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ADA_MOUSE_4_352

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

Composition of the binding site

Protein chains monomer
A1 (ADA_MOUSE):15, 17, 19, 58, 61, 62, 65, 102, 103, 106, 153, 155, 183, 184, 214, 217, 238, 295, 29615, 17, 19, 58, 61, 62, 65, 102, 103, 106, 153, 155, 183, 184, 214, 217, 238, 295, 296
Metals (Me):Zn

Full PDB list

1a4l, 1a4m, 1add, 1fkw, 1fkx, 1uio, 1uip, 2ada, 3km8, 3mvi, 3mvt, 3t1g (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
5
H
1
7
D
1
9
L
5
8
F
6
1
L
6
2
F
6
5
Y
1
0
2
S
1
0
3
L
1
0
6
C
1
5
3
M
1
5
5
A
1
8
3
G
1
8
4
H
2
1
4
E
2
1
7
H
2
3
8
D
2
9
5
D
2
9
6
[1]1a4l.c dcf19 . . . . . . . . . . . . . . . . . . . Zn
[1]1a4m.a prh19 . . . . . . . . . . . . . . . . . . . Zn
[1]1add.a 1da19 . . . . . . . . . . . . . . . . . . . Zn
[1]1fkw.a pur18 . . . . . . . . . . . . . . . . . E . Zn
[1]1fkx.a prh19 . . . . . . . . . . . . . . . . . . A Zn
[1]1uio.a hpr19 . . . . . . . . . . . . . . . . A . . Zn
[1]1uip.a pur18 . . . . . . . . . . . . . . . . E . . Zn
[1]2ada.a hpr19 . . . . . . . . . . . . . . . . . . . Zn
[1]3km8.a 9di19 . . . . . . . . . . . . . . . Q . . . Zn
[1]3mvi.a none . . . . . . . . . . . . . . . . . . . Zn
[1]3t1g.a none . . S Q T . W . . . . . I . . . . . A 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

