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AMYS_NEIPO_12_636

Amylosucrase [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer
A1 (AMYS_NEIPO):152, 155, 195, 234, 236, 237, 258, 262, 292, 294, 295, 297, 298, 336:340, 400:402, 404:407, 409, 423, 444, 452, 454, 517152, 155, 195, 234, 236, 237, 258, 262, 292, 294, 295, 297, 298, 336:340, 400:402, 404:407, 409, 423, 444, 452, 454, 517

Full PDB list

1g5a, 1jg9, 1jgi, 1mvy, 1mw0, 1mw1, 1mw2, 1mw3, 1s46, 1zs2, 3ueq, 4flo, 4flq, 4flr, 4fls, 5n6v, 5n7j (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
1
5
2
Y
1
5
5
H
1
9
5
R
2
3
4
I
2
3
6
F
2
3
7
F
2
5
8
Q
2
6
2
R
2
9
2
D
2
9
4
A
2
9
5
F
2
9
8
E
3
3
6
A
3
3
7
I
3
3
8
V
3
3
9
H
3
4
0
H
4
0
0
D
4
0
1
D
4
0
2
G
4
0
4
W
4
0
5
T
4
0
6
F
4
0
7
D
4
0
9
R
4
2
3
F
4
4
4
D
4
5
2
R
4
5
4
R
5
1
7
[1]1jg9.a glc12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jgi.a suc23 . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . .
[1]1mvy.a none . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . .
[1]1mw0.a glc.glc.glc.glc.glc.glc.glc78 . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . .
[1]1mw2.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1s46.a none . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . .
[1]3ueq.a otu23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4flo.a none . . . . . . . . . . . C . . . . . . . . . . . . . . . . . .
[1]4flq.a none . . . . . . . . . . . I . . . . . . . . . . . . . . . . . .
[1]4flr.a none . . . . . . . . . . . L . . . . . . . . . . . . . . . . . .
[1]4fls.a suc23 . . . . . . . . . . . K Q . . . . . . . . . . . . . . . . .
[1]5n6v.a none . . . . . . . . . . . . . . . D . . . . . . . . . . . . . .
[1]5n7j.a none . . . K V . . . . . . Y . . . T . . . . . . . . . . . . . .

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
D
1
5
2
Y
1
5
5
H
1
9
5
R
2
3
4
I
2
3
6
F
2
3
7
F
2
5
8
Q
2
6
2
R
2
9
2
D
2
9
4
A
2
9
5
A
2
9
7
F
2
9
8
E
3
3
6
A
3
3
7
I
3
3
8
V
3
3
9
H
3
4
0
H
4
0
0
D
4
0
1
D
4
0
2
G
4
0
4
W
4
0
5
T
4
0
6
F
4
0
7
D
4
0
9
R
4
2
3
F
4
4
4
D
4
5
2
R
4
5
4
R
5
1
7
[1]1jg9.a . . . * . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]1jgi.a . . . * . . . . . * . . . Q . . . . . . . . . * . . . . . . .
[1]1mvy.a . . . . . . . . . * . . . Q . . . . . . . . . * . . . . . . .
[1]1mw0.a . . . . . . . . . * . . . Q . . . . . . . . . . . . . . . . .
[1]1mw2.a . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . .
[1]1s46.a . . . * . . . . . * . . . Q . . . . . . . . . * . . . . . . .
[1]3ueq.a . . . * . . . . . * . . . . . . . . . . . . . * . . . . . . .
[1]4flo.a . . . * . . . . . * . P C . . . . . . . . . . * . . . . . . .
[1]4flq.a . . . * . . . . . * . P I . . . . . . . . . . * . . . . . . .
[1]4flr.a . . . * . . . . . . . P L . . . . . . . . . . * . . . . . . .
[1]4fls.a . . . * . . . . . * . . K Q . . . . . . . . . * . . . . . . .
[1]5n6v.a . . . * . . . . . * . . . . . . D . . . . . . * . . . . . . .
[1]5n7j.a . . . K V . . . . . . I Y . . . T . . . . . . * . . . . . . .

