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KLK6_HUMAN_22_244

Kallikrein-6 [Peptidase S1 family. Kallikrein subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KLK6_HUMAN):D: Peptidase S1 (45:47, 62, 63, 103, 151, 191:197, 211:218, 225)45:47, 62, 63, 103, 151, 191:197, 211:218, 225

Full PDB list

1gvl, 1l2e, 1lo6, 3vfe, 4d8n (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
4
5
L
4
6
C
4
7
H
6
2
C
6
3
H
1
0
3
F
1
5
1
D
1
9
1
S
1
9
2
C
1
9
3
Q
1
9
4
G
1
9
5
D
1
9
6
S
1
9
7
V
2
1
1
S
2
1
2
W
2
1
3
G
2
1
4
N
2
1
5
I
2
1
6
C
2
1
8
G
2
2
5
[1]1gvl.a none . . . . . . - - - . . . . . . . . . . . . .
[1]1lo6.a ben9 . . . . . . . . . . . . . . . . . . . . . .
[1]3vfe.a 0hl37 . . . . . . . . . . . . . . . . . . . . . .
[1]4d8n.a 0hm31 . . . . . . . . . . . . . . . . . . . . . .

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
L
4
5
L
4
6
C
4
7
H
6
2
C
6
3
H
1
0
3
F
1
5
1
D
1
9
1
S
1
9
2
C
1
9
3
Q
1
9
4
G
1
9
5
D
1
9
6
S
1
9
7
V
2
1
1
S
2
1
2
W
2
1
3
G
2
1
4
N
2
1
5
I
2
1
6
P
2
1
7
C
2
1
8
G
2
2
5
[1]1gvl.a . . . . . . - - - . . . . . . . . . * * . . .
[1]1lo6.a . . . . . . . . . . * . . . . . . . . . . . .
[1]3vfe.a . . . . . . . . . . . . . . . . . . . . . . .
[1]4d8n.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
1gvl.a is apo
1lo6.a:ben
3vfe.a:0hl
4d8n.a:0hm
[1] 1gvl.a
-
4.3 4.1 4.0
[1] 1lo6.a -
0
1.3 0.2
[1] 3vfe.a - 0
0
0.6
[1] 4d8n.a - 0.1 1.3
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
1gvl.a
1lo6.a
3vfe.a
4d8n.a
[1] 1gvl.a
0
.25 .21 .25
[1] 1lo6.a .25
0
.07 .01
[1] 3vfe.a .21 .07
0
.07
[1] 4d8n.a .25 .01 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1gvl.a
1lo6.a
3vfe.a
4d8n.a
[1] 1gvl.a
0
4.3 4.3 4.2
[1] 1lo6.a 4.3
0
0.3 0.3
[1] 3vfe.a 4.3 0.3
0
0.3
[1] 4d8n.a 4.2 0.3 0.3
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
1gvl.a
1lo6.a
3vfe.a
4d8n.a
[1] 1gvl.a
0
4.6 4.7 4.6
[1] 1lo6.a 4.6
0
0.7 0.4
[1] 3vfe.a 4.7 0.7
0
0.8
[1] 4d8n.a 4.6 0.4 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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