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AMPA_HELPY_1_496

Cytosol aminopeptidase [Peptidase M17 family]

Composition of the binding site

Protein chains monomer
A1 (AMPA_HELPY):258, 263, 270, 278, 281, 338, 340, 342, 344, 367:370, 428, 461258, 263, 270, 278, 281, 338, 340, 342, 344, 367:370, 428, 461
Metals (Me):Na/Zn

Full PDB list

4zi6, 4zla

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
2
5
8
D
2
6
3
K
2
7
0
M
2
7
8
D
2
8
1
N
3
3
8
D
3
4
0
E
3
4
2
R
3
4
4
T
3
6
7
L
3
6
8
T
3
6
9
G
3
7
0
I
4
2
8
A
4
6
1
[1]4zi6.a none . . . . . . . . . . . . . . . Na,Zn
[1]4zla.a bes22 . . . . . . . . . . . . . . . Na,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
K
2
5
8
D
2
6
3
K
2
7
0
M
2
7
8
D
2
8
1
N
3
3
8
D
3
4
0
E
3
4
2
R
3
4
4
T
3
6
7
L
3
6
8
T
3
6
9
G
3
7
0
I
4
2
8
A
4
6
1
[1]4zi6.a . . . . . . . . . . . . . . . Na,Zn
[1]4zla.a . . . . . . . . . . . . . . . Na,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
4zi6.a is apo
4zla.a:bes
[1] 4zi6.a
-
0.1
[1] 4zla.a -
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
4zi6.a
4zla.a
[1] 4zi6.a
0
0
[1] 4zla.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
4zi6.a
4zla.a
[1] 4zi6.a
0
0.1
[1] 4zla.a 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
4zi6.a
4zla.a
[1] 4zi6.a
0
0.2
[1] 4zla.a 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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