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HEPS_HUMAN_46_417

Serine protease hepsin [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (HEPS_HUMAN):D: Peptidase S1 (187, 188, 203, 204, 206, 209, 243, 252, 254, 301, 331, 347:351, 353, 375:381, 388, 389)187, 188, 203, 204, 206, 209, 243, 252, 254, 301, 331, 347:351, 353, 375:381, 388, 389

Full PDB list

1o5e, 1o5f, 1p57, 1z8g, 3t2n, 5ce1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
8
7
C
1
8
8
H
2
0
3
C
2
0
4
P
2
0
6
Y
2
4
3
E
2
5
2
N
2
5
4
Y
3
0
1
Q
3
3
1
D
3
4
7
A
3
4
8
C
3
4
9
Q
3
5
0
G
3
5
1
S
3
5
3
V
3
7
5
S
3
7
6
W
3
7
7
G
3
7
8
T
3
7
9
G
3
8
0
C
3
8
1
G
3
8
8
[1]1o5e.h 13226 . . . . . . - . . . . . . . . . . . . . . . . .
[1]1o5f.h cr928 . . . . . . - . . . . . . . . . . . . . . . . .
[1]1p57.b cr419 . . . . . . - . . . . . . . . . . . . . . . . .
[1]1z8g.a aceKQLar7.0qe41 . . * . . . . . . . . . . . . * . . . . . . . .
[1]3t2n.a none . . . . . . . . - . - - - - . . . . - - - - - .
[1]5ce1.a 50k25 . . . . . . - . . . . . . . . . . . . . . . . .

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
L
1
8
7
C
1
8
8
H
2
0
3
C
2
0
4
P
2
0
6
N
2
0
9
Y
2
4
3
E
2
5
2
N
2
5
4
Y
3
0
1
Q
3
3
1
D
3
4
7
A
3
4
8
C
3
4
9
Q
3
5
0
G
3
5
1
S
3
5
3
V
3
7
5
S
3
7
6
W
3
7
7
G
3
7
8
T
3
7
9
G
3
8
0
C
3
8
1
G
3
8
8
V
3
8
9
[1]1o5e.h . . * . . . . - . . . . . . . . * . . . . . . . . .
[1]1o5f.h . . . . . . . - . . . . . . . . * . . . . . . . . .
[1]1p57.b . . * . . . . - . . . . . . . . * . . . . . . . . .
[1]1z8g.a . . * . . . . . . . . . . . * . * . . . . . . . . .
[1]3t2n.a . . . . . . . . . - . - - - - . * . . - - - - - . .
[1]5ce1.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
1o5e.h:132
1o5f.h:cr9
1p57.b:cr4
1z8g.a:aceKQLar7.0qe
3t2n.a is apo
5ce1.a:50k
[1] 1o5e.h
0.1
0.4 0.2 1.7 - 0.1
[1] 1o5f.h 0.4
0.1
0.3 1.5 - 0
[1] 1p57.b 0.1 0.1
0.1
1.6 - 0.1
[1] 1z8g.a 1.1 0.8 1.0
1.6
- 1.3
[1] 3t2n.a 0.5 0.6 0.6 2.1
-
0
[1] 5ce1.a 0.2 0.4 0.3 2.4 -
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
1o5e.h
1o5f.h
1p57.b
1z8g.a
3t2n.a
5ce1.a
[1] 1o5e.h
0
.04 .02 .07 .07 .03
[1] 1o5f.h .04
0
.03 .08 .04 .05
[1] 1p57.b .02 .03
0
.06 .06 .04
[1] 1z8g.a .07 .08 .06
0
.11 .09
[1] 3t2n.a .07 .04 .06 .11
0
.08
[1] 5ce1.a .03 .05 .04 .09 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1o5e.h
1o5f.h
1p57.b
1z8g.a
3t2n.a
5ce1.a
[1] 1o5e.h
0
0.3 0.2 0.3 1.8 0.3
[1] 1o5f.h 0.3
0
0.2 0.4 1.8 0.4
[1] 1p57.b 0.2 0.2
0
0.3 1.8 0.3
[1] 1z8g.a 0.3 0.4 0.3
0
1.8 0.3
[1] 3t2n.a 1.8 1.8 1.8 1.8
0
1.7
[1] 5ce1.a 0.3 0.4 0.3 0.3 1.7
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
1o5e.h
1o5f.h
1p57.b
1z8g.a
3t2n.a
5ce1.a
[1] 1o5e.h
0
0.3 0.2 0.8 2.4 0.5
[1] 1o5f.h 0.3
0
0.2 0.9 2.5 0.6
[1] 1p57.b 0.2 0.2
0
0.8 2.5 0.5
[1] 1z8g.a 0.8 0.9 0.8
0
2.6 0.8
[1] 3t2n.a 2.4 2.5 2.5 2.6
0
2.5
[1] 5ce1.a 0.5 0.6 0.5 0.8 2.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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