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AMYP_PIG_16_511

Pancreatic alpha-amylase [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer
A1 (AMYP_PIG):68, 73, 74, 77, 78, 116, 119:122, 160:164, 166, 167, 177:180, 210, 212, 213, 215, 216, 248, 250, 252:255, 314, 315, 319:323, 371, 37268, 73, 74, 77, 78, 116, 119:122, 160:164, 166, 167, 177:180, 210, 212, 213, 215, 216, 248, 250, 252:255, 314, 315, 319:323, 371, 372
Metals (Me):Ca

Full PDB list

1bvn, 1dhk, 1hx0, 1jfh, 1kxq, 1kxt, 1kxv, 1ose, 1pif, 1pig, 1ppi, 1ua3, 1vah, 1wo2, 3l2l, 3l2m, 4x0n (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
6
8
W
7
3
W
7
4
Y
7
7
Q
7
8
H
1
1
6
G
1
1
9
S
1
2
0
G
1
2
1
A
1
2
2
S
1
6
0
G
1
6
2
Y
1
6
6
L
1
7
7
V
1
7
8
G
1
7
9
L
1
8
0
R
2
1
0
D
2
1
2
A
2
1
3
K
2
1
5
H
2
1
6
E
2
4
8
I
2
5
0
L
2
5
2
G
2
5
3
G
2
5
4
E
2
5
5
H
3
1
4
D
3
1
5
H
3
2
0
G
3
2
1
A
3
2
2
D
3
7
1
W
3
7
2
[1]1bvn.p SWRYSQ-ITTVGDGYIGS133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1dhk.a DS-V-F-SGAYQW82 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1hx0.a ac1.glc,glc.ac165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1jfh.a glc.ma1,ma2.ma348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxq.b YRRTGYT-VR82 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxq.d YRRTGYT-V71 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxv.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ose.a bgc.ac1.glc.ac165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1pig.a bgc.glc.agl.hmc.glc.agl65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ppi.a bgc.daf.glc.glc55 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ua3.a mlr34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1vah.a npo10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1wo2.a bgc.glc.glc34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]3l2l.a glc,glc.glc.glc.glc.glc67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]3l2m.a glc.glc.glc.glc.glc.glc66 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4x0n.a YIYHG-MGV-YKTPW115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
N
6
8
W
7
3
W
7
4
Y
7
7
Q
7
8
H
1
1
6
G
1
1
9
S
1
2
0
G
1
2
1
A
1
2
2
S
1
6
0
G
1
6
1
G
1
6
2
I
1
6
3
E
1
6
4
Y
1
6
6
N
1
6
7
L
1
