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CHXA_VIBCL_459_665

Cholix toxin

Composition of the binding site

Protein chains monomer
A1 (CHXA_VIBCL):388, 492:494, 498, 501, 502, 506, 507, 509:512, 517, 518, 521, 522, 524:527, 532, 533, 536, 540, 580, 581, 613, 618388, 492:494, 498, 501, 502, 506, 507, 509:512, 517, 518, 521, 522, 524:527, 532, 533, 536, 540, 580, 581, 613, 618

Full PDB list

2q5t, 2q6m, 3ess, 3ki0, 3ki1, 3ki2, 3ki3, 3ki4, 3ki5, 3ki6, 3ki7, 3ny6, 3q9o

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
3
8
8
H
4
9
2
G
4
9
3
T
4
9
4
T
5
0
1
I
5
0
2
A
5
0
7
V
5
0
9
R
5
1
1
N
5
1
7
E
5
1
8
W
5
2
1
L
5
2
4
Y
5
2
5
V
5
2
6
A
5
2
7
V
5
3
2
A
5
3
3
Y
5
3
6
K
5
4
0
L
5
8
0
E
5
8
1
E
6
1
3
W
6
1
8
[1]2q5t.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]2q6m.a p3422 - . . . . . . . - . . . . . . . . . . . . . . .
[1]3ess.a 18n15 - . . . . . . . - - - . . . . . . . . . . . . .
[1]3ki0.a g9d21 - . . . . . . . - . . . . . . . . . . . . . . .
[1]3ki1.a g9f27 - . . . . . . - - - - . . . . . . . . . . . . .
[1]3ki2.a g9g22 - . . . . . . - - . . . . . . . . . . . . . . .
[1]3ki3.a g9h18 - . . . . . . - - - - . . . . . . . . . . . . .
[1]3ki4.a g9p22 - . . . . . . . - . . . . . . . . . . . . . . .
[1]3ki5.a g9m30 - . . . . . . . - . . . . . . . . . . . . . . .
[1]3ki6.a g9l26 - . . . . . . - - . . . . . . . . . . . . . . .
[1]3ki7.a g9i28 - . . . . . . . - - - . . . . . . . . . . . . .
[1]3ny6.a v3020 - . . . . . . . - . . . . . . . . . . . . . . .
[1]3q9o.a nad44 . . . . . . . . . . . . . . . . . . . . . . . .

