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AMPA_PSEPU_1_497

Cytosol aminopeptidase [Peptidase M17 family]

Composition of the binding site

Protein chains monomer
A1 (AMPA_PSEPU):267, 272, 279, 287, 290, 347, 349:351, 353, 376:379, 382, 437, 466, 470267, 272, 279, 287, 290, 347, 349:351, 353, 376:379, 382, 437, 466, 470
Metals (Me):Mn/Zn/K

Full PDB list

3h8e, 3h8f, 3h8g (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
2
6
7
D
2
7
2
K
2
7
9
M
2
8
7
D
2
9
0
N
3
4
7
D
3
4
9
E
3
5
1
R
3
5
3
T
3
7
6
L
3
7
7
T
3
7
8
G
3
7
9
I
3
8
2
I
4
3
7
A
4
6
6
W
4
7
0
[1]3h8f.a none . . . . . . . . . . . . . . . . . Mn,Zn,K
[1]3h8g.f bes22 . . . . . . . . . . . . . . . . . Mn,Zn,K

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

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PDB.ch
A1 Me
K
2
6
7
D
2
7
2
K
2
7
9
M
2
8
7
D
2
9
0
N
3
4
7
D
3
4
9
A
3
5
0
E
3
5
1
R
3
5
3
T
3
7
6
L
3
7
7
T
3
7
8
G
3
7
9
I
3
8
2
I
4
3
7
A
4
6
6
W
4
7
0
[1]3h8f.a . . . . . . . . . . . . . . . . . . Mn,Zn,K
[1]3h8g.f . . . . . . . . . . . . . . . . . . Mn,Zn,K

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
3h8f.a is apo
3h8g.f:bes
[1] 3h8f.a
-
0.2
[1] 3h8g.f -
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
3h8f.a
3h8g.f
[1] 3h8f.a
0
.01
[1] 3h8g.f .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3h8f.a
3h8g.f
[1] 3h8f.a
0
0.1
[1] 3h8g.f 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
3h8f.a
3h8g.f
[1] 3h8f.a
0
0.4
[1] 3h8g.f 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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