7
7
V
1
7
8
G
1
7
9
L
1
8
0
R
2
1
0
D
2
1
2
A
2
1
3
K
2
1
5
H
2
1
6
E
2
4
8
I
2
5
0
L
2
5
2
G
2
5
3
G
2
5
4
E
2
5
5
H
3
1
4
D
3
1
5
G
3
1
9
H
3
2
0
G
3
2
1
A
3
2
2
G
3
2
3
D
3
7
1
W
3
7
2
[1]1bvn.p . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1dhk.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1hx0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . Ca
[1]1jfh.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . Ca
[1]1kxq.b . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxq.d . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1kxv.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ose.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . Ca
[1]1pig.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . Ca
[1]1ppi.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . Ca
[1]1ua3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1vah.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1wo2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]3l2l.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]3l2m.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4x0n.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
1bvn.p:SWRYSQ-ITTVGDGYIGS
1dhk.a:DS-V-F-SGAYQW
1hx0.a:ac1.glc,glc.ac1
1jfh.a:glc.ma1,ma2.ma3
1kxq.b:YRRTGYT-VR
1kxq.d:YRRTGYT-V
1kxv.b is apo
1ose.a:bgc.ac1.glc.ac1
1pig.a:bgc.glc.agl.hmc.glc.agl
1ppi.a:bgc.daf.glc.glc
1ua3.a:mlr
1vah.a:npo
1wo2.a:bgc.glc.glc
3l2l.a:glc,glc.glc.glc.glc.glc
3l2m.a:glc.glc.glc.glc.glc.glc
4x0n.a:YIYHG-MGV-YKTPW
[1] 1bvn.p
0.2
0.8 1.0 0.5 0.5 0.3 - 0.8 1.3 1.0 0.4 0 0.6 0.2 0.1 0.5
[1] 1dhk.a 0.6
0
0.3 0.1 0 0 - 0.1 0.2 0.2 0.3 0 0.5 0.1 0 0.6
[1] 1hx0.a 2.6 1.7
0
0 1.5 1.2 - 0.2 0.5 0.2 0.2 0 0.4 0.1 1.0 3.6
[1] 1jfh.a 2.4 0.8 0.3
0
1.3 1.2 - 0.6 0.9 0.4 0.2 0 0.3 0.1 0.8 5.0
[1] 1kxq.b 0.5 0.2 0.2 0.2
0
0.1 - 0.4 0.4 0.2 0.3 0 0.5 0 1.3 0.4
[1] 1kxq.d 1.3 0.4 0.3 0.2 0
0
- 0.5 0.6 0.2 0.4 0 0.5 0 1.0 0.9
[1] 1kxv.b 0.6 0.4 0.3 0.3 1.1 0.7
-
0.3 0.7 0.2 0.3 0 0.4 0 0 0.8
[1] 1ose.a 2.0 1.1 0 0.1 1.2 1.2 -
0
0.2 0.1 0.1 0 0.2 0.1 1.0 3.3
[1] 1pig.a 2.1 1.3 0 0.1 1.2 1.2 - 0
0.1
0 0.4 0 0.3 0.1 1.2 3.5
[1] 1ppi.a 2.5 1.2 0 0.1 1.6 1.5 - 0.2 0.3
0
0.3 0 0.2 0.1 1.0 4.3
[1] 1ua3.a 1.3 0.3 0.1 0 0.5 0.2 - 0.3 0.5 0.3
