
[1] 1g9a.a 0.4
0
0.4 1.1
[1] 1g9b.a 0.4 0.4
0
1.1
[1] 2np0.a 1.1 1.1 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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