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CBH_CLOPE_1_329

Choloylglycine hydrolase [Peptidase C59 family]

Composition of the binding site

Protein chains monomer
A1 (CBH_CLOPE):2, 18, 20, 26, 59, 61, 66, 68, 80, 82, 103, 133, 137:140, 1422, 18, 20, 26, 59, 61, 66, 68, 80, 82, 103, 133, 137:140, 142

Full PDB list

2bjf, 2bjg, 2rf8, 2rg2, 2rlc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
C
2
R
1
8
M
2
0
F
2
6
T
5
9
F
6
1
T
6
6
A
6
8
G
8
0
N
8
2
I
1
3
3
I
1
3
7
P
1
3
8
T
1
4
0
L
1
4
2
[1]2bjf.a dxc28 . . . . . . . . . . . . . . .
[1]2bjg.b none . . . . . . . . . . . . . . .
[1]2rf8.a none A . . . . . . . . . . . . . .
[1]2rg2.a none * L . . . . . . . . . . . . .
[1]2rlc.a chd29 * . * . . . . . . . . . . . .

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
C
2
R
1
8
M
2
0
F
2
6
T
5
9
F
6
1
T
6
6
A
6
8
G
8
0
N
8
2
Y
1
0
3
I
1
3
3
I
1
3
7
P
1
3
8
N
1
3
9
T
1
4
0
L
1
4
2
[1]2bjf.a . . . . . . . . . . . . . . . . .
[1]2bjg.b . . . . . * . . . . . . * . . . .
[1]2rf8.a A . . . . . . . . . . . . . . . .
[1]2rg2.a * L . . . . . . . . . . . . . . .
[1]2rlc.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
2bjf.a:dxc
2bjg.b is apo
2rf8.a is apo
2rg2.a is apo
2rlc.a:chd
[1] 2bjf.a
0
- - - 0
[1] 2bjg.b 1.6
-
- - 2.1
[1] 2rf8.a 0.2 -
-
- 0.2
[1] 2rg2.a 0.8 - -
-
1.1
[1] 2rlc.a 0.1 - - -
0
[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
2bjf.a
2bjg.b
2rf8.a
2rg2.a
2rlc.a
[1] 2bjf.a
0
.14 .01 .08 .01
[1] 2bjg.b .14
0
.12 .07 .14
[1] 2rf8.a .01 .12
0
.06 .02
[1] 2rg2.a .08 .07 .06
0
.08
[1] 2rlc.a .01 .14 .02 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
2bjf.a
2bjg.b
2rf8.a
2rg2.a
2rlc.a
[1] 2bjf.a
0
1.3 1.0 1.1 0.2
[1] 2bjg.b 1.3
0
0.9 0.9 1.2
[1] 2rf8.a 1.0 0.9
0
0.4 0.8
[1] 2rg2.a 1.1 0.9 0.4
0
1.0
[1] 2rlc.a 0.2 1.2 0.8 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
2bjf.a
2bjg.b
2rf8.a
2rg2.a
2rlc.a
[1] 2bjf.a
0
1.5 1.2 1.5 0.6
[1] 2bjg.b 1.5
0
1.3 1.4 1.5
[1] 2rf8.a 1.2 1.3
0
0.7 1.1
[1] 2rg2.a 1.5 1.4 0.7
0
1.3
[1] 2rlc.a 0.6 1.5 1.1 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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