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ADE_PSEAE_1_316

Adenine deaminase [Metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenine deaminase type 2 subfamily]

Composition of the binding site

Protein chains monomer
A1 (ADE_PSEAE):16, 54, 57, 58, 61, 166, 167, 194, 197, 218, 275, 27616, 54, 57, 58, 61, 166, 167, 194, 197, 218, 275, 276
Metals (Me):Zn

Full PDB list

3ou8, 3pan, 3pao, 3pbm

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
6
L
5
4
F
5
7
L
5
8
Y
6
1
D
1
6
6
S
1
6
7
H
1
9
4
E
1
9
7
H
2
1
8
D
2
7
5
D
2
7
6
[1]3ou8.a none . . . . . . . . . . . . Zn
[1]3pan.a hpa10 . . . . . . . . . . . . Zn
[1]3pao.a ade10 . . . . . . . . . . . . Zn
[1]3pbm.a es410 . . . . . . . . . . . . Zn

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 Me
H
1
6
L
5
4
F
5
7
L
5
8
Y
6
1
D
1
6
6
S
1
6
7
H
1
9
4
E
1
9
7
H
2
1
8
D
2
7
5
D
2
7
6
[1]3ou8.a . . . . . . . . . . . . Zn
[1]3pan.a . . . . . . . . . . . . Zn
[1]3pao.a . . . . . . . . . . . . Zn
[1]3pbm.a . . . . . . . . . . . . Zn

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
3ou8.a is apo
3pan.a:hpa
3pao.a:ade
3pbm.a:es4
[1] 3ou8.a
-
0 0 0.2
[1] 3pan.a -
0
0 0.3
[1] 3pao.a - 0.1
0
0.1
[1] 3pbm.a - 0.1 0
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
3ou8.a
3pan.a
3pao.a
3pbm.a
[1] 3ou8.a
0
.01 .03 .03
[1] 3pan.a .01
0
.03 .03
[1] 3pao.a .03 .03
0
.01
[1] 3pbm.a .03 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3ou8.a
3pan.a
3pao.a
3pbm.a
[1] 3ou8.a
0
0.1 0.1 0.1
[1] 3pan.a 0.1
0
0.1 0.1
[1] 3pao.a 0.1 0.1
0
0.1
[1] 3pbm.a 0.1 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3ou8.a
3pan.a
3pao.a
3pbm.a
[1] 3ou8.a
0
0.4 0.2 0.2
[1] 3pan.a 0.4
0
0.4 0.4
[1] 3pao.a 0.2 0.4
0
0.1
[1] 3pbm.a 0.2 0.4 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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