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AMYG_ASPNG_25_495

Glucoamylase [Glycosyl hydrolase 15 family]

Composition of the binding site

Protein chains monomer
A1 (AMYG_ASPNG):63, 72, 76, 78, 79, 143:145, 199, 201:204, 329, 335, 341, 439, 44163, 72, 76, 78, 79, 143:145, 199, 201:204, 329, 335, 341, 439, 441

Full PDB list

1agm, 1dog, 1gah, 1gai, 1glm, 3eqa, 3gly (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
A
6
3
Y
7
2
W
7
6
R
7
8
D
7
9
S
1
4
3
W
1
4
4
G
1
4
5
Y
1
9
9
L
2
0
1
W
2
0
2
E
2
0
3
E
2
0
4
R
3
2
9
Y
3
3
5
W
3
4
1
L
4
3
9
W
4
4
1
[1]1agm.a acr,acr88 . . . . . . . . . . . . . . . . . .
[1]1dog.a noj,noj22 . . . . . . . . . . . . . . . . . .
[1]1gah.a acr44 . . . . . . . . . . . . . . . . . .
[1]1gai.a gac44 . . . . . . . . . . . . . . . . . .
[1]3eqa.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

[download in TSV format]
   
PDB.ch
A1
A
6
3
Y
7
2
W
7
6
R
7
8
D
7
9
S
1
4
3
W
1
4
4
G
1
4
5
Y
1
9
9
L
2
0
1
W
2
0
2
E
2
0
3
E
2
0
4
R
3
2
9
Y
3
3
5
W
3
4
1
L
4
3
9
W
4
4
1
[1]1agm.a . . . . . . . . . . . . . . . . . .
[1]1dog.a . . . . . . . . . . . . . . . . . .
[1]1gah.a . . . . . . . . . . . . . . . . . .
[1]1gai.a . . . . . . . . . . . . . . . . . .
[1]3eqa.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
1agm.a:acr
1dog.a:noj
1gah.a:acr
1gai.a:gac
3eqa.a is apo
[1] 1agm.a
0.1
0.2 0 0 -
[1] 1dog.a 0
0.2
0 0 -
[1] 1gah.a 0.1 0.1
0
0 -
[1] 1gai.a 0.1 0.4 0
0
-
[1] 3eqa.a 0.1 0.4 0.1 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
1agm.a
1dog.a
1gah.a
1gai.a
3eqa.a
[1] 1agm.a
0
.01 .01 .01 .02
[1] 1dog.a .01
0
0 .02 .02
[1] 1gah.a .01 0
0
.02 .02
[1] 1gai.a .01 .02 .02
0
.01
[1] 3eqa.a .02 .02 .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1agm.a
1dog.a
1gah.a
1gai.a
3eqa.a
[1] 1agm.a
0
0.1 0.1 0.1 0.2
[1] 1dog.a 0.1
0
0.2 0.1 0.2
[1] 1gah.a 0.1 0.2
0
0.1 0.2
[1] 1gai.a 0.1 0.1 0.1
0
0.2
[1] 3eqa.a 0.2 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1agm.a
1dog.a
1gah.a
1gai.a
3eqa.a
[1] 1agm.a
0
0.2 0.3 0.3 0.3
[1] 1dog.a 0.2
0
0.3 0.3 0.3
[1] 1gah.a 0.3 0.3
0
0.1 0.3
[1] 1gai.a 0.3 0.3 0.1
0
0.3
[1] 3eqa.a 0.3 0.3 0.3 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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