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APEH_AERPE_2_582

Acylamino-acid-releasing enzyme [Peptidase S9C family]

Composition of the binding site

Protein chains monomer
A1 (APEH_AERPE):113, 115, 153, 155, 368, 369, 445, 446, 471, 474, 477, 485, 488, 489, 492, 526, 527, 556113, 115, 153, 155, 368, 369, 445, 446, 471, 474, 477, 485, 488, 489, 492, 526, 527, 556

Full PDB list

1ve6, 1ve7, 2hu5, 2hu7, 2hu8, 2qr5, 2qzp, 3o4g, 3o4h, 3o4i, 3o4j, 4re5, 4re6 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
L
1
1
5
G
3
6
8
G
3
6
9
S
4
4
5
Y
4
4
6
V
4
7
1
W
4
7
4
M
4
7
7
F
4
8
5
F
4
8
8
I
4
8
9
L
4
9
2
R
5
2
6
T
5
2
7
H
5
5
6
[1]1ve7.b 4np14 . . . . . . . . . . . . . . .
[1]2hu5.a GF16 . . . . . . . . . . . . . . .
[1]2hu7.a aceF15 . . . . . . . . . . . . . . .
[1]2hu8.b be2GF25 . . . A . . . . . . . . . . .
[1]3o4h.c none . . . . . . . . . . . . . . .
[1]4re5.a y3a20 . . . * . . . . . . . . . . *

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
R
1
1
3
L
1
1
5
F
1
5
3
F
1
5
5
G
3
6
8
G
3
6
9
S
4
4
5
Y
4
4
6
V
4
7
1
W
4
7
4
M
4
7
7
F
4
8
5
F
4
8
8
I
4
8
9
L
4
9
2
R
5
2
6
T
5
2
7
H
5
5
6
[1]1ve7.b . . . . . . . . . . . . . . . . . .
[1]2hu5.a . . . . . . * . . . . . . . . . . .
[1]2hu7.a . . . . . . * . . . . . . . . . . .
[1]2hu8.b . . . . . . A . . . . . . . . . . .
[1]3o4h.c . . . . . . * . . . . . . . . . . .
[1]4re5.a . . . . . . * . . . . . . . . . . *

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
1ve7.b:4np
2hu5.a:GF
2hu7.a:aceF
2hu8.b:be2GF
3o4h.c is apo
4re5.a:y3a
[1] 1ve7.b
0.1
0 0 0 - 1.0
[1] 2hu5.a 0.8
0.1
0 0.1 - 1.3
[1] 2hu7.a 0.5 0.2
0.1
0.1 - 1.3
[1] 2hu8.b 0.3 0 0
0
- 0.8
[1] 3o4h.c 0.9 0.5 0.5 0.5
-
1.6
[1] 4re5.a 0.8 0.2 0.3 0.1 -
1.5
[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
1ve7.b
2hu5.a
2hu7.a
2hu8.b
3o4h.c
4re5.a
[1] 1ve7.b
0
.04 .03 .03 .05 .06
[1] 2hu5.a .04
0
.02 .04 .03 .02
[1] 2hu7.a .03 .02
0
.04 .05 .03
[1] 2hu8.b .03 .04 .04
0
.06 .06
[1] 3o4h.c .05 .03 .05 .06
0
.02
[1] 4re5.a .06 .02 .03 .06 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1ve7.b
2hu5.a
2hu7.a
2hu8.b
3o4h.c
4re5.a
[1] 1ve7.b
0
0.4 0.3 0.3 0.6 0.5
[1] 2hu5.a 0.4
0
0.1 0.3 0.6 0.3
[1] 2hu7.a 0.3 0.1
0
0.3 0.6 0.3
[1] 2hu8.b 0.3 0.3 0.3
0
0.6 0.4
[1] 3o4h.c 0.6 0.6 0.6 0.6
0
0.6
[1] 4re5.a 0.5 0.3 0.3 0.4 0.6
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

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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
1ve7.b
2hu5.a
2hu7.a
2hu8.b
3o4h.c
4re5.a
[1] 1ve7.b
0
0.6 0.5 0.5 0.7 0.9
[1] 2hu5.a 0.6
0
0.1 0.3 0.7 0.7
[1] 2hu7.a 0.5 0.1
0
0.3 0.7 0.7
[1] 2hu8.b 0.5 0.3 0.3
0
0.7 0.8
[1] 3o4h.c 0.7 0.7 0.7 0.7
0
1.0
[1] 4re5.a 0.9 0.7 0.7 0.8 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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