If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

AMY1_HORVU_25_431

Alpha-amylase type A isozyme [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMY1_HORVU):R: Substrate binding (404:406)
R: Substrate binding (416, 419:422)
399, 407, 423, 424, 426
399, 404:407, 416, 419:424, 426

Full PDB list

1ht6, 1p6w, 1rp8, 1rp9, 1rpk, 2qps, 2qpu, 3bsg, 3bsh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
3
9
9
Y
4
0
4
D
4
0
5
V
4
0
6
G
4
0
7
T
4
1
6
H
4
1
9
G
4
2
0
N
4
2
1
D
4
2
2
Y
4
2
3
A
4
2
4
W
4
2
6
[1]1ht6.a none . . . . . . . . . . . . .
[1]1p6w.a gtm.sgc.sgc.bgc46 . . . . . . . . . . . . .
[1]1rp8.a glc.glc.glc.glc.glc56 . . . . . . . . . . . . .
[1]1rp9.a daf.glc.glc44 . . . . . . . . . . . . .
[1]2qpu.a qpu32 . . . . . . . . . . . . .
[1]2qpu.b qps44 . . . . . . . . . . . . .
[1]3bsg.a none . . . . . . A . . . . . .
[1]3bsh.a none . A . . . . . . . . . . .

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
K
3
9
9
Y
4
0
4
D
4
0
5
V
4
0
6
G
4
0
7
T
4
1
6
H
4
1
9
G
4
2
0
N
4
2
1
D
4
2
2
Y
4
2
3
A
4
2
4
W
4
2
6
[1]1ht6.a . . . . . . . . . . . . .
[1]1p6w.a . . . . . . . . . . . . .
[1]1rp8.a . . . . . . . . . . . . .
[1]1rp9.a . . . . . . . . . . . . .
[1]2qpu.a . . . . . . . . . . . . .
[1]2qpu.b . . . . . . . . . . . . .
[1]3bsg.a . . . . . . A . . . . . .
[1]3bsh.a . 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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1ht6.a is apo
1p6w.a:gtm.sgc.sgc.bgc
1rp8.a:glc.glc.glc.glc.glc
1rp9.a:daf.glc.glc
2qpu.a:qpu
2qpu.b:qps
3bsg.a is apo
3bsh.a is apo
[1] 1ht6.a
-
0.4 0.2 0.2 0.1 0.2 - -
[1] 1p6w.a -
0
0 0 0.1 0 - -
[1] 1rp8.a - 0
0
0.1 0 0.2 - -
[1] 1rp9.a - 0 0
0
0.1 0.1 - -
[1] 2qpu.a - 0.1 0.1 0
0
0.1 - -
[1] 2qpu.b - 0.1 0 0 0
0
- -
[1] 3bsg.a - 0.3 0.2 0.1 0 0.1
-
-
[1] 3bsh.a - 0.2 0.1 0.3 0 0.1 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1ht6.a
1p6w.a
1rp8.a
1rp9.a
2qpu.a
2qpu.b
3bsg.a
3bsh.a
[1] 1ht6.a
0
.02 .03 .03 .02 .04 .04 .06
[1] 1p6w.a .02
0
.01 .01 0 .02 .03 .04
[1] 1rp8.a .03 .01
0
.02 .01 .02 .02 .03
[1] 1rp9.a .03 .01 .02
0
.01 .02 .04 .05
[1] 2qpu.a .02 0 .01 .01
0
.02 .03 .04
[1] 2qpu.b .04 .02 .02 .02 .02
0
.02 .02
[1] 3bsg.a .04 .03 .02 .04 .03 .02
0
.02
[1] 3bsh.a .06 .04 .03 .05 .04 .02 .02
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

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
1ht6.a
1p6w.a
1rp8.a
1rp9.a
2qpu.a
2qpu.b
3bsg.a
3bsh.a
[1] 1ht6.a
0
0.4 0.4 0.5 0.5 0.4 0.3 0.4
[1] 1p6w.a 0.4
0
0.2 0.2 0.1 0.1 0.3 0.6
[1] 1rp8.a 0.4 0.2
0
0.2 0.2 0.2 0.3 0.5
[1] 1rp9.a 0.5 0.2 0.2
0
0.1 0.2 0.4 0.6
[1] 2qpu.a 0.5 0.1 0.2 0.1
0
0.1 0.4 0.6
[1] 2qpu.b 0.4 0.1 0.2 0.2 0.1
0
0.3 0.5
[1] 3bsg.a 0.3 0.3 0.3 0.4 0.4 0.3
0
0.5
[1] 3bsh.a 0.4 0.6 0.5 0.6 0.6 0.5 0.5
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
1ht6.a
1p6w.a
1rp8.a
1rp9.a
2qpu.a
2qpu.b
3bsg.a
3bsh.a
[1] 1ht6.a
0
1.1 1.0 1.1 1.0 0.8 0.4 0.8
[1] 1p6w.a 1.1
0
0.7 0.5 0.6 0.8 1.0 1.0
[1] 1rp8.a 1.0 0.7
0
0.7 0.8 0.6 1.0 1.0
[1] 1rp9.a 1.1 0.5 0.7
0
0.6 0.8 1.1 1.1
[1] 2qpu.a 1.0 0.6 0.8 0.6
0
0.5 1.0 1.0
[1] 2qpu.b 0.8 0.8 0.6 0.8 0.5
0
0.8 0.9
[1] 3bsg.a 0.4 1.0 1.0 1.1 1.0 0.8
0
0.8
[1] 3bsh.a 0.8 1.0 1.0 1.1 1.0 0.9 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...