0.1
0 0.3 0 0 0.5
[1] 1vah.a 0.6 0.2 0.3 0.1 0.7 0.4 - 0.4 0.6 0.5 0.2
0
0.3 0 0 1.1
[1] 1wo2.a 1.8 0.3 0 0 0.4 0.2 - 0.3 0.4 0.3 0.4 0
0
0 0 0.7
[1] 3l2l.a 0.9 0.3 0.1 0.1 0.3 0.2 - 0.4 0.4 0.4 0.3 0 0.3
0
0.1 0.9
[1] 3l2m.a 1.2 0.2 0.1 0.1 0.4 0.2 - 0.4 0.4 0.4 0.3 0 0.4 0
0
1.0
[1] 4x0n.a 0.5 0.3 0.3 0.1 0.1 0.1 - 0.2 0.5 0.3 0.5 0 0.6 0.1 0
0.1
[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
1bvn.p
1dhk.a
1hx0.a
1jfh.a
1kxq.b
1kxq.d
1kxv.b
1ose.a
1pig.a
1ppi.a
1ua3.a
1vah.a
1wo2.a
3l2l.a
3l2m.a
4x0n.a
[1] 1bvn.p
0
.05 .13 .16 .07 .08 .05 .13 .14 .16 .05 .06 .07 .06 .07 .05
[1] 1dhk.a .05
0
.13 .15 .06 .07 .06 .11 .12 .14 .05 .05 .07 .04 .04 .03
[1] 1hx0.a .13 .13
0
.06 .14 .12 .13 .04 .04 .05 .10 .13 .10 .10 .11 .12
[1] 1jfh.a .16 .15 .06
0
.15 .16 .14 .06 .07 .05 .13 .12 .13 .13 .13 .15
[1] 1kxq.b .07 .06 .14 .15
0
.05 .07 .12 .12 .15 .07 .07 .09 .06 .07 .06
[1] 1kxq.d .08 .07 .12 .16 .05
0
.09 .13 .12 .14 .07 .08 .06 .06 .07 .07
[1] 1kxv.b .05 .06 .13 .14 .07 .09
0
.12 .13 .14 .05 .03 .07 .05 .06 .06
[1] 1ose.a .13 .11 .04 .06 .12 .13 .12
0
.04 .05 .11 .12 .10 .09 .09 .11
[1] 1pig.a .14 .12 .04 .07 .12 .12 .13 .04
0
.05 .12 .11 .11 .09 .10 .12
[1] 1ppi.a .16 .14 .05 .05 .15 .14 .14 .05 .05
0
.14 .14 .14 .11 .12 .14
[1] 1ua3.a .05 .05 .10 .13 .07 .07 .05 .11 .12 .14
0
.05 .03 .03 .04 .05
[1] 1vah.a .06 .05 .13 .12 .07 .08 .03 .12 .11 .14 .05
0
.07 .05 .05 .07
[1] 1wo2.a .07 .07 .10 .13 .09 .06 .07 .10 .11 .14 .03 .07
0
.05 .05 .07
[1] 3l2l.a .06 .04 .10 .13 .06 .06 .05 .09 .09 .11 .03 .05 .05
0
.01 .05
[1] 3l2m.a .07 .04 .11 .13 .07 .07 .06 .09 .10 .12 .04 .05 .05 .01
0
.06
[1] 4x0n.a .05 .03 .12 .15 .06 .07 .06 .11 .12 .14 .05 .07 .07 .05 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1bvn.p
1dhk.a
1hx0.a
1jfh.a
1kxq.b
1kxq.d
1kxv.b
1ose.a
1pig.a
1ppi.a
1ua3.a
1vah.a
1wo2.a
3l2l.a
3l2m.a
4x0n.a
[1] 1bvn.p
0
3.7 1.3 1.6 0.8 0.8 0.7 1.3 1.3 1.3 0.8 0.9 0.8 0.7 0.8 0.6
[1] 1dhk.a 3.7
0
4.2 4.2 3.8 3.9 3.8 4.2 4.2 4.2 3.8 3.9 3.8 3.8 3.8 3.8
[1] 1hx0.a 1.3 4.2
0
0.9 1.1 1.1 1.1 0.4 0.5 0.6 1.0 1.0 1.0 1.0 1.0 1.2
[1] 1jfh.a 1.6 4.2 0.9
0
1.5 1.5 1.5 0.8 0.9 0.7 1.4 1.3 1.4 1.4 1.4 1.5
[1] 1kxq.b 0.8 3.8 1.1 1.5
0
0.2 0.7 1.1 1.1 1.2 0.6 0.8 0.6 0.6 0.6 0.6
