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APT_HUMAN_1_180

Adenine phosphoribosyltransferase [Purine/pyrimidine phosphoribosyltransferase family]

Composition of the binding site

Protein chains homodimer
A1 (APT_HUMAN):24:27, 65:67, 88, 103, 127:129, 131:135, 15924:27, 65:67, 88, 103, 127:129, 131:135, 159
A2 (APT_HUMAN):87, 9187, 91

Full PDB list

1ore, 1zn7, 1zn8, 1zn9, 4x44, 4x45 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
V
2
5
F
2
6
R
2
7
S
6
6
R
6
7
K
8
8
D
1
2
7
D
1
2
8
L
1
2
9
A
1
3
1
T
1
3
2
G
1
3
3
G
1
3
4
T
1
3
5
L
1
5
9
R
8
7
K
9
1
[1]1zn7.a ade,hsx,mg,prp47 . . . . . . . . . . . . . . . . .
[1]1zn7.b ade,hsx,prp46 . . . . . . . . . . . . . . . . .
[1]1zn9.b amp23 . . . . . . . . . . . . . . . . .
[1]4x45.a none . . . . . . . . . . . . . . . . .

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 A2
V
2
4
V
2
5
F
2
6
R
2
7
D
6
5
S
6
6
R
6
7
K
8
8
L
1
0
3
D
1
2
7
D
1
2
8
L
1
2
9
A
1
3
1
T
1
3
2
G
1
3
3
G
1
3
4
T
1
3
5
L
1
5
9
R
8
7
K
9
1
[1]1zn7.a . . . . . . . . . . . . . . . . . . . .
[1]1zn7.b . . . . . . . . . . . . . . . . . . . .
[1]1zn9.b . . . . . . . . . . . . . . . . . . . .
[1]4x45.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
1zn7.a:ade,hsx,mg,prp
1zn7.b:ade,hsx,prp
1zn9.b:amp
4x45.a is apo
[1] 1zn7.a
0.4
0.4 0.1 -
[1] 1zn7.b 0.6
0.6
0.1 -
[1] 1zn9.b 0.5 0.2
0.1
-
[1] 4x45.a 1.6 1.4 0.9
-
[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
1zn7.a
1zn7.b
1zn9.b
4x45.a
[1] 1zn7.a
0
.01 .02 .08
[1] 1zn7.b .01
0
.02 .08
[1] 1zn9.b .02 .02
0
.08
[1] 4x45.a .08 .08 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1zn7.a
1zn7.b
1zn9.b
4x45.a
[1] 1zn7.a
0
0.2 0.8 0.5
[1] 1zn7.b 0.2
0
0.7 0.6
[1] 1zn9.b 0.8 0.7
0
0.9
[1] 4x45.a 0.5 0.6 0.9
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
1zn7.a
1zn7.b
1zn9.b
4x45.a
[1] 1zn7.a
0
0.6 1.2 1.0
[1] 1zn7.b 0.6
0
1.2 1.1
[1] 1zn9.b 1.2 1.2
0
1.2
[1] 4x45.a 1.0 1.1 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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