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PDB.ch
A1 Me
H
1
5
H
1
7
D
1
9
L
5
8
F
6
1
L
6
2
F
6
5
Y
1
0
2
S
1
0
3
L
1
0
6
C
1
5
3
M
1
5
5
A
1
8
3
G
1
8
4
H
2
1
4
E
2
1
7
H
2
3
8
D
2
9
5
D
2
9
6
[1]1a4l.c . . . . . . . . . . . . . . . . . . . Zn
[1]1a4m.a . . . . . . . . . . . . . . . . . . . Zn
[1]1add.a . . . . . . . . . . . . . . . . . . . Zn
[1]1fkw.a . . . . . . . . . . . . . . . . . E . Zn
[1]1fkx.a . . . . . . . . . . . . . . . . . . A Zn
[1]1uio.a . . . . . . . . . . . . . . . . A . . Zn
[1]1uip.a . . . . . . . . . . . . . . . . E . . Zn
[1]2ada.a . . . . . . . . . . . . . . . . . . . Zn
[1]3km8.a . . . . . . . . . . . . . . . Q . . . Zn
[1]3mvi.a . . . . . . . . . . . . . . . . . . . Zn
[1]3t1g.a . . S Q T . W . . . . . I . . . . . 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
1a4l.c:dcf
1a4m.a:prh
1add.a:1da
1fkw.a:pur
1fkx.a:prh
1uio.a:hpr
1uip.a:pur
2ada.a:hpr
3km8.a:9di
3mvi.a is apo
3t1g.a is apo
[1] 1a4l.c
0.3
0.1 0.2 0.1 0.3 0.2 0.1 0.2 0.3 - -
[1] 1a4m.a 0.3
0
0.1 0.1 0.1 0.1 0.1 0.1 0.1 - -
[1] 1add.a 0.3 0
0
0 0 0 0 0.1 0 - -
[1] 1fkw.a 1.2 1.0 0.1
0.1
0.5 1.0 0.2 1.2 0.1 - -
[1] 1fkx.a 0.7 0.2 0.1 0
0
0.2 0 0.3 0.3 - -
[1] 1uio.a 0.2 0 0.2 0.1 0.2
0.1
0.1 0.1 0.1 - -
[1] 1uip.a 0.4 0.2 0.1 0.1 0.2 0.2
0.1
0.3 0.1 - -
[1] 2ada.a 0.2 0 0 0 0.1 0 0
0
0.2 - -
[1] 3km8.a 0.3 0.2 0.1 0 0.1 0.2 0 0.2
0.1
- -
[1] 3mvi.a 0.3 0 0.1 0.1 0.2 0.1 0.1 0.1 0.1
-
-
[1] 3t1g.a 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 -
-
[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
1a4l.c
1a4m.a
1add.a
1fkw.a
1fkx.a
1uio.a
1uip.a
2ada.a
3km8.a
3mvi.a
3t1g.a
[1] 1a4l.c
0
.03 .03 .07 .02 .03 .04 .02 .03 .04 .03
[1] 1a4m.a .03
0
.01 .05 .04 .02 .03 .02 .01 .03 .02
[1] 1add.a .03 .01
0
.05 .04 .01 .02 .01 .02 .03 .02
[1] 1fkw.a .07 .05 .05
0
.06 .06 .05 .06 .06 .08 .07
[1] 1fkx.a .02 .04 .04 .06
0
.05 .04 .04 .05 .06 .05
[1] 1uio.a .03 .02 .01 .06 .05
0
.01 .01 .02 .02 .02
[1] 1uip.a .04 .03 .02 .05 .04 .01
0
.02 .03 .03 .03
[1] 2ada.a .02 .02 .01 .06 .04 .01 .02
0
.02 .03 .02
[1] 3km8.a .03 .01 .02 .06 .05 .02 .03 .02
0
.02 .02
[1] 3mvi.a .04 .03 .03 .08 .06 .02 .03 .03 .02
0
.02
[1] 3t1g.a .03 .02 .02 .07 .05 .02 .03 .02 .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1a4l.c
1a4m.a
1add.a
1fkw.a
1fkx.a
1uio.a
1uip.a
2ada.a
3km8.a
3mvi.a
3t1g.a
[1] 1a4l.c
0
0.2 0.3 0.3 0.3 0.2 0.3 0.2 0.4 0.2 0.6
[1] 1a4m.a 0.2
0
0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.2 0.6
[1] 1add.a 0.3 0.2
0
0.3 0.2 0.3 0.3 0.2 0.3 0.2 0.6
[1] 1fkw.a 0.3 0.2 0.3
0
0.2 0.3 0.2 0.2 0.3 0.2 0.6
[1] 1fkx.a 0.3 0.2 0.2 0.2
0
0.2 0.2 0.2 0.4 0.2 0.6
[1] 1uio.a 0.2 0.2 0.3 0.3 0.2
0
0.2 0.2 0.3 0.2 0.6
[1] 1uip.a 0.3 0.2 0.3 0.2 0.2 0.2
0
0.2 0.4 0.2 0.6
[1] 2ada.a 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
0.3 0.2 0.6
[1] 3km8.a 0.4 0.3 0.3 0.3 0.4 0.3 0.4 0.3
0
0.3 0.7
[1] 3mvi.a 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3
0
0.6
[1] 3t1g.a 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.6
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
1a4l.c
1a4m.a
1add.a
1fkw.a
1fkx.a
1uio.a
1uip.a
2ada.a
3km8.a
3mvi.a
3t1g.a
[1] 1a4l.c
0
0.4 0.6 0.5 0.4 0.6 0.6 0.6 0.7 0.5 0.8
[1] 1a4m.a 0.4
0
0.5 0.4 0.3 0.5 0.6 0.6 0.6 0.2 0.7
[1] 1add.a 0.6 0.5
0
0.5 0.5 0.6 0.7 0.6 0.5 0.5 0.8
[1] 1fkw.a 0.5 0.4 0.5
0
0.4 0.6 0.5 0.5 0.6 0.5 0.8
[1] 1fkx.a 0.4 0.3 0.5 0.4
0
0.5 0.5 0.5 0.6 0.3 0.8
[1] 1uio.a 0.6 0.5 0.6 0.6 0.5
0
0.3 0.3 0.7 0.5 0.9
[1] 1uip.a 0.6 0.6 0.7 0.5 0.5 0.3
0
0.4 0.8 0.6 0.9
[1] 2ada.a 0.6 0.6 0.6 0.5 0.5 0.3 0.4
0
0.8 0.6 0.9
[1] 3km8.a 0.7 0.6 0.5 0.6 0.6 0.7 0.8 0.8
0
0.6 0.8
[1] 3mvi.a 0.5 0.2 0.5 0.5 0.3 0.5 0.6 0.6 0.6
0
0.7
[1] 3t1g.a 0.8 0.7 0.8 0.8 0.8 0.9 0.9 0.9 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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