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
1jg9.a:glc
1jgi.a:suc
1mvy.a is apo
1mw0.a:glc.glc.glc.glc.glc.glc.glc
1mw2.a is apo
1s46.a is apo
3ueq.a:otu
4flo.a is apo
4flq.a is apo
4flr.a is apo
4fls.a:suc
5n6v.a is apo
5n7j.a is apo
[1] 1jg9.a
0
0.2 - 1.9 - - 0.2 - - - 0.1 - -
[1] 1jgi.a 0.9
0.2
- 1.7 - - 0.2 - - - 0 - -
[1] 1mvy.a 0.7 0.2
-
1.6 - - 0.1 - - - 0.1 - -
[1] 1mw0.a 0.8 0.1 -
0.1
- - 0.4 - - - 0.1 - -
[1] 1mw2.a 0.9 0.2 - 1.5
-
- 0.2 - - - 0.2 - -
[1] 1s46.a 1.6 0.7 - 2.4 -
-
0.6 - - - 0.3 - -
[1] 3ueq.a 0.6 0.2 - 1.7 - -
0.1
- - - 0.1 - -
[1] 4flo.a 0.8 0.3 - 2.4 - - 0.5
-
- - 0.3 - -
[1] 4flq.a 0.8 0.3 - 2.1 - - 0.3 -
-
- 0.1 - -
[1] 4flr.a 0.6 0.3 - 2.2 - - 0.3 - -
-
0.3 - -
[1] 4fls.a 1.0 0.2 - 1.5 - - 0.2 - - -
0
- -
[1] 5n6v.a 0.9 0.4 - 2.0 - - 0.3 - - - 0.2
-
-
[1] 5n7j.a 0.6 0.4 - 1.2 - - 0.3 - - - 0.4 -
-
[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
1jg9.a
1jgi.a
1mvy.a
1mw0.a
1mw2.a
1s46.a
3ueq.a
4flo.a
4flq.a
4flr.a
4fls.a
5n6v.a
5n7j.a
[1] 1jg9.a
0
.05 .03 .10 .04 .07 .02 .05 .04 .04 .05 .05 .05
[1] 1jgi.a .05
0
.03 .07 .04 .05 .03 .04 .04 .05 .02 .05 .05
[1] 1mvy.a .03 .03
0
.07 .01 .05 .01 .04 .03 .05 .03 .03 .04
[1] 1mw0.a .10 .07 .07
0
.08 .11 .07 .10 .09 .11 .07 .09 .07
[1] 1mw2.a .04 .04 .01 .08
0
.06 .02 .04 .03 .04 .04 .03 .03
[1] 1s46.a .07 .05 .05 .11 .06
0
.05 .06 .07 .08 .05 .07 .08
[1] 3ueq.a .02 .03 .01 .07 .02 .05
0
.03 .02 .04 .03 .03 .05
[1] 4flo.a .05 .04 .04 .10 .04 .06 .03
0
.04 .05 .06 .04 .05
[1] 4flq.a .04 .04 .03 .09 .03 .07 .02 .04
0
.03 .05 .03 .05
[1] 4flr.a .04 .05 .05 .11 .04 .08 .04 .05 .03
0
.06 .04 .03
[1] 4fls.a .05 .02 .03 .07 .04 .05 .03 .06 .05 .06
0
.04 .05
[1] 5n6v.a .05 .05 .03 .09 .03 .07 .03 .04 .03 .04 .04
0
.04
[1] 5n7j.a .05 .05 .04 .07 .03 .08 .05 .05 .05 .03 .05 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1jg9.a
1jgi.a
1mvy.a
1mw0.a
1mw2.a
1s46.a
3ueq.a
4flo.a
4flq.a
4flr.a
4fls.a
5n6v.a
5n7j.a
[1] 1jg9.a
0
0.1 0.3 0.4 0.1 0.2 0.1 0.2 0.2 0.2 0.3 0.2 0.2
[1] 1jgi.a 0.1
0
0.3 0.5 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3
[1] 1mvy.a 0.3 0.3
0
0.5 0.3 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.3
[1] 1mw0.a 0.4 0.5 0.5
0
0.5 0.5 0.4 0.5 0.4 0.5 0.5 0.5 0.5
[1] 1mw2.a 0.1 0.2 0.3 0.5
0
0.2 0.1 0.2 0.2 0.2 0.3 0.2 0.2
[1] 1s46.a 0.2 0.2 0.3 0.5 0.2
0
0.2 0.3 0.3 0.3 0.3 0.3 0.3
[1] 3ueq.a 0.1 0.2 0.2 0.4 0.1 0.2
0
0.2 0.2 0.2 0.2 0.2 0.2
[1] 4flo.a 0.2 0.2 0.3 0.5 0.2 0.3 0.2
0
0.2 0.2 0.3 0.3 0.2
[1] 4flq.a 0.2 0.2 0.3 0.4 0.2 0.3 0.2 0.2
0
0.1 0.3 0.3 0.3
[1] 4flr.a 0.2 0.2 0.3 0.5 0.2 0.3 0.2 0.2 0.1
0
0.3 0.2 0.2
[1] 4fls.a 0.3 0.2 0.3 0.5 0.3 0.3 0.2 0.3 0.3 0.3
0
0.3 0.3
[1] 5n6v.a 0.2 0.3 0.3 0.5 0.2 0.3 0.2 0.3 0.3 0.2 0.3
0
0.3
[1] 5n7j.a 0.2 0.3 0.3 0.5 0.2 0.3 0.2 0.2 0.3 0.2 0.3 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

