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8ODP_MOUSE_2_156

7,8-dihydro-8-oxoguanine triphosphatase [Nudix hydrolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (8ODP_MOUSE):D: Nudix hydrolase (23, 27, 33, 36:38, 52, 56, 72, 74, 81, 83, 100, 117, 119, 120, 123)
R: Substrate binding (36:38)
R: Substrate binding (117, 119, 120)
7:9, 139
7:9, 23, 27, 33, 36:38, 52, 56, 72, 74, 81, 83, 100, 117, 119, 120, 123, 139

Full PDB list

5mze, 5mzg, 6ehh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
7
T
8
L
9
K
2
3
F
2
7
N
3
3
G
3
6
G
3
7
K
3
8
E
5
2
E
5
6
F
7
2
F
7
4
M
8
1
V
8
3
E
1
0
0
W
1
1
7
D
1
1
9
D
1
2
0
W
1
2
3
F
1
3
9
[1]5mze.a 8dg32 . . . . . . . . . . . . . . . . . . . . .
[1]5mzg.a 2ge19 . . . . . . . . . . . . . . . . . . . . .

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
Y
7
T
8
L
9
K
2
3
F
2
7
N
3
3
G
3
6
G
3
7
K
3
8
E
5
2
E
5
6
F
7
2
F
7
4
M
8
1
V
8
3
E
1
0
0
W
1
1
7
D
1
1
9
D
1
2
0
W
1
2
3
F
1
3
9
[1]5mze.a . . . . . . . . . . . . . . . . . . . . .
[1]5mzg.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
5mze.a:8dg
5mzg.a:2ge
[1] 5mze.a
0.3
0.4
[1] 5mzg.a 0.6
0
[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
5mze.a
5mzg.a
[1] 5mze.a
0
.03
[1] 5mzg.a .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
5mze.a
5mzg.a
[1] 5mze.a
0
0.3
[1] 5mzg.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
5mze.a
5mzg.a
[1] 5mze.a
0
0.6
[1] 5mzg.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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