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ADA2_HUMAN_28_511

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ADA2_HUMAN):R: Substrate binding (204, 207, 208, 211)
114, 115, 248, 293, 325, 326, 356, 359, 384, 415, 441, 442
114, 115, 204, 207, 208, 211, 248, 293, 325, 326, 356, 359, 384, 415, 441, 442
Metals (Me):Zn

Full PDB list

3lgd, 3lgg

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
1
4
D
1
1
5
W
2
0
4
F
2
0
7
E
2
0
8
F
2
1
1
R
2
4
8
H
2
9
3
V
3
2
5
G
3
2
6
H
3
5
6
E
3
5
9
H
3
8
4
L
4
1
5
D
4
4
1
D
4
4
2
[1]3lgd.a none . . . . . . . . . . . . . . . . Zn
[1]3lgg.a cfe20 . . . . . . . . . . . . . . . . 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
1
4
D
1
1
5
W
2
0
4
F
2
0
7
E
2
0
8
F
2
1
1
R
2
4
8
H
2
9
3
V
3
2
5
G
3
2
6
H
3
5
6
E
3
5
9
H
3
8
4
L
4
1
5
D
4
4
1
D
4
4
2
[1]3lgd.a . . . . . . . . . . . . . . . . Zn
[1]3lgg.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
3lgd.a is apo
3lgg.a:cfe
[1] 3lgd.a
-
0.2
[1] 3lgg.a -
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
3lgd.a
3lgg.a
[1] 3lgd.a
0
.01
[1] 3lgg.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3lgd.a
3lgg.a
[1] 3lgd.a
0
0.2
[1] 3lgg.a 0.2
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
3lgd.a
3lgg.a
[1] 3lgd.a
0
0.8
[1] 3lgg.a 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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