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CDD_ECOLI_1_294

Cytidine deaminase [Cytidine and deoxycytidylate deaminase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDD_ECOLI):D: CMP/dCMP-type deaminase 1 (69, 71, 73, 89, 91, 100:104, 126:129, 132)
R: Substrate binding (89, 91)
69, 71, 73, 89, 91, 100:104, 126:129, 132
Metals (Me):Zn

Full PDB list

1af2, 1aln, 1ctt, 1ctu

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
7
1
V
7
3
N
8
9
E
9
1
T
1
0
0
V
1
0
1
H
1
0
2
A
1
0
3
E
1
0
4
Y
1
2
6
T
1
2
7
P
1
2
8
C
1
2
9
C
1
3
2
[1]1af2.a U17 . . . . . . . . . . . . . . Zn
[1]1aln.a ctd17 . . . . . . . . . . . . . . Zn
[1]1ctt.a dhz16 . . . . . . . . . . . . . . Zn
[1]1ctu.a zeb17 . . . . . . . . . . . . . . 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 Me
S
6
9
F
7
1
V
7
3
N
8
9
E
9
1
T
1
0
0
V
1
0
1
H
1
0
2
A
1
0
3
E
1
0
4
Y
1
2
6
T
1
2
7
P
1
2
8
C
1
2
9
C
1
3
2
[1]1af2.a . . . . . . . . . . . . . . . Zn
[1]1aln.a . . . . . . . . . . . . . . . Zn
[1]1ctt.a . . . . . . . . . . . . . . . Zn
[1]1ctu.a . . . . . . . . . . . . . . . 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
1af2.a:U
1aln.a:ctd
1ctt.a:dhz
1ctu.a:zeb
[1] 1af2.a
0
0.1 0 0.2
[1] 1aln.a 0.1
0
0 0.1
[1] 1ctt.a 0.1 0
0
0.3
[1] 1ctu.a 0.1 0 0
0.2
[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
1af2.a
1aln.a
1ctt.a
1ctu.a
[1] 1af2.a
0
.02 .02 .01
[1] 1aln.a .02
0
.01 .01
[1] 1ctt.a .02 .01
0
.01
[1] 1ctu.a .01 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1af2.a
1aln.a
1ctt.a
1ctu.a
[1] 1af2.a
0
0.1 0.2 0.2
[1] 1aln.a 0.1
0
0.2 0.2
[1] 1ctt.a 0.2 0.2
0
0.1
[1] 1ctu.a 0.2 0.2 0.1
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

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
1af2.a
1aln.a
1ctt.a
1ctu.a
[1] 1af2.a
0
0.6 0.4 0.3
[1] 1aln.a 0.6
0
0.5 0.6
[1] 1ctt.a 0.4 0.5
0
0.4
[1] 1ctu.a 0.3 0.6 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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