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CBBY_RHOSH_1_230

Protein CbbY [HAD-like hydrolase superfamily. CbbY/CbbZ/Gph/YieH family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CBBY_RHOSH):R: Substrate binding (50, 51, 54)
R: Substrate binding (75, 78)
R: Substrate binding (115:118, 121)
8:10, 17, 20, 46, 49, 151
8:10, 17, 20, 46, 49:51, 54, 75, 78, 115:118, 121, 151
Metals (Me):Mg

Full PDB list

4uar, 4uas, 4uat, 4uau (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
D
8
V
9
D
1
0
E
1
7
H
2
0
T
4
9
G
5
0
G
5
1
R
5
4
H
7
5
K
7
8
T
1
1
5
T
1
1
6
T
1
1
7
S
1
1
8
N
1
2
1
[1]4uar.a none . . . . . . . . . . . . . . . .
[1]4uau.b xbp18 . . N . . . . . . . . . . . . . Mg

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 Me
D
8
V
9
D
1
0
E
1
7
H
2
0
L
4
6
T
4
9
G
5
0
G
5
1
R
5
4
H
7
5
K
7
8
T
1
1
5
T
1
1
6
T
1
1
7
S
1
1
8
N
1
2
1
K
1
5
1
[1]4uar.a . . . . . . . . . . . . . . . . . .
[1]4uau.b . . N . . . . . . . . . . . . . . . Mg

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
4uar.a is apo
4uau.b:xbp
[1] 4uar.a
-
0.8
[1] 4uau.b -
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
4uar.a
4uau.b
[1] 4uar.a
0
.04
[1] 4uau.b .04
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
4uar.a
4uau.b
[1] 4uar.a
0
0.4
[1] 4uau.b 0.4
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
4uar.a
4uau.b
[1] 4uar.a
0
0.6
[1] 4uau.b 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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