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CBP2_WHEAT_3_441

Serine carboxypeptidase 2 [Peptidase S10 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CBP2_WHEAT):R: Substrate binding (157:159)
60:62, 65, 70, 251, 293, 413, 414
60:62, 65, 70, 157:159, 251, 293, 413, 414

Full PDB list

1bcr, 1bcs, 1whs, 1wht, 3sc2 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
N
6
0
G
6
1
G
6
2
C
6
5
Y
7
0
E
1
5
7
S
1
5
8
Y
1
5
9
Y
2
5
1
H
4
1
3
E
4
1
4
[1]1bcr.a R12 . . . . . . . . . . .
[1]1bcs.a R12 . . . . . . . . . . .
[1]1wht.a bzs15 . . . . . . . . . . .
[1]3sc2.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
N
6
0
G
6
1
G
6
2
C
6
5
Y
7
0
E
1
5
7
S
1
5
8
Y
1
5
9
Y
2
5
1
E
2
9
3
H
4
1
3
E
4
1
4
[1]1bcr.a . . . . . . . . . . . .
[1]1bcs.a . . . . . . . . . . . .
[1]1wht.a . . . . . . . . . . . .
[1]3sc2.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
1bcr.a:R
1bcs.a:R
1wht.a:bzs
3sc2.a is apo
[1] 1bcr.a
0.3
0 0.3 -
[1] 1bcs.a 0.3
0
0.8 -
[1] 1wht.a 0.3 0.1
0.1
-
[1] 3sc2.a 0.3 0 0.3
-
[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
1bcr.a
1bcs.a
1wht.a
3sc2.a
[1] 1bcr.a
0
.04 .02 .01
[1] 1bcs.a .04
0
.06 .05
[1] 1wht.a .02 .06
0
.01
[1] 3sc2.a .01 .05 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1bcr.a
1bcs.a
1wht.a
3sc2.a
[1] 1bcr.a
0
0.2 0.2 0.2
[1] 1bcs.a 0.2
0
0.2 0.2
[1] 1wht.a 0.2 0.2
0
0.2
[1] 3sc2.a 0.2 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

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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
1bcr.a
1bcs.a
1wht.a
3sc2.a
[1] 1bcr.a
0
0.4 0.7 0.6
[1] 1bcs.a 0.4
0
0.6 0.7
[1] 1wht.a 0.7 0.6
0
0.6
[1] 3sc2.a 0.6 0.7 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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