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CATS_MOUSE_116_340

Cathepsin S [Peptidase C1 family]

Composition of the binding site

Protein chains monomer
A1 (CATS_MOUSE):141, 145:148, 187, 190:194, 260, 285:288, 334141, 145:148, 187, 190:194, 260, 285:288, 334

Full PDB list

4bpv, 4bqv, 4bs5, 4bs6, 4bsq, 4mzo, 4mzs

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
1
4
1
G
1
4
5
C
1
4
7
W
1
4
8
K
1
8
7
G
1
9
0
G
1
9
1
G
1
9
2
Y
1
9
3
M
1
9
4
G
2
6
0
V
2
8
5
N
2
8
6
H
2
8
7
G
2
8
8
Y
3
3
4
[1]4bpv.c ofh39 . . * . . . . . . . . . . . . .
[1]4bqv.b 8pw38 . . * . . . . . . . . . . . . .
[1]4bs5.a mg226 . . * . . . . . . . . . . . . .
[1]4bs6.a jg740 . . * . . . . . . . . . . . . .
[1]4bsq.a qqv28 . . * . . . . . . . . . . . . .
[1]4mzo.c 2ew28 . . * . . . . . . . . . . . . .
[1]4mzs.a 2ev29 . . * . . . . . . . . . . . . .

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
Q
1
4
1
G
1
4
5
A
1
4
6
C
1
4
7
W
1
4
8
K
1
8
7
G
1
9
0
G
1
9
1
G
1
9
2
Y
1
9
3
M
1
9
4
G
2
6
0
V
2
8
5
N
2
8
6
H
2
8
7
G
2
8
8
Y
3
3
4
[1]4bpv.c . . . * . . . . . . . . . . . . .
[1]4bqv.b . . . * . . . . . . . . . . . . .
[1]4bs5.a . . . * . . . . . . . . . . . . .
[1]4bs6.a . . . * . . . . . . . . . . . . .
[1]4bsq.a . . . * . . . . . . . . . . . . *
[1]4mzo.c . . . * . . . . . . . . . . . . .
[1]4mzs.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
4bpv.c:ofh
4bqv.b:8pw
4bs5.a:mg2
4bs6.a:jg7
4bsq.a:qqv
4mzo.c:2ew
4mzs.a:2ev
[1] 4bpv.c
0.4
0.4 0.4 0.4 1.0 0.6 1.1
[1] 4bqv.b 0.6
0.4
0.4 0.6 0.8 0.8 1.2
[1] 4bs5.a 0.7 0.4
0.4
0.6 0.4 0.6 0.7
[1] 4bs6.a 0.6 0.4 0.4
0.6
1.0 0.5 0.9
[1] 4bsq.a 1.8 2.4 2.1 1.8
0.5
2.0 1.4
[1] 4mzo.c 0.6 0.4 0.4 0.6 0.4
0.6
0.6
[1] 4mzs.a 0.6 0.4 0.4 0.4 0.4 0.4
0.4
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4bpv.c
4bqv.b
4bs5.a
4bs6.a
4bsq.a
4mzo.c
4mzs.a
[1] 4bpv.c
0
.02 .05 .01 .16 .04 .05
[1] 4bqv.b .02
0
.05 .01 .15 .02 .04
[1] 4bs5.a .05 .05
0
.04 .12 .02 .01
[1] 4bs6.a .01 .01 .04
0
.15 .03 .04
[1] 4bsq.a .16 .15 .12 .15
0
.12 .11
[1] 4mzo.c .04 .02 .02 .03 .12
0
.01
[1] 4mzs.a .05 .04 .01 .04 .11 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4bpv.c
4bqv.b
4bs5.a
4bs6.a
4bsq.a
4mzo.c
4mzs.a
[1] 4bpv.c
0
0.2 0.2 0.1 0.2 0.2 0.2
[1] 4bqv.b 0.2
0
0.2 0.1 0.2 0.2 0.1
[1] 4bs5.a 0.2 0.2
0
0.2 0.2 0.3 0.2
[1] 4bs6.a 0.1 0.1 0.2
0
0.2 0.2 0.1
[1] 4bsq.a 0.2 0.2 0.2 0.2
0
0.2 0.2
[1] 4mzo.c 0.2 0.2 0.3 0.2 0.2
0
0.2
[1] 4mzs.a 0.2 0.1 0.2 0.1 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
4bpv.c
4bqv.b
4bs5.a
4bs6.a
4bsq.a
4mzo.c
4mzs.a
[1] 4bpv.c
0
0.8 1.0 0.8 1.7 0.7 0.8
[1] 4bqv.b 0.8
0
0.7 0.1 1.5 1.1 1.1
[1] 4bs5.a 1.0 0.7
0
0.6 1.6 1.0 0.9
[1] 4bs6.a 0.8 0.1 0.6
0
1.5 1.0 1.1
[1] 4bsq.a 1.7 1.5 1.6 1.5
0
1.8 1.8
[1] 4mzo.c 0.7 1.1 1.0 1.0 1.8
0
0.3
[1] 4mzs.a 0.8 1.1 0.9 1.1 1.8 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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