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AMPE_HUMAN_76_957

Glutamyl aminopeptidase [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPE_HUMAN):R: Substrate binding (357:360)
221:223, 356, 371, 386, 390, 393, 394, 397, 416, 474, 479, 887, 891
221:223, 356:360, 371, 386, 390, 393, 394, 397, 416, 474, 479, 887, 891
Metals (Me):Zn

Full PDB list

4kx7, 4kx8, 4kx9, 4kxa, 4kxb, 4kxc, 4kxd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
2
2
1
E
2
2
3
T
3
5
6
G
3
5
7
A
3
5
8
M
3
5
9
E
3
6
0
N
3
7
1
R
3
8
6
V
3
9
0
H
3
9
3
E
3
9
4
H
3
9
7
E
4
1
6
F
4
7
4
Y
4
7
9
R
8
8
7
[1]4kx7.a none . . . . . . . . . . . . . . . . . Zn
[1]4kx8.a l2oVVD33 . . . . . . . . . . . . . . . . . Zn
[1]4kx9.a R12 . . . . . . . . . . . . . . . . . Zn
[1]4kxa.a ca,D10 . . . . . . . . . . . . . . . . . Zn
[1]4kxb.a bes22 . . . . . . . . . . . . . . . . . Zn
[1]4kxc.a E10 . . . . . . . . . . . . . . . . . Zn
[1]4kxd.a ca,E11 . . . . . . . . . . . . . . . . . Zn

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
D
2
2
1
H
2
2
2
E
2
2
3
T
3
5
6
G
3
5
7
A
3
5
8
M
3
5
9
E
3
6
0
N
3
7
1
R
3
8
6
V
3
9
0
H
3
9
3
E
3
9
4
H
3
9
7
E
4
1
6
F
4
7
4
Y
4
7
9
R
8
8
7
R
8
9
1
[1]4kx7.a . . . . . . . . . . . . . . . . . * . Zn
[1]4kx8.a . . . . . . . . . . . . . . . . . . . Zn
[1]4kx9.a . . . . . . . . . . . . . . . . . * . Zn
[1]4kxa.a . . . . . . . . . . . . . . . . . * . Zn
[1]4kxb.a . . . . . . . . . . . . . . . . . . . Zn
[1]4kxc.a . . . . . . . . . . . . . . . . . . . Zn
[1]4kxd.a . . . . . . . . . . . . . . . . . * . Zn

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
4kx7.a is apo
4kx8.a:l2oVVD
4kx9.a:R
4kxa.a:D,ca
4kxb.a:bes
4kxc.a:E
4kxd.a:E,ca
[1] 4kx7.a
-
0.6 0.2 0.2 1.4 0.1 0.3
[1] 4kx8.a -
0.4
0.5 0.2 1.2 0 0.2
[1] 4kx9.a - 0.8
0.2
0.2 1.5 0.1 0.3
[1] 4kxa.a - 0.6 0.2
0.2
1.4 0.2 0.4
[1] 4kxb.a - 1.0 0.1 0.2
0.2
0 0.3
[1] 4kxc.a - 0.7 0.2 0.2 1.2
0.1
0.3
[1] 4kxd.a - 0.6 0.2 0.2 1.4 0.1
0.3
[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
4kx7.a
4kx8.a
4kx9.a
4kxa.a
4kxb.a
4kxc.a
4kxd.a
[1] 4kx7.a
0
.01 .02 0 .04 .02 0
[1] 4kx8.a .01
0
.03 .01 .04 .02 .01
[1] 4kx9.a .02 .03
0
.02 .05 .02 .02
[1] 4kxa.a 0 .01 .02
0
.04 .02 0
[1] 4kxb.a .04 .04 .05 .04
0
.04 .04
[1] 4kxc.a .02 .02 .02 .02 .04
0
.02
[1] 4kxd.a 0 .01 .02 0 .04 .02
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
4kx7.a
4kx8.a
4kx9.a
4kxa.a
4kxb.a
4kxc.a
4kxd.a
[1] 4kx7.a
0
0.1 0.1 0.1 0.1 0.1 0.1
[1] 4kx8.a 0.1
0
0.1 0.2 0.1 0.2 0.2
[1] 4kx9.a 0.1 0.1
0
0.1 0.1 0.1 0.1
[1] 4kxa.a 0.1 0.2 0.1
0
0.1 0.1 0.1
[1] 4kxb.a 0.1 0.1 0.1 0.1
0
0.1 0.1
[1] 4kxc.a 0.1 0.2 0.1 0.1 0.1
0
0.1
[1] 4kxd.a 0.1 0.2 0.1 0.1 0.1 0.1
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

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
4kx7.a
4kx8.a
4kx9.a
4kxa.a
4kxb.a
4kxc.a
4kxd.a
[1] 4kx7.a
0
0.3 0.1 0.1 1.0 0.3 0.1
[1] 4kx8.a 0.3
0
0.2 0.3 1.0 0.4 0.3
[1] 4kx9.a 0.1 0.2
0
0.1 0.9 0.3 0.1
[1] 4kxa.a 0.1 0.3 0.1
0
0.9 0.3 0.1
[1] 4kxb.a 1.0 1.0 0.9 0.9
0
0.9 0.9
[1] 4kxc.a 0.3 0.4 0.3 0.3 0.9
0
0.3
[1] 4kxd.a 0.1 0.3 0.1 0.1 0.9 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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