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ADA_HUMAN_2_358

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

Composition of the binding site

Protein chains monomer
A1 (ADA_HUMAN):15, 17, 19, 52, 56:62, 65, 102, 103, 106, 117, 153, 155, 157, 183:186, 214, 217, 218, 238, 268, 269, 295, 29615, 17, 19, 52, 56:62, 65, 102, 103, 106, 117, 153, 155, 157, 183:186, 214, 217, 218, 238, 268, 269, 295, 296
Metals (Me):Ni/Zn

Full PDB list

1krm, 1ndv, 1ndw, 1ndy, 1ndz, 1o5r, 1qxl, 1uml, 1v79, 1v7a, 1vfl, 1w1i, 1wxy, 1wxz, 2bgn, 2e1w, 2z7g, 3iar (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
5
H
1
7
D
1
9
M
5
2
L
5
6
T
5
7
L
5
8
F
6
1
L
6
2
F
6
5
Y
1
0
2
S
1
0
3
L
1
0
6
W
1
1
7
C
1
5
3
M
1
5
5
H
1
5
7
A
1
8
3
G
1
8
4
D
1
8
5
H
2
1
4
E
2
1
7
V
2
1
8
H
2
3
8
T
2
6
9
D
2
9
5
D
2
9
6
[1]1ndv.a fr025 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndw.a fr219 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndy.a fr323 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndz.a fr537 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1o5r.a fr933 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1qxl.a fr835 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1uml.a fr433 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1v79.a fr722 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1v7a.a frc25 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1vfl.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1wxy.a frk27 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1wxz.a frl30 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2e1w.a fr624 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2z7g.a eh920 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]1krm.a prh19 . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]3iar.a 3d118 . . . . . . . . . . . . . . . . . . . . . . . . . . . Ni

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
5
H
1
7
D
1
9
M
5
2
L
5
6
T
5
7
L
5
8
P
5
9
D
6
0
F
6
1
L
6
2
F
6
5
Y
1
0
2
S
1
0
3
L
1
0
6
W
1
1
7
C
1
5
3
M
1
5
5
H
1
5
7
A
1
8
3
G
1
8
4
D
1
8
5
E
1
8
6
H
2
1
4
E
2
1
7
V
2
1
8
H
2
3
8
L
2
6
8
T
2
6
9
D
2
9
5
D
2
9
6
[1]1ndv.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndw.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndy.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . Zn
[1]1ndz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1o5r.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1qxl.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1uml.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1v79.a . . . . . . . . . * * . . . . . . . . . . . . . . . . . . . . Zn
[1]1v7a.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1vfl.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . Zn
[1]1wxy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1wxz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2e1w.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2z7g.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]1krm.a . . . . . * * . . * * . . . . . . . . . . . . . . . . . . . . Zn
[2]3iar.a . . . . . * * . . * * . . . . . . . . . . . . . . . . . . . . Ni