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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
1jg9.a
1jgi.a
1mvy.a
1mw0.a
1mw2.a
1s46.a
3ueq.a
4flo.a
4flq.a
4flr.a
4fls.a
5n6v.a
5n7j.a
[1] 1jg9.a
0
0.4 0.5 0.7 0.4 0.6 0.4 0.5 0.5 0.5 0.5 0.6 0.7
[1] 1jgi.a 0.4
0
0.4 0.6 0.3 0.5 0.3 0.3 0.3 0.4 0.3 0.5 0.6
[1] 1mvy.a 0.5 0.4
0
0.7 0.4 0.7 0.4 0.4 0.5 0.5 0.5 0.6 0.7
[1] 1mw0.a 0.7 0.6 0.7
0
0.7 0.8 0.7 0.7 0.6 0.7 0.7 0.8 0.7
[1] 1mw2.a 0.4 0.3 0.4 0.7
0
0.5 0.2 0.2 0.2 0.3 0.5 0.5 0.6
[1] 1s46.a 0.6 0.5 0.7 0.8 0.5
0
0.5 0.6 0.6 0.6 0.6 0.6 0.7
[1] 3ueq.a 0.4 0.3 0.4 0.7 0.2 0.5
0
0.2 0.2 0.3 0.4 0.5 0.6
[1] 4flo.a 0.5 0.3 0.4 0.7 0.2 0.6 0.2
0
0.2 0.3 0.5 0.4 0.6
[1] 4flq.a 0.5 0.3 0.5 0.6 0.2 0.6 0.2 0.2
0
0.2 0.4 0.4 0.6
[1] 4flr.a 0.5 0.4 0.5 0.7 0.3 0.6 0.3 0.3 0.2
0
0.5 0.4 0.6
[1] 4fls.a 0.5 0.3 0.5 0.7 0.5 0.6 0.4 0.5 0.4 0.5
0
0.6 0.7
[1] 5n6v.a 0.6 0.5 0.6 0.8 0.5 0.6 0.5 0.4 0.4 0.4 0.6
0
0.6
[1] 5n7j.a 0.7 0.6 0.7 0.7 0.6 0.7 0.6 0.6 0.6 0.6 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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