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DXO_MOUSE_26_389_RNA

Decapping and exoribonuclease protein [DXO/Dom3Z family]

Composition of the binding site

Protein chains monomer
A1 (DXO_MOUSE):58, 95, 97, 101, 131:134, 136, 137, 146, 147, 164, 181, 184, 185, 188, 189, 192, 215, 217, 233, 234, 236, 253, 255:258, 273, 276, 277, 280, 29458, 95, 97, 101, 131:134, 136, 137, 146, 147, 164, 181, 184, 185, 188, 189, 192, 215, 217, 233, 234, 236, 253, 255:258, 273, 276, 277, 280, 294
Metals (Me):Ca/Mg

Full PDB list

3fqi, 3fqj, 4j7l, 4j7m, 4j7n, 5uli

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
5
8
R
9
5
E
9
7
E
1
0
1
W
1
3
1
R
1
3
2
G
1
3
3
H
1
3
4
T
1
3
6
K
1
3
7
Q
1
4
6
E
1
6
4
L
1
8
1
L
1
8
4
M
1
8
5
G
1
8
8
Y
1
8
9
E
1
9
2
C
2
1
7
G
2
3
3
E
2
3
4
D
2
3
6
E
2
5
3
K
2
5
5
T
2
5
6
K
2
5
8
K
2
7
3
K
2
7
6
W
2
7
7
Q
2
8
0
R
2
9
4
[1]3fqi.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3fqj.a gdp28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4j7l.a UUUU81 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4j7m.a Uu37.u37UU85 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4j7n.a 9mg,gtg64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5uli.a 0wd48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca

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
R
5
8
R
9
5
E
9
7
E
1
0
1
W
1
3
1
R
1
3
2
G
1
3
3
H
1
3
4
T
1
3
6
K
1
3
7
Q
1
4
6
E
1
4
7
E
1
6
4
L
1
8
1
L
1
8
4
M
1
8
5
G
1
8
8
Y
1
8
9
E
1
9
2
A
2
1
5
C
2
1
7
G
2
3
3
E
2
3
4
D
2
3
6
E
2
5
3
K
2
5
5
T
2
5
6
S
2
5
7
K
2
5
8
K
2
7
3
K
2
7
6
W
2
7
7
Q
2
8
0
R
2
9
4
[1]3fqi.a . * . . . . . . . . * . . . * . . . . . . . * . . . . . . . . . . . Mg
[1]3fqj.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4j7l.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4j7m.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4j7n.a . * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]5uli.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca

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
3fqi.a is apo
3fqj.a:gdp
4j7l.a:UUUU
4j7m.a:Uu37.u37UU
4j7n.a:9mg,gtg
5uli.a:0wd
[1] 3fqi.a
-
3.2 2.6 2.0 3.3 1.7
[1] 3fqj.a -
0
0.9 2.3 0.5 1.6
[1] 4j7l.a - 2.3
0
0.7 2.1 1.4
[1] 4j7m.a - 0.8 0
0.3
0.9 0.6
[1] 4j7n.a - 0 1.2 2.6
0
1.4
[1] 5uli.a - 0.8 1.0 1.7 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
3fqi.a
3fqj.a
4j7l.a
4j7m.a
4j7n.a
5uli.a
[1] 3fqi.a
0
.18 .13 .19 .17 .20
[1] 3fqj.a .18
0
.10 .10 .09 .09
[1] 4j7l.a .13 .10
0
.06 .09 .12
[1] 4j7m.a .19 .10 .06
0
.10 .08
[1] 4j7n.a .17 .09 .09 .10
0
.09
[1] 5uli.a .20 .09 .12 .08 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3fqi.a
3fqj.a
4j7l.a
4j7m.a
4j7n.a
5uli.a
[1] 3fqi.a
0
0.4 0.3 0.2 0.4 0.4
[1] 3fqj.a 0.4
0
0.4 0.4 0.4 0.4
[1] 4j7l.a 0.3 0.4
0
0.2 0.3 0.3
[1] 4j7m.a 0.2 0.4 0.2
0
0.3 0.3
[1] 4j7n.a 0.4 0.4 0.3 0.3
0
0.2
[1] 5uli.a 0.4 0.4 0.3 0.3 0.2
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

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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
3fqi.a
3fqj.a
4j7l.a
4j7m.a
4j7n.a
5uli.a
[1] 3fqi.a
0
1.1 1.1 1.0 1.1 1.0
[1] 3fqj.a 1.1
0
1.0 0.9 0.9 0.8
[1] 4j7l.a 1.1 1.0
0
0.5 0.9 0.9
[1] 4j7m.a 1.0 0.9 0.5
0
0.9 0.8
[1] 4j7n.a 1.1 0.9 0.9 0.9
0
0.9
[1] 5uli.a 1.0 0.8 0.9 0.8 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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