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
1ndv.a:fr0
1ndw.a:fr2
1ndy.a:fr3
1ndz.a:fr5
1o5r.a:fr9
1qxl.a:fr8
1uml.a:fr4
1v79.a:fr7
1v7a.a:frc
1vfl.a is apo
1wxy.a:frk
1wxz.a:frl
2e1w.a:fr6
2z7g.a:eh9
1krm.a:prh
3iar.a:3d1
[1] 1ndv.a
0.2
0.2 0.1 0.8 0.2 0.1 0.2 0.3 0.2 - 0.3 0.5 0.3 0.8 0.5 0.4
[1] 1ndw.a 0.2
0
0.1 0.8 0.1 0.3 0.1 0.1 0.3 - 0.3 0.3 0.4 0.8 0.6 0.2
[1] 1ndy.a 0.3 0.2
0
0.8 0 0.1 0.1 0.1 0.2 - 0.3 0.5 0.3 0.6 0.6 0.3
[1] 1ndz.a 0 0.1 0.1
0.1
0.2 0.2 0.3 0.2 0.2 - 0.1 0.3 0.3 0.6 0.6 0.4
[1] 1o5r.a 0.4 0.1 0 0.8
0
0.2 0 0.1 0.1 - 0.3 0.5 0.1 0.5 0.5 0.3
[1] 1qxl.a 0.2 0 0 0.7 0
0.1
0 0.1 0.1 - 0.1 0.2 0.1 0.4 0.4 0.1
[1] 1uml.a 0.1 0.2 0 0.3 0.1 0.1
0
0.1 0.1 - 0.3 0.3 0.2 0.6 0.5 0.4
[1] 1v79.a 0.8 0.2 0 1.3 0.2 0.2 0.1
0.1
0.2 - 0.3 0.3 0.3 0.7 0.6 0.3
[1] 1v7a.a 0.2 0.1 0 0.8 0 0.1 0 0.1
0
- 0.1 0.1 0.2 0.5 0.4 0.2
[1] 1vfl.a 0.8 0.2 0.2 1.7 0.5 0.4 0.5 0.3 0.4
-
0.6 0.7 0.5 0.9 0.5 0.1
[1] 1wxy.a 0.4 0.2 0.1 1.0 0.4 0.5 0.3 0.3 0.5 -
0
0.8 0.4 0.6 0.6 0.1
[1] 1wxz.a 0.9 0 0 1.6 0.3 0.8 0.4 0.1 0.1 - 0.4
0
0.1 0.4 0.5 0.3
[1] 2e1w.a 0.3 0.3 0 0.9 0 0.1 0 0 0 - 0.4 0.3
0
0.4 0.4 0.2
[1] 2z7g.a 0.3 0 0 0.7 0 0.2 0 0.1 0 - 0 0.1 0.1
0.1
0.4 0.3
[2] 1krm.a 7.7 0.3 1.6 7.9 7.2 7.5 6.9 0.9 2.8 - 6.5 3.2 1.7 1.4
0.2
0.3
[2] 3iar.a 7.5 0.5 1.8 8.1 7.2 8.3 7.4 1.0 2.0 - 6.0 3.3 2.1 1.7 0.8
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1ndv.a
1ndw.a
1ndy.a
1ndz.a
1o5r.a
1qxl.a
1uml.a
1v79.a
1v7a.a
1vfl.a
1wxy.a
1wxz.a
2e1w.a
2z7g.a
1krm.a
3iar.a
[1] 1ndv.a
0
.03 .04 .05 .04 .02 .04 .05 .03 .06 .05 .09 .04 .04 .34 .35
[1] 1ndw.a .03
0
.02 .04 .04 .03 .05 .03 .03 .05 .05 .08 .05 .05 .33 .34
[1] 1ndy.a .04 .02
0
.04 .04 .04 .05 .03 .04 .05 .05 .08 .04 .05 .33 .35
[1] 1ndz.a .05 .04 .04
0
.05 .04 .03 .06 .04 .08 .06 .09 .06 .05 .36 .37
[1] 1o5r.a .04 .04 .04 .05
0
.02 .04 .04 .03 .06 .03 .08 .02 .04 .32 .35
[1] 1qxl.a .02 .03 .04 .04 .02
0
.03 .05 .01 .06 .04 .07 .03 .02 .34 .35
[1] 1uml.a .04 .05 .05 .03 .04 .03
0
.06 .04 .07 .06 .09 .05 .03 .35 .37
[1] 1v79.a .05 .03 .03 .06 .04 .05 .06
0
.04 .04 .06 .07 .05 .05 .32 .33
[1] 1v7a.a .03 .03 .04 .04 .03 .01 .04 .04
0
.06 .04 .07 .03 .02 .33 .35
[1] 1vfl.a .06 .05 .05 .08 .06 .06 .07 .04 .06
0
.07 .08 .06 .07 .31 .31
[1] 1wxy.a .05 .05 .05 .06 .03 .04 .06 .06 .04 .07
0
.09 .04 .06 .32 .34
[1] 1wxz.a .09 .08 .08 .09 .08 .07 .09 .07 .07 .08 .09
0
.07 .09 .28 .31
[1] 2e1w.a .04 .05 .04 .06 .02 .03 .05 .05 .03 .06 .04 .07
0
.04 .31 .35
[1] 2z7g.a .04 .05 .05 .05 .04 .02 .03 .05 .02 .07 .06 .09 .04
0
.35 .37
[2] 1krm.a .34 .33 .33 .36 .32 .34 .35 .32 .33 .31 .32 .28 .31 .35
0
.14
[2] 3iar.a .35 .34 .35 .37 .35 .35 .37 .33 .35 .31 .34 .31 .35 .37 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1ndv.a
