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GRAM_HUMAN_26_257_pep

Granzyme M [Peptidase S1 family. Granzyme subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (GRAM_HUMAN):D: Peptidase S1 (50, 51, 66, 105:108, 182, 185, 202:207, 223:228)50, 51, 66, 105:108, 182, 185, 202:207, 223:228

Full PDB list

2zgc, 2zgh, 2zgj, 2zks

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
5
0
C
5
1
H
6
6
V
1
0
5
P
1
0
6
A
1
0
7
L
1
0
8
W
1
8
2
S
1
8
5
P
2
0
2
C
2
0
3
K
2
0
4
G
2
0
5
D
2
0
6
S
2
0
7
L
2
2
3
S
2
2
4
F
2
2
5
S
2
2
6
S
2
2
7
R
2
2
8
[1]2zgh.a SGKVPL42 . . . . . . . . . . . . . . . . . . . . .
[1]2zgj.a SGKVPLS48 . . . . . . . . . . . . . . . . . . . . .
[1]2zks.a aceKVPL0qe35 . . * . . . . . . . . . . . . . . . . . .
[2]2zgc.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

[download in TSV format]
   
PDB.ch
A1
L
5
0
C
5
1
H
6
6
V
1
0
5
P
1
0
6
A
1
0
7
L
1
0
8
W
1
8
2
S
1
8
5
P
2
0
2
C
2
0
3
K
2
0
4
G
2
0
5
D
2
0
6
S
2
0
7
L
2
2
3
S
2
2
4
F
2
2
5
S
2
2
6
S
2
2
7
R
2
2
8
[1]2zgh.a . . . . . . . . . . . . . . . . . . . . .
[1]2zgj.a . . * . . . . . . . . . . . . . . . . . .
[1]2zks.a . . * . . . . . . . . . . . . . . . . . .
[2]2zgc.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
2zgh.a:SGKVPL
2zgj.a:SGKVPLS
2zks.a:aceKVPL0qe
2zgc.a is apo
[1] 2zgh.a
0
0.1 0.6 -
[1] 2zgj.a 0
0
0.7 -
[1] 2zks.a 0.5 0.4
1.0
-
[2] 2zgc.a 6.8 7.0 8.9
-
[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
2zgh.a
2zgj.a
2zks.a
2zgc.a
[1] 2zgh.a
0
.02 .05 .41
[1] 2zgj.a .02
0
.03 .40
[1] 2zks.a .05 .03
0
.40
[2] 2zgc.a .41 .40 .40
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
2zgh.a
2zgj.a
2zks.a
2zgc.a
[1] 2zgh.a
0
0.4 0.5 1.3
[1] 2zgj.a 0.4
0
0.3 1.3
[1] 2zks.a 0.5 0.3
0
1.3
[2] 2zgc.a 1.3 1.3 1.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2zgh.a
2zgj.a
2zks.a
2zgc.a
[1] 2zgh.a
0
0.5 0.7 2.0
[1] 2zgj.a 0.5
0
0.8 2.0
[1] 2zks.a 0.7 0.8
0
2.0
[2] 2zgc.a 2.0 2.0 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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