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AMY_PSEHA_25_475

Alpha-amylase [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMY_PSEHA):R: Substrate binding (71, 74, 75)
R: Substrate binding (201, 202)
70, 113, 116, 151, 163:166, 196, 198, 199, 224, 226, 228, 231, 287, 288, 293, 294
70, 71, 74, 75, 113, 116, 151, 163:166, 196, 198, 199, 201, 202, 224, 226, 228, 231, 287, 288, 293, 294
Metals (Me):Ca

Full PDB list

1aqh, 1aqm, 1b0i, 1g94, 1g9h, 1jd7, 1jd9, 1kxh, 1l0p (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
W
7
0
W
7
1
Y
7
4
Q
7
5
H
1
1
3
A
1
1
6
Y
1
5
1
L
1
6
3
V
1
6
4
G
1
6
5
L
1
6
6
R
1
9
6
D
1
9
8
A
1
9
9
K
2
0
1
H
2
0
2
E
2
2
4
I
2
2
6
Q
2
2
8
E
2
3
1
H
2
8
7
D
2
8
8
H
2
9
3
G
2
9
4
[1]1g94.a daf.glc.daf.glc.glc76 . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1g9h.a none . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxh.a acr44 . . . . . . . . . . . . N . . . . . . . . . . . Ca

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 Me
W
7
0
W
7
1
Y
7
4
Q
7
5
H
1
1
3
A
1
1
6
Y
1
5
1
L
1
6
3
V
1
6
4
G
1
6
5
L
1
6
6
R
1
9
6
D
1
9
8
A
1
9
9
K
2
0
1
H
2
0
2
E
2
2
4
I
2
2
6
Q
2
2
8
E
2
3
1
H
2
8
7
D
2
8
8
H
2
9
3
G
2
9
4
[1]1g94.a . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1g9h.a . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxh.a . . . . . . . . . . . . N . . . . . . . . . . . Ca

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
1g94.a:daf.glc.daf.glc.glc
1g9h.a is apo
1kxh.a:acr
[1] 1g94.a
0
- 0.2
[1] 1g9h.a 0.1
-
0.1
[1] 1kxh.a 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
1g94.a
1g9h.a
1kxh.a
[1] 1g94.a
0
.01 .03
[1] 1g9h.a .01
0
.02
[1] 1kxh.a .03 .02
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

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
1g94.a
1g9h.a
1kxh.a
[1] 1g94.a
0
0.5 0.4
[1] 1g9h.a 0.5
0
0.3
[1] 1kxh.a 0.4 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

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
1g94.a
1g9h.a
1kxh.a
[1] 1g94.a
0
0.5 0.5
[1] 1g9h.a 0.5
0
0.4
[1] 1kxh.a 0.5 0.4
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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