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
Q
3
8
8
H
4
9
2
G
4
9
3
T
4
9
4
A
4
9
8
T
5
0
1
I
5
0
2
I
5
0
6
A
5
0
7
V
5
0
9
P
5
1
0
R
5
1
1
G
5
1
2
N
5
1
7
E
5
1
8
W
5
2
1
G
5
2
2
L
5
2
4
Y
5
2
5
V
5
2
6
A
5
2
7
V
5
3
2
A
5
3
3
Y
5
3
6
K
5
4
0
L
5
8
0
E
5
8
1
E
6
1
3
W
6
1
8
[1]2q5t.a . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]2q6m.a - . . . . . . . . . - - - . . . . . . . . . . . . . . . .
[1]3ess.a - . . . . . . . . . - - - - - . . . . . . . . . . . . . .
[1]3ki0.a - . . . . . . . . . - - - . . . . . . . . . . . . . . . .
[1]3ki1.a - . . . . . . . . - - - - - - . . . . . . . . . . . . . .
[1]3ki2.a - . . . . . . . . - - - - . . . . . . . . . . . . . . . .
[1]3ki3.a - . . . . . . . . - - - - - - . . . . . . . . . . . . . .
[1]3ki4.a - . . . . . . . . . - - - . . . . . . . . . . . . . . . .
[1]3ki5.a - . . . . . . . . . - - - . . . . . . . . . . . . . . . .
[1]3ki6.a - . . . . . . . . - - - - . . . . . . . . . . . . . . . .
[1]3ki7.a - . . . . . . . . . - - - - - . . . . . . . . . . . . . .
[1]3ny6.a - . . . . . . . . . - - - . . . . . . . . . . . . . . . .
[1]3q9o.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
2q5t.a is apo
2q6m.a:p34
3ess.a:18n
3ki0.a:g9d
3ki1.a:g9f
3ki2.a:g9g
3ki3.a:g9h
3ki4.a:g9p
3ki5.a:g9m
3ki6.a:g9l
3ki7.a:g9i
3ny6.a:v30
3q9o.a:nad
[1] 2q5t.a
-
0.3 0 0 3.1 0.2 0 0.1 0.6 3.3 0.4 0.5 0.4
[1] 2q6m.a -
0
0 0.3 0.1 0 0 0 0 0.1 0.3 0.1 0.4
[1] 3ess.a - 0
0
0 0 0 0 0 0 0 0 0.2 0.3
[1] 3ki0.a - 0 0
0
0 0 0 0.1 0.4 0.2 0.1 0.1 0.3
[1] 3ki1.a - 0 0 0
0
0 0 0 0.3 0 0 0 0.3
[1] 3ki2.a - 0 0 0.3 0.2
0
0.3 0 0.4 0.1 0.3 0.1 0.6
[1] 3ki3.a - 0 0 0 0 0
0
0 0.2 0 0 0.1 0.2
[1] 3ki4.a - 0 0 0 0 0 0
0
0.1 0 0 0.2 0.3
[1] 3ki5.a - 0 0 0.1 0.1 0 0 0
0
0 0 0.1 0.2
[1] 3ki6.a - 0 0 0.1 0 0 0 0 0
0
0 0.1 0.4
[1] 3ki7.a - 0 0 0 0 0 0 0 0 0
0
0.1 0.1
[1] 3ny6.a - 0 0 0 0 0 0.1 0 0.2 0 0
0
0.3
[1] 3q9o.a - 0 0 0 2.5 0.2 0.1 0.1 0.5 3.2 0.5 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
2q5t.a
2q6m.a
3ess.a
3ki0.a
3ki1.a
3ki2.a
3ki3.a
3ki4.a
3ki5.a
3ki6.a
3ki7.a
3ny6.a
3q9o.a
[1] 2q5t.a
0
.17 .15 .18 .17 .17 .16 .15 .16 .17 .16 .17 .03
[1] 2q6m.a .17
0
.02 .03 .03 .02 .03 .02 .01 0 .02 .02 .16
[1] 3ess.a .15 .02
0
.03 .02 .03 .01 0 .01 .01 .01 .01 .14
[1] 3ki0.a .18 .03 .03
0
.02 .02 .03 .03 .03 .04 .03 .03 .16
[1] 3ki1.a .17 .03 .02 .02
0
.02 .01 .02 .02 .03 .02 .01 .16
[1] 3ki2.a .17 .02 .03 .02 .02
0
.03 .03 .02 .02 .04 .03 .17
