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CUCM1_CUCME_111_731

Cucumisin [Peptidase S8 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CUCM1_CUCME):D: Peptidase S8 (204, 273:275, 304, 307, 522:526)204, 273:275, 304, 307, 522:526

Full PDB list

3vta, 4yn3

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
2
0
4
G
2
7
5
S
3
0
4
N
3
0
7
S
5
2
2
G
5
2
3
T
5
2
4
S
5
2
5
M
5
2
6
[1]3vta.a dfp10 . . . . . . . * .
[1]4yn3.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
H
2
0
4
S
2
7
3
V
2
7
4
G
2
7
5
S
3
0
4
N
3
0
7
S
5
2
2
G
5
2
3
T
5
2
4
S
5
2
5
M
5
2
6
[1]3vta.a . . . . . . . . . * .
[1]4yn3.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
3vta.a:dfp
4yn3.a is apo
[1] 3vta.a
0.9
-
[1] 4yn3.a 0.7
-
[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
3vta.a
4yn3.a
[1] 3vta.a
0
.02
[1] 4yn3.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3vta.a
4yn3.a
[1] 3vta.a
0
0.6
[1] 4yn3.a 0.6
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
3vta.a
4yn3.a
[1] 3vta.a
0
0.6
[1] 4yn3.a 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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