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DEOD1_VIBCH_1_241

Purine nucleoside phosphorylase DeoD-type 1 [PNP/UDP phosphorylase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DEOD1_VIBCH):R: Phosphate binding (88, 91)
R: Purine nucleoside binding (180:182)
65, 92, 93, 160, 179, 207
65, 88, 91:93, 160, 179:182, 204, 205, 207
A2 (DEOD1_VIBCH):5, 44, 725, 44, 72

Full PDB list

1vhj, 1vhw, 3of3

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
M
6
5
R
8
8
S
9
1
C
9
2
G
9
3
F
1
6
0
V
1
7
9
E
1
8
0
M
1
8
1
E
1
8
2
S
2
0
4
D
2
0
5
H
5
R
4
4
[1]1vhj.a none . . . . . . . . . . . . . .
[1]1vhw.a adn19 . . . . . . . . . . . . . .
[1]3of3.a dih19 . . . . . . . . . . . . . .

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 A2
M
6
5
R
8
8
S
9
1
C
9
2
G
9
3
F
1
6
0
V
1
7
9
E
1
8
0
M
1
8
1
E
1
8
2
S
2
0
4
D
2
0
5
I
2
0
7
H
5
R
4
4
I
7
2
[1]1vhj.a . . . . . . . . . . . . . . . .
[1]1vhw.a . . . . . . . . . . . . . . . .
[1]3of3.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
1vhj.a is apo
1vhw.a:adn
3of3.a:dih
[1] 1vhj.a
-
0.2 0.2
[1] 1vhw.a -
0
0.2
[1] 3of3.a - 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
1vhj.a
1vhw.a
3of3.a
[1] 1vhj.a
0
.01 .01
[1] 1vhw.a .01
0
.01
[1] 3of3.a .01 .01
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
1vhj.a
1vhw.a
3of3.a
[1] 1vhj.a
0
0.3 0.6
[1] 1vhw.a 0.3
0
0.6
[1] 3of3.a 0.6 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
1vhj.a
1vhw.a
3of3.a
[1] 1vhj.a
0
0.5 0.8
[1] 1vhw.a 0.5
0
0.6
[1] 3of3.a 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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