[1] 3ki3.a .16 .03 .01 .03 .01 .03
0
.01 .02 .02 .01 .01 .15
[1] 3ki4.a .15 .02 0 .03 .02 .03 .01
0
.01 .01 .01 .01 .14
[1] 3ki5.a .16 .01 .01 .03 .02 .02 .02 .01
0
.01 .01 .02 .15
[1] 3ki6.a .17 0 .01 .04 .03 .02 .02 .01 .01
0
.02 .02 .15
[1] 3ki7.a .16 .02 .01 .03 .02 .04 .01 .01 .01 .02
0
.02 .14
[1] 3ny6.a .17 .02 .01 .03 .01 .03 .01 .01 .02 .02 .02
0
.16
[1] 3q9o.a .03 .16 .14 .16 .16 .17 .15 .14 .15 .15 .14 .16
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2q5t.a
2q6m.a
3ess.a
3ki0.a
3ki1.a
3ki2.a
3ki3.a
3ki4.a
3ki5.a
3ki6.a
3ki7.a
3ny6.a
3q9o.a
[1] 2q5t.a
0
0.8 0.5 0.9 0.4 0.7 0.3 0.6 0.7 0.7 0.5 0.4 0.3
[1] 2q6m.a 0.8
0
0.3 0.2 0.2 0.1 0.2 0.5 0.2 0.3 0.3 0.8 0.9
[1] 3ess.a 0.5 0.3
0
0.2 0.2 0.2 0.1 0.3 0.3 0.3 0.1 0.5 0.5
[1] 3ki0.a 0.9 0.2 0.2
0
0.2 0.2 0.2 0.6 0.3 0.3 0.3 0.9 1.0
[1] 3ki1.a 0.4 0.2 0.2 0.2
0
0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.4
[1] 3ki2.a 0.7 0.1 0.2 0.2 0.1
0
0.2 0.5 0.3 0.3 0.2 0.7 0.8
[1] 3ki3.a 0.3 0.2 0.1 0.2 0.2 0.2
0
0.1 0.2 0.3 0.1 0.2 0.3
[1] 3ki4.a 0.6 0.5 0.3 0.6 0.2 0.5 0.1
0
0.4 0.4 0.3 0.6 0.7
[1] 3ki5.a 0.7 0.2 0.3 0.3 0.2 0.3 0.2 0.4
0
0.3 0.3 0.7 0.8
[1] 3ki6.a 0.7 0.3 0.3 0.3 0.2 0.3 0.3 0.4 0.3
0
0.3 0.7 0.8
[1] 3ki7.a 0.5 0.3 0.1 0.3 0.2 0.2 0.1 0.3 0.3 0.3
0
0.5 0.6
[1] 3ny6.a 0.4 0.8 0.5 0.9 0.2 0.7 0.2 0.6 0.7 0.7 0.5
0
0.4
[1] 3q9o.a 0.3 0.9 0.5 1.0 0.4 0.8 0.3 0.7 0.8 0.8 0.6 0.4
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
2q5t.a
2q6m.a
3ess.a
3ki0.a
3ki1.a
3ki2.a
3ki3.a
3ki4.a
3ki5.a
3ki6.a
3ki7.a
3ny6.a
3q9o.a
[1] 2q5t.a
0
1.3 0.6 1.3 0.8 1.3 0.5 0.8 1.2 1.2 0.6 0.9 0.5
[1] 2q6m.a 1.3
0
0.9 0.7 0.9 0.6 0.9 1.0 0.3 0.7 0.9 1.2 1.4
[1] 3ess.a 0.6 0.9
0
0.8 0.5 0.9 0.1 0.3 0.8 0.8 0.2 0.9 0.6
[1] 3ki0.a 1.3 0.7 0.8
0
0.8 0.5 0.8 1.0 0.6 0.5 0.9 1.3 1.4
[1] 3ki1.a 0.8 0.9 0.5 0.8
0
0.7 0.5 0.6 0.8 0.8 0.6 0.8 0.6
[1] 3ki2.a 1.3 0.6 0.9 0.5 0.7
0
0.9 1.0 0.6 0.6 0.9 1.1 1.4
[1] 3ki3.a 0.5 0.9 0.1 0.8 0.5 0.9
0
0.3 0.8 0.9 0.1 0.8 0.5
[1] 3ki4.a 0.8 1.0 0.3 1.0 0.6 1.0 0.3
0
0.9 0.9 0.3 1.0 0.9
[1] 3ki5.a 1.2 0.3 0.8 0.6 0.8 0.6 0.8 0.9
0
0.6 0.8 1.1 1.3
[1] 3ki6.a 1.2 0.7 0.8 0.5 0.8 0.6 0.9 0.9 0.6
0
0.9 1.0 1.3
[1] 3ki7.a 0.6 0.9 0.2 0.9 0.6 0.9 0.1 0.3 0.8 0.9
0
0.9 0.7
[1] 3ny6.a 0.9 1.2 0.9 1.3 0.8 1.1 0.8 1.0 1.1 1.0 0.9
0
0.8
[1] 3q9o.a 0.5 1.4 0.6 1.4 0.6 1.4 0.5 0.9 1.3 1.3 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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