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PRSS8_HUMAN_51_303

Prostasin [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PRSS8_HUMAN):D: Peptidase S1 (69, 70, 85, 86, 126, 128:134, 212:216, 221, 232:238, 256:262, 267, 269)69, 70, 85, 86, 126, 128:134, 212:216, 221, 232:238, 256:262, 267, 269

Full PDB list

3dfj, 3dfl, 3e0n, 3e0p, 3e16, 3e1x, 3fvf, 3gyl, 3gym (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
6
9
C
7
0
H
8
5
C
8
6
Y
1
2
6
E
1
2
9
G
1
3
0
S
1
3
1
Q
1
3
2
D
1
3
4
E
2
1
3
P
2
1
4
H
2
1
5
F
2
1
6
M
2
2
1
D
2
3
2
A
2
3
3
C
2
3
4
Q
2
3
5
G
2
3
6
D
2
3
7
S
2
3
8
V
2
5
6
S
2
5
7
W
2
5
8
G
2
5
9
D
2
6
0
A
2
6
1
C
2
6
2
R
2
6
7
G
2
6
9
[1]3dfl.a gbs12 . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]3e0n.b dpnFarm34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e0p.b b3c53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3e16.b b4c49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fvf.b 1jz12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gym.a GPCKA-YGGCR68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3dfj.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]3gyl.b ca1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
V
6
9
C
7
0
H
8
5
C
8
6
Y
1
2
6
Q
1
2
8
E
1
2
9
G
1
3
0
S
1
3
1
Q
1
3
2
G
1
3
3
D
1
3
4
E
2
1
2
E
2
1
3
P
2
1
4
H
2
1
5
F
2
1
6
M
2
2
1
D
2
3
2
A
2
3
3
C
2
3
4
Q
2
3
5
G
2
3
6
D
2
3
7
S
2
3
8
V
2
5
6
S
2
5
7
W
2
5
8
G
2
5
9
D
2
6
0
A
2
6
1
C
2
6
2
R
2
6
7
G
2
6
9
[1]3dfl.a . . . . . . * . * . . . . . . . . . . . . * . . * . . . . . . . . .
[1]3e0n.b . . . . . . * * * . . . . . * . . . . . . * . . . . . . . . . . . .
[1]3e0p.b . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]3e16.b . . . . . . * . * . . . . . . . . . . . . . . . * . . . . . . . . .
[1]3fvf.b . . . . . . * . * . . . . . . . . . . . . * . . * . . . . . . . . .
[1]3gym.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3dfj.a . . . . . . * . * . . . . * * * . . . . . . . . . . . * * * * . . .
[3]3gyl.b . . . . . . * . * . . . . . . . . . . . . . . . * . . . * * . . . .

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
3dfl.a:gbs
3e0n.b:dpnFarm
3e0p.b:b3c
3e16.b:b4c
3fvf.b:1jz
3gym.a:GPCKA-YGGCR
3dfj.a is apo
3gyl.b:ca
[1] 3dfl.a
0.6
4.2 5.9 3.5 0.8 4.9 - 0.1
[1] 3e0n.b 0.5
0.9
6.8 3.9 0.3 5.0 - 0.2
[1] 3e0p.b 0.3 0.9
0.6
1.2 0.4 1.1 - 0.1
[1] 3e16.b 0.2 1.6 2.9
0.4
0.4 3.6 - 0.1
[1] 3fvf.b 0.6 1.5 4.3 2.5
0.6
4.2 - 0.1
[1] 3gym.a 0.5 1.3 0.7 0.3 0.5
0
- 0.2
[2] 3dfj.a 5.8 13 12 9.0 5.6 10
-
0.3
[3] 3gyl.b 0.5 7.0 9.6 7.2 0.7 6.8 -
0.5
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
3dfl.a
3e0n.b
3e0p.b
3e16.b
3fvf.b
3gym.a
3dfj.a
3gyl.b
[1] 3dfl.a
0
.18 .23 .13 .09 .26 .39 .28
[1] 3e0n.b .18
0
.29 .22 .19 .31 .52 .36
[1] 3e0p.b .23 .29
0
.17 .20 .09 .52 .37
[1] 3e16.b .13 .22 .17
0
.10 .19 .42 .29
[1] 3fvf.b .09 .19 .20 .10
0
.24 .45 .29
[1] 3gym.a .26 .31 .09 .19 .24
0
.52 .39
[2] 3dfj.a .39 .52 .52 .42 .45 .52
0
.29
[3] 3gyl.b .28 .36 .37 .29 .29 .39 .29
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.8 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
3dfl.a
3e0n.b
3e0p.b
3e16.b
3fvf.b
3gym.a
3dfj.a
3gyl.b
[1] 3dfl.a
0
1.7 2.5 0.7 0.6 2.0 1.8 1.0
[1] 3e0n.b 1.7
0
2.9 1.9 1.7 2.5 2.3 1.9
[1] 3e0p.b 2.5 2.9
0
2.4 2.4 1.1 3.0 2.7
[1] 3e16.b 0.7 1.9 2.4
0
0.8 1.8 1.7 1.3
[1] 3fvf.b 0.6 1.7 2.4 0.8
0
1.9 1.9 1.1
[1] 3gym.a 2.0 2.5 1.1 1.8 1.9
0
2.5 2.2
[2] 3dfj.a 1.8 2.3 3.0 1.7 1.9 2.5
0
1.6
[3] 3gyl.b 1.0 1.9 2.7 1.3 1.1 2.2 1.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.8 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
3dfl.a
3e0n.b
3e0p.b
3e16.b
3fvf.b
3gym.a
3dfj.a
3gyl.b
[1] 3dfl.a
0
3.0 3.5 1.2 1.1 2.9 2.4 1.5
[1] 3e0n.b 3.0
0
4.2 3.1 2.8 3.9 3.6 3.0
[1] 3e0p.b 3.5 4.2
0
3.3 3.3 1.4 4.3 3.6
[1] 3e16.b 1.2 3.1 3.3
0
1.3 2.6 2.5 1.9
[1] 3fvf.b 1.1 2.8 3.3 1.3
0
2.9 2.8 1.4
[1] 3gym.a 2.9 3.9 1.4 2.6 2.9
0
3.7 3.2
[2] 3dfj.a 2.4 3.6 4.3 2.5 2.8 3.7
0
2.2
[3] 3gyl.b 1.5 3.0 3.6 1.9 1.4 3.2 2.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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