1ndw.a
1ndy.a
1ndz.a
1o5r.a
1qxl.a
1uml.a
1v79.a
1v7a.a
1vfl.a
1wxy.a
1wxz.a
2e1w.a
2z7g.a
1krm.a
3iar.a
[1] 1ndv.a
0
0.5 0.7 0.4 0.5 0.6 0.6 0.7 0.7 0.7 0.5 0.8 0.6 0.7 1.6 1.5
[1] 1ndw.a 0.5
0
0.4 0.3 0.6 0.4 0.6 0.5 0.6 0.4 0.4 0.8 0.4 0.4 1.7 1.5
[1] 1ndy.a 0.7 0.4
0
0.5 0.7 0.5 0.7 0.4 0.5 0.5 0.6 1.1 0.4 0.4 1.8 1.7
[1] 1ndz.a 0.4 0.3 0.5
0
0.5 0.5 0.5 0.6 0.6 0.6 0.5 0.9 0.5 0.5 1.7 1.6
[1] 1o5r.a 0.5 0.6 0.7 0.5
0
0.5 0.5 0.7 0.7 0.7 0.6 0.7 0.6 0.7 1.6 1.5
[1] 1qxl.a 0.6 0.4 0.5 0.5 0.5
0
0.5 0.6 0.5 0.6 0.6 0.9 0.5 0.5 1.8 1.7
[1] 1uml.a 0.6 0.6 0.7 0.5 0.5 0.5
0
0.7 0.5 0.7 0.7 0.8 0.6 0.7 1.7 1.6
[1] 1v79.a 0.7 0.5 0.4 0.6 0.7 0.6 0.7
0
0.6 0.5 0.6 1.1 0.5 0.4 1.7 1.6
[1] 1v7a.a 0.7 0.6 0.5 0.6 0.7 0.5 0.5 0.6
0
0.6 0.7 1.0 0.6 0.6 1.8 1.7
[1] 1vfl.a 0.7 0.4 0.5 0.6 0.7 0.6 0.7 0.5 0.6
0
0.5 0.9 0.5 0.3 1.5 1.4
[1] 1wxy.a 0.5 0.4 0.6 0.5 0.6 0.6 0.7 0.6 0.7 0.5
0
0.8 0.5 0.6 1.5 1.4
[1] 1wxz.a 0.8 0.8 1.1 0.9 0.7 0.9 0.8 1.1 1.0 0.9 0.8
0
0.9 1.0 1.6 1.4
[1] 2e1w.a 0.6 0.4 0.4 0.5 0.6 0.5 0.6 0.5 0.6 0.5 0.5 0.9
0
0.5 1.7 1.6
[1] 2z7g.a 0.7 0.4 0.4 0.5 0.7 0.5 0.7 0.4 0.6 0.3 0.6 1.0 0.5
0
1.7 1.5
[2] 1krm.a 1.6 1.7 1.8 1.7 1.6 1.8 1.7 1.7 1.8 1.5 1.5 1.6 1.7 1.7
0
0.7
[2] 3iar.a 1.5 1.5 1.7 1.6 1.5 1.7 1.6 1.6 1.7 1.4 1.4 1.4 1.6 1.5 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1ndv.a
1ndw.a
1ndy.a
1ndz.a
1o5r.a
1qxl.a
1uml.a
1v79.a
1v7a.a
1vfl.a
1wxy.a
1wxz.a
2e1w.a
2z7g.a
1krm.a
3iar.a
[1] 1ndv.a
0
0.7 0.8 0.6 0.7 0.8 0.7 0.8 0.8 0.9 0.7 0.9 0.8 1.0 1.8 1.7
[1] 1ndw.a 0.7
0
0.6 0.5 0.7 0.6 0.7 0.6 0.7 0.7 0.6 1.0 0.7 0.8 1.9 1.8
[1] 1ndy.a 0.8 0.6
0
0.6 0.8 0.7 0.8 0.5 0.7 0.7 0.7 1.2 0.7 0.7 2.0 1.9
[1] 1ndz.a 0.6 0.5 0.6
0
0.7 0.7 0.7 0.6 0.7 0.8 0.6 1.0 0.7 0.8 1.9 1.8
[1] 1o5r.a 0.7 0.7 0.8 0.7
0
0.7 0.6 0.8 0.8 0.8 0.7 0.8 0.7 0.8 1.8 1.7
[1] 1qxl.a 0.8 0.6 0.7 0.7 0.7
0
0.6 0.7 0.6 0.7 0.8 1.0 0.6 0.8 1.9 1.8
[1] 1uml.a 0.7 0.7 0.8 0.7 0.6 0.6
0
0.8 0.6 0.8 0.8 0.8 0.7 0.9 1.8 1.7
[1] 1v79.a 0.8 0.6 0.5 0.6 0.8 0.7 0.8
0
0.7 0.7 0.7 1.1 0.7 0.8 1.9 1.8
[1] 1v7a.a 0.8 0.7 0.7 0.7 0.8 0.6 0.6 0.7
0
0.8 0.8 1.1 0.6 0.8 2.0 1.9
[1] 1vfl.a 0.9 0.7 0.7 0.8 0.8 0.7 0.8 0.7 0.8
0
0.8 1.1 0.8 0.6 1.7 1.6
[1] 1wxy.a 0.7 0.6 0.7 0.6 0.7 0.8 0.8 0.7 0.8 0.8
0
1.0 0.8 0.9 1.8 1.7
[1] 1wxz.a 0.9 1.0 1.2 1.0 0.8 1.0 0.8 1.1 1.1 1.1 1.0
0
1.1 1.2 1.7 1.6
[1] 2e1w.a 0.8 0.7 0.7 0.7 0.7 0.6 0.7 0.7 0.6 0.8 0.8 1.1
0
0.8 1.9 1.8
[1] 2z7g.a 1.0 0.8 0.7 0.8 0.8 0.8 0.9 0.8 0.8 0.6 0.9 1.2 0.8
0
1.9 1.8
[2] 1krm.a 1.8 1.9 2.0 1.9 1.8 1.9 1.8 1.9 2.0 1.7 1.8 1.7 1.9 1.9
0
0.9
[2] 3iar.a 1.7 1.8 1.9 1.8 1.7 1.8 1.7 1.8 1.9 1.6 1.7 1.6 1.8 1.8 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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