[1] 1kxq.d 0.8 3.9 1.1 1.5 0.2
0
0.7 1.1 1.1 1.2 0.6 0.8 0.6 0.6 0.6 0.6
[1] 1kxv.b 0.7 3.8 1.1 1.5 0.7 0.7
0
1.1 1.1 1.1 0.5 0.5 0.4 0.5 0.5 0.8
[1] 1ose.a 1.3 4.2 0.4 0.8 1.1 1.1 1.1
0
0.3 0.5 0.9 0.9 1.0 0.9 0.9 1.1
[1] 1pig.a 1.3 4.2 0.5 0.9 1.1 1.1 1.1 0.3
0
0.5 0.9 0.8 0.9 0.9 0.9 1.1
[1] 1ppi.a 1.3 4.2 0.6 0.7 1.2 1.2 1.1 0.5 0.5
0
1.1 0.9 1.1 1.1 1.1 1.2
[1] 1ua3.a 0.8 3.8 1.0 1.4 0.6 0.6 0.5 0.9 0.9 1.1
0
0.5 0.2 0.2 0.3 0.6
[1] 1vah.a 0.9 3.9 1.0 1.3 0.8 0.8 0.5 0.9 0.8 0.9 0.5
0
0.5 0.5 0.5 0.9
[1] 1wo2.a 0.8 3.8 1.0 1.4 0.6 0.6 0.4 1.0 0.9 1.1 0.2 0.5
0
0.3 0.3 0.7
[1] 3l2l.a 0.7 3.8 1.0 1.4 0.6 0.6 0.5 0.9 0.9 1.1 0.2 0.5 0.3
0
0.1 0.6
[1] 3l2m.a 0.8 3.8 1.0 1.4 0.6 0.6 0.5 0.9 0.9 1.1 0.3 0.5 0.3 0.1
0
0.7
[1] 4x0n.a 0.6 3.8 1.2 1.5 0.6 0.6 0.8 1.1 1.1 1.2 0.6 0.9 0.7 0.6 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1bvn.p
1dhk.a
1hx0.a
1jfh.a
1kxq.b
1kxq.d
1kxv.b
1ose.a
1pig.a
1ppi.a
1ua3.a
1vah.a
1wo2.a
3l2l.a
3l2m.a
4x0n.a
[1] 1bvn.p
0
3.1 1.8 1.9 1.3 1.3 1.2 1.7 1.6 1.7 1.1 1.1 1.2 1.1 1.2 0.9
[1] 1dhk.a 3.1
0
3.6 3.6 3.3 3.4 3.2 3.5 3.5 3.6 3.3 3.2 3.3 3.2 3.2 3.1
[1] 1hx0.a 1.8 3.6
0
1.0 1.5 1.6 1.4 0.8 0.8 0.8 1.1 1.6 1.1 1.2 1.2 1.6
[1] 1jfh.a 1.9 3.6 1.0
0
1.7 1.8 1.6 0.9 0.8 0.6 1.5 1.7 1.5 1.4 1.5 1.7
[1] 1kxq.b 1.3 3.3 1.5 1.7
0
0.6 1.0 1.6 1.5 1.6 1.1 1.1 1.0 1.0 1.1 1.3
[1] 1kxq.d 1.3 3.4 1.6 1.8 0.6
0
1.2 1.7 1.6 1.7 1.2 1.2 1.1 1.1 1.2 1.4
[1] 1kxv.b 1.2 3.2 1.4 1.6 1.0 1.2
0
1.5 1.4 1.4 0.9 0.9 0.9 0.9 1.0 1.2
[1] 1ose.a 1.7 3.5 0.8 0.9 1.6 1.7 1.5
0
0.6 0.7 1.2 1.6 1.2 1.2 1.3 1.5
[1] 1pig.a 1.6 3.5 0.8 0.8 1.5 1.6 1.4 0.6
0
0.6 1.2 1.5 1.2 1.1 1.2 1.5
[1] 1ppi.a 1.7 3.6 0.8 0.6 1.6 1.7 1.4 0.7 0.6
0
1.3 1.6 1.3 1.3 1.4 1.5
[1] 1ua3.a 1.1 3.3 1.1 1.5 1.1 1.2 0.9 1.2 1.2 1.3
0
1.0 0.5 0.7 0.8 1.0
[1] 1vah.a 1.1 3.2 1.6 1.7 1.1 1.2 0.9 1.6 1.5 1.6 1.0
0
1.0 1.1 1.1 1.2
[1] 1wo2.a 1.2 3.3 1.1 1.5 1.0 1.1 0.9 1.2 1.2 1.3 0.5 1.0
0
0.7 0.8 1.1
[1] 3l2l.a 1.1 3.2 1.2 1.4 1.0 1.1 0.9 1.2 1.1 1.3 0.7 1.1 0.7
0
0.5 1.0
[1] 3l2m.a 1.2 3.2 1.2 1.5 1.1 1.2 1.0 1.3 1.2 1.4 0.8 1.1 0.8 0.5
0
1.1
[1] 4x0n.a 0.9 3.1 1.6 1.7 1.3 1.4 1.2 1.5 1.5 1.5 1.0 1.2 1.1 1.0 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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