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ATOX1_HUMAN_1_68

Copper transport protein ATOX1 [ATX1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ATOX1_HUMAN):D: HMA (11:15, 18, 21, 60)11:15, 18, 21, 60
Metals (Me):Ag/Cd/Hg

Full PDB list

1fe0, 1fe4, 1fee, 3cjk, 3iwl, 3iwx, 4qot, 4ydx, 4yea, 5f0w, 5t7l (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
1
1
C
1
2
G
1
4
C
1
5
A
1
8
K
6
0
[1]1fe0.a none . . . . . . Cd
[1]1fe4.a none . . . . . . Hg
[1]3cjk.a cd,CNS-F32 . . . . . .
[1]3iwl.a pt,tce17 . . . . . .
[1]3iwx.a cpt3 . . . . . .
[1]5f0w.a ag,ag,ag3 . . . . . . Ag
[1]5t7l.a CNS-F,cu,cu33 . . . . . .

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
T
1
1
C
1
2
G
1
3
G
1
4
C
1
5
A
1
8
R
2
1
K
6
0
[1]1fe0.a . . . . . . . . Cd
[1]1fe4.a . . . . . . . . Hg
[1]3cjk.a . * . . . . . .
[1]3iwl.a . . . . . . . .
[1]3iwx.a . * . . . . . .
[1]5f0w.a . . . . . . . . Ag
[1]5t7l.a . . . . . . . .

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
1fe0.a is apo
1fe4.a is apo
3cjk.a:CNS-F,cd
3iwl.a:pt,tce
3iwx.a:cpt
5f0w.a:ag
5t7l.a:CNS-F,cu
[1] 1fe0.a
-
- 0.3 1.0 0.8 0.5 0.2
[1] 1fe4.a -
-
0.3 1.2 1.2 0.7 0.4
[1] 3cjk.a - -
0.1
1.2 1.3 0.9 0.3
[1] 3iwl.a - - 0.1
1.0
0.9 0.6 0.2
[1] 3iwx.a - - 0.3 1.1
1.0
0.9 0.2
[1] 5f0w.a - - 0.3 0.4 0.5
0.2
0.3
[1] 5t7l.a - - 0.1 1.1 0.8 0.8
0.3
[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
1fe0.a
1fe4.a
3cjk.a
3iwl.a
3iwx.a
5f0w.a
5t7l.a
[1] 1fe0.a
0
.05 .05 .05 .05 .10 .05
[1] 1fe4.a .05
0
.05 .05 0 .15 .05
[1] 3cjk.a .05 .05
0
.10 .05 .15 .10
[1] 3iwl.a .05 .05 .10
0
.05 .13 .02
[1] 3iwx.a .05 0 .05 .05
0
.15 .05
[1] 5f0w.a .10 .15 .15 .13 .15
0
.13
[1] 5t7l.a .05 .05 .10 .02 .05 .13
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1fe0.a
1fe4.a
3cjk.a
3iwl.a
3iwx.a
5f0w.a
5t7l.a
[1] 1fe0.a
0
0.2 0.4 0.5 0.3 0.6 0.5
[1] 1fe4.a 0.2
0
0.4 0.6 0.3 0.7 0.5
[1] 3cjk.a 0.4 0.4
0
0.5 0.4 0.6 0.4
[1] 3iwl.a 0.5 0.6 0.5
0
0.6 0.6 0.5
[1] 3iwx.a 0.3 0.3 0.4 0.6
0
0.5 0.4
[1] 5f0w.a 0.6 0.7 0.6 0.6 0.5
0
0.6
[1] 5t7l.a 0.5 0.5 0.4 0.5 0.4 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1fe0.a
1fe4.a
3cjk.a
3iwl.a
3iwx.a
5f0w.a
5t7l.a
[1] 1fe0.a
0
0.2 1.5 1.1 0.9 1.3 1.8
[1] 1fe4.a 0.2
0
1.5 1.1 0.9 1.3 1.8
[1] 3cjk.a 1.5 1.5
0
1.5 1.4 1.7 1.0
[1] 3iwl.a 1.1 1.1 1.5
0
1.0 1.0 1.8
[1] 3iwx.a 0.9 0.9 1.4 1.0
0
1.3 1.7
[1] 5f0w.a 1.3 1.3 1.7 1.0 1.3
0
1.9
[1] 5t7l.a 1.8 1.8 1.0 1.8 1.7 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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