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.

AMPN_HUMAN_65_967

Aminopeptidase N [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPN_HUMAN):R: Metalloprotease (211, 213, 214, 350:355, 363, 381, 385, 388, 389, 392, 411, 442, 469, 472, 477, 864, 894:897, 900, 903, 904, 907)
R: Substrate binding (352:355)
211, 213, 214, 350:355, 363, 381, 385, 388, 389, 392, 411, 442, 469, 472, 477, 864, 894:897, 900, 903, 904, 907
Metals (Me):Zn

Full PDB list

4fyq, 4fyr, 4fys, 4fyt, 5lhd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
2
1
1
Q
2
1
3
A
2
1
4
A
3
5
1
G
3
5
2
A
3
5
3
M
3
5
4
E
3
5
5
R
3
6
3
R
3
8
1
V
3
8
5
H
3
8
8
E
3
8
9
H
3
9
2
E
4
1
1
R
4
4
2
S
4
6
9
F
4
7
2
Y
4
7
7
I
8
6
4
G
8
9
4
S
8
9
5
F
8
9
6
S
8
9
7
N
9
0
0
Q
9
0
3
A
9
0
4
R
9
0
7
[1]4fyq.a none . . . . . . . . . . . . . . . . . . . . - - - - . . . . Zn
[1]4fyr.a bes22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4fys.a VYIHPF56 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4fyt.a l2oVVD33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
Q
2
1
1
Q
2
1
3
A
2
1
4
N
3
5
0
A
3
5
1
G
3
5
2
A
3
5
3
M
3
5
4
E
3
5
5
R
3
6
3
R
3
8
1
V
3
8
5
H
3
8
8
E
3
8
9
H
3
9
2
E
4
1
1
R
4
4
2
S
4
6
9
F
4
7
2
Y
4
7
7
I
8
6
4
G
8
9
4
S
8
9
5
F
8
9
6
S
8
9
7
N
9
0
0
Q
9
0
3
A
9
0
4
R
9
0
7
[1]4fyq.a . . . . . . . . . . . . . . . . . . . . . - - - - . . . . Zn
[1]4fyr.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . . Zn
[1]4fys.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]4fyt.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4fyq.a is apo
4fyr.a:bes
4fys.a:VYIHPF
4fyt.a:l2oVVD
[1] 4fyq.a
-
0 0.4 0.3
[1] 4fyr.a -
0
0.9 2.1
[1] 4fys.a - 4.8
0
1.0
[1] 4fyt.a - 4.3 0.2
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
4fyq.a
4fyr.a
4fys.a
4fyt.a
[1] 4fyq.a
0
.11 .20 .16
[1] 4fyr.a .11
0
.28 .24
[1] 4fys.a .20 .28
0
.06
[1] 4fyt.a .16 .24 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4fyq.a
4fyr.a
4fys.a
4fyt.a
[1] 4fyq.a
0
0.3 0.3 0.3
[1] 4fyr.a 0.3
0
1.6 1.7
[1] 4fys.a 0.3 1.6
0
0.4
[1] 4fyt.a 0.3 1.7 0.4
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
4fyq.a
4fyr.a
4fys.a
4fyt.a
[1] 4fyq.a
0
0.8 0.4 0.4
[1] 4fyr.a 0.8
0
2.3 2.2
[1] 4fys.a 0.4 2.3
0
0.5
[1] 4fyt.a 0.4 2.2 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...