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CASP6_HUMAN_18_293

Caspase-6 [Peptidase C14A family]

Composition of the binding site

Protein chains monomer
A1 (CASP6_HUMAN):61, 62, 121:124, 128, 129, 163:168, 191:193, 219, 220, 261, 264:266, 269, 27261, 62, 121:124, 128, 129, 163:168, 191:193, 219, 220, 261, 264:266, 269, 272

Full PDB list

2wdp, 3k7e, 3nkf, 3nr2, 3od5, 3p45, 3qnw, 3s70, 3s8e, 3v6l, 3v6m, 4ejf, 4fxo, 4hva, 4iyr, 4n5d, 4n6g, 4n7j, 4n7m, 4nbk, 4nbl, 4nbn (redundant Pocketome entry); 3p4u (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
6
1
P
6
2
H
1
2
1
G
1
2
2
Y
1
2
8
H
1
6
8
H
2
1
9
V
2
6
1
C
2
6
4
K
2
6
5
D
2
6
6
A
2
6
9
[1]3od5.a none . . . . . . . . . . . .
[1]3qnw.a none . . . . . - . . . . . .
[1]4hva.b 4hv30 . . . . . . . . . . . .
[2]3v6l.a none . . . . . - . . - - - .
[2]4iyr.a none . . A . . . . . . . . .
[2]4nbl.a none . . . . . . . . . . . .

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
6
1
P
6
2
H
1
2
1
G
1
2
2
E
1
2
3
G
1
2
4
Y
1
2
8
A
1
2
9
C
1
6
3
R
1
6
4
G
1
6
5
N
1
6
6
Q
1
6
7
H
1
6
8
E
1
9
1
V
1
9
2
D
1
9
3
H
2
1
9
R
2
2
0
V
2
6
1
C
2
6
4
K
2
6
5
D
2
6
6
A
2
6
9
K
2
7
2
[1]3od5.a . . . . . . . . . . . . . . - - - . . . . . . . .
[1]3qnw.a . . . . * . . . . . - - - - - - - . . . . . . . .
[1]4hva.b . . . . . . . . . . . . . . - - - . . . . . . . .
[2]3v6l.a . . . . . . . . . * * * - - . * . . . . - - - . .
[2]4iyr.a . . A . . . . . . * * * . * . * . . . . . . . . .
[2]4nbl.a . . . . . . . . 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
3od5.a is apo
3qnw.a is apo
4hva.b:4hv
3v6l.a is apo
4iyr.a is apo
4nbl.a is apo
[1] 3od5.a
-
- 0 - - -
[1] 3qnw.a -
-
5.4 - - -
[1] 4hva.b - -
0
- - -
[2] 3v6l.a - - 8.8
-
- -
[2] 4iyr.a - - 14 -
-
-
[2] 4nbl.a - - 9.3 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
3od5.a
3qnw.a
4hva.b
3v6l.a
4iyr.a
4nbl.a
[1] 3od5.a
0
.17 0 .28 .43 .29
[1] 3qnw.a .17
0
.17 .44 .59 .45
[1] 4hva.b 0 .17
0
.28 .43 .29
[2] 3v6l.a .28 .44 .28
0
.16 .12
[2] 4iyr.a .43 .59 .43 .16
0
.25
[2] 4nbl.a .29 .45 .29 .12 .25
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 5.5 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
3od5.a
3qnw.a
4hva.b
3v6l.a
4iyr.a
4nbl.a
[1] 3od5.a
0
6.8 0.7 3.6 5.8 5.9
[1] 3qnw.a 6.8
0
6.9 7.1 6.7 6.6
[1] 4hva.b 0.7 6.9
0
3.8 6.0 6.1
[2] 3v6l.a 3.6 7.1 3.8
0
1.3 1.1
[2] 4iyr.a 5.8 6.7 6.0 1.3
0
1.7
[2] 4nbl.a 5.9 6.6 6.1 1.1 1.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 4.8 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
3od5.a
3qnw.a
4hva.b
3v6l.a
4iyr.a
4nbl.a
[1] 3od5.a
0
7.6 1.0 4.5 6.7 6.4
[1] 3qnw.a 7.6
0
7.8 7.8 7.5 7.4
[1] 4hva.b 1.0 7.8
0
4.6 6.9 6.6
[2] 3v6l.a 4.5 7.8 4.6
0
1.7 1.7
[2] 4iyr.a 6.7 7.5 6.9 1.7
0
2.8
[2] 4nbl.a 6.4 7.4 6.6 1.7 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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