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CDD_MOUSE_1_146

Cytidine deaminase [Cytidine and deoxycytidylate deaminase family]

Composition of the binding site

Protein chains homotrimer [domain annotation]
A1 (CDD_MOUSE):D: CMP/dCMP-type deaminase (34, 36, 38, 54, 56, 65:67, 96:99, 102)
R: Substrate binding (54, 56)
34, 36, 38, 54, 56, 65:67, 96:99, 102
A2 (CDD_MOUSE):D: CMP/dCMP-type deaminase (58:61)58:61
A3 (CDD_MOUSE):D: CMP/dCMP-type deaminase (137)
142
137, 142
Metals (Me):Zn

Full PDB list

1zab, 2fr5, 2fr6

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3 Me
F
3
6
V
3
8
N
5
4
E
5
6
C
6
5
A
6
6
E
6
7
I
9
6
S
9
7
P
9
8
C
9
9
C
1
0
2
A
5
8
C
5
9
Y
6
0
P
6
1
F
1
3
7
L
1
4
2
[1]1zab.b urd17 . . . . . . . . . . . . . . . . . . Zn
[1]2fr5.b tyu17 . . . . . . . . . . . . . . . . . . Zn
[1]2fr6.a ctn17 . . . . . . . . . . . . . . . . . . Zn
[1]2fr6.b uri17 . . . . . . . . . . . . . . . . . . Zn

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 A3 Me
S
3
4
F
3
6
V
3
8
N
5
4
E
5
6
C
6
5
A
6
6
E
6
7
I
9
6
S
9
7
P
9
8
C
9
9
C
1
0
2
A
5
8
C
5
9
Y
6
0
P
6
1
F
1
3
7
L
1
4
2
[1]1zab.b . . . . . . . . . . . . . . . . . . . Zn
[1]2fr5.b . . . . . . . . . . . . . . . . . . . Zn
[1]2fr6.a . . . . . . . . . . . . . . . . . . . Zn
[1]2fr6.b . . . . . . . . . . . . . . . . . . . Zn

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
1zab.b:urd
2fr5.b:tyu
2fr6.a:ctn
2fr6.b:uri
[1] 1zab.b
0
0.1 0.1 0.1
[1] 2fr5.b 0.1
0.1
0.2 0
[1] 2fr6.a 0 0
0
0
[1] 2fr6.b 0.1 0 0.1
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
1zab.b
2fr5.b
2fr6.a
2fr6.b
[1] 1zab.b
0
.01 .01 .01
[1] 2fr5.b .01
0
.02 .01
[1] 2fr6.a .01 .02
0
.01
[1] 2fr6.b .01 .01 .01
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
1zab.b
2fr5.b
2fr6.a
2fr6.b
[1] 1zab.b
0
0.2 0.2 0.1
[1] 2fr5.b 0.2
0
0.2 0.1
[1] 2fr6.a 0.2 0.2
0
0.2
[1] 2fr6.b 0.1 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1zab.b
2fr5.b
2fr6.a
2fr6.b
[1] 1zab.b
0
0.2 0.2 0.4
[1] 2fr5.b 0.2
0
0.3 0.5
[1] 2fr6.a 0.2 0.3
0
0.5
[1] 2fr6.b 0.4 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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