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BXB_CLOBO_856_1291

Botulinum neurotoxin type B [Peptidase M27 family]

Composition of the binding site

Protein chains monomer
A1 (BXB_CLOBO):1189, 1190, 1238:1242, 1244, 1258, 1260, 1262, 12631189, 1190, 1238:1242, 1244, 1258, 1260, 1262, 1263

Full PDB list

1epw, 1f31, 1g9a, 1g9b, 1g9c, 1g9d, 1i1e, 1s0b, 1s0c, 1s0d, 1s0e, 1s0f, 1s0g, 1z0h, 2nm1, 2np0, 4kbb, 5vid, 5vmr (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
1
1
8
9
E
1
1
9
0
G
1
2
3
9
I
1
2
4
0
H
1
2
4
1
R
1
2
4
2
C
1
2
5
8
S
1
2
6
0
W
1
2
6
2
Y
1
2
6
3
[1]1f31.a agc.gla.sia43 . . . . . . . . . .
[1]1i1e.a dm239 . . . . . . . . . .
[1]2nm1.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

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PDB.ch
A1
E
1
1
8
9
E
1
1
9
0
I
1
2
3
8
G
1
2
3
9
I
1
2
4
0
H
1
2
4
1
R
1
2
4
2
Y
1
2
4
4
C
1
2
5
8
S
1
2
6
0
W
1
2
6
2
Y
1
2
6
3
[1]1f31.a . . . . . . . . . . . .
[1]1i1e.a . . . . . . . . . . . .
[1]2nm1.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
1f31.a:agc.gla.sia
1i1e.a:dm2
2nm1.a is apo
[1] 1f31.a
0.2
2.4 -
[1] 1i1e.a 1.1
0.9
-
[1] 2nm1.a 4.0 4.0
-
[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
1f31.a
1i1e.a
2nm1.a
[1] 1f31.a
0
.13 .25
[1] 1i1e.a .13
0
.24
[1] 2nm1.a .25 .24
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1f31.a
1i1e.a
2nm1.a
[1] 1f31.a
0
0.3 0.8
[1] 1i1e.a 0.3
0
0.7
[1] 2nm1.a 0.8 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

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
1f31.a
1i1e.a
2nm1.a
[1] 1f31.a
0
0.7 2.1
[1] 1i1e.a 0.7
0
2.0
[1] 2nm1.a 2.1 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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