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CODA_ECOLI_2_427

Cytosine deaminase [Metallo-dependent hydrolases superfamily. Cytosine deaminase family]

Composition of the binding site

Protein chains monomer
A1 (CODA_ECOLI):64, 82, 86, 155, 157, 184, 215, 218, 247, 279, 283, 314, 315, 318, 32064, 82, 86, 155, 157, 184, 215, 218, 247, 279, 283, 314, 315, 318, 320
Metals (Me):Fe/Zn

Full PDB list

1k6w, 1k70, 1r9x, 1r9y, 1r9z, 1ra0, 1ra5, 1rak, 3g77, 3o7u, 3r0d, 3rn6

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
6
4
L
8
2
F
1
5
5
Q
1
5
7
I
1
8
4
H
2
1
5
E
2
1
8
H
2
4
7
D
3
1
4
D
3
1
5
W
3
2
0
[1]1k6w.a none . . . . . . . . . . . Fe
[1]1k70.a hpy8 . . . . . . . . . . . Fe
[1]1r9x.a none . . . . . . . . . G . Fe
[1]1r9y.a none . . . . . . . . . A . Fe
[1]1r9z.a none . . . . . . . . . S . Fe
[1]1ra0.a fpy9 . . . . . . . . . G . Fe
[1]1ra5.a fpy9 . . . . . . . . . A . Fe
[1]1rak.a fpy9 . . . . . . . . . S . Fe
[1]3g77.a none . . . . . . . . . . . Fe
[1]3o7u.a o7u9 . . . . . . . . . . . Zn
[1]3r0d.a zn1 . . . . . . . . . . . Zn
[1]3rn6.a iga11 . . . . . . . . . . . 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
H
6
4
L
8
2
I
8
6
F
1
5
5
Q
1
5
7
I
1
8
4
H
2
1
5
E
2
1
8
H
2
4
7
V
2
7
9
L
2
8
3
D
3
1
4
D
3
1
5
D
3
1
8
W
3
2
0
[1]1k6w.a . . . . . . . . . . . . . . . Fe
[1]1k70.a . . . . . . . . . . . . . . . Fe
[1]1r9x.a . . . . . . . . . . . . G . . Fe
[1]1r9y.a . . . . . . . . . . . . A . . Fe
[1]1r9z.a . . . . . . . . . . . . S . . Fe
[1]1ra0.a . . . . . . . . . . . . G . . Fe
[1]1ra5.a . . . . . . . . . . . . A . . Fe
[1]1rak.a . . . . . . . . . . . . S . . Fe
[1]3g77.a . . . . . . . . . . . . . G . Fe
[1]3o7u.a . . . . . . . . . . . . . . . Zn
[1]3r0d.a . . . . . . . . . . . . . . . Zn
[1]3rn6.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
1k6w.a is apo
1k70.a:hpy
1r9x.a is apo
1r9y.a is apo
1r9z.a is apo
1ra0.a:fpy
1ra5.a:fpy
1rak.a:fpy
3g77.a is apo
3o7u.a:o7u
3r0d.a:zn
3rn6.a:iga
[1] 1k6w.a
-
0 - - - 0.1 0.1 0.1 - 0 0.2 0
[1] 1k70.a -
0
- - - 0.1 0.1 0.1 - 0 0.2 0.5
[1] 1r9x.a - 0
-
- - 0 0 0 - 0 0.3 0
[1] 1r9y.a - 0 -
-
- 0 0 0 - 0 0.3 0
[1] 1r9z.a - 0 - -
-
0.1 0.1 0.1 - 0 0.3 0
[1] 1ra0.a - 0 - - -
0
0 0 - 0 0.2 0.4
[1] 1ra5.a - 0 - - - 0
0
0 - 0 0.2 0.4
[1] 1rak.a - 0 - - - 0 0
0
- 0 0.2 0.4
[1] 3g77.a - 0.2 - - - 0.3 0.3 0.3
-
0.4 0.3 1.2
[1] 3o7u.a - 0 - - - 0.1 0.2 0.2 -
0
0.2 0.3
[1] 3r0d.a - 0 - - - 0.1 0.2 0.2 - 0
0.3
0.3
[1] 3rn6.a - 0 - - - 0.1 0.1 0.1 - 0 0.4
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
1k6w.a
1k70.a
1r9x.a
1r9y.a
1r9z.a
1ra0.a
1ra5.a
1rak.a
3g77.a
3o7u.a
3r0d.a
3rn6.a
[1] 1k6w.a
0
.03 .01 .01 .01 .03 .03 .03 .09 .02 .03 .02
[1] 1k70.a .03
0
.04 .04 .04 .01 .01 .01 .07 .02 .03 .05
[1] 1r9x.a .01 .04
0
0 0 .03 .03 .03 .08 .03 .03 .02
[1] 1r9y.a .01 .04 0
0
0 .03 .03 .03 .08 .03 .03 .02
[1] 1r9z.a .01 .04 0 0
0
.03 .03 .03 .08 .03 .03 .02
[1] 1ra0.a .03 .01 .03 .03 .03
0
0 0 .06 .03 .03 .05
[1] 1ra5.a .03 .01 .03 .03 .03 0
0
0 .06 .03 .03 .05
[1] 1rak.a .03 .01 .03 .03 .03 0 0
0
.06 .03 .03 .05
[1] 3g77.a .09 .07 .08 .08 .08 .06 .06 .06
0
.09 .08 .10
[1] 3o7u.a .02 .02 .03 .03 .03 .03 .03 .03 .09
0
.01 .03
[1] 3r0d.a .03 .03 .03 .03 .03 .03 .03 .03 .08 .01
0
.02
[1] 3rn6.a .02 .05 .02 .02 .02 .05 .05 .05 .10 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1k6w.a
1k70.a
1r9x.a
1r9y.a
1r9z.a
1ra0.a
1ra5.a
1rak.a
3g77.a
3o7u.a
3r0d.a
3rn6.a
[1] 1k6w.a
0
1.8 0.2 0.1 0.1 1.8 1.8 1.8 1.7 1.7 1.7 1.7
[1] 1k70.a 1.8
0
1.8 1.8 1.8 0.2 0.1 0.1 0.2 0.1 0.2 0.3
[1] 1r9x.a 0.2 1.8
0
0.1 0.1 1.8 1.8 1.8 1.8 1.8 1.7 1.7
[1] 1r9y.a 0.1 1.8 0.1
0
0.1 1.8 1.8 1.8 1.8 1.8 1.7 1.7
[1] 1r9z.a 0.1 1.8 0.1 0.1
0
1.9 1.9 1.9 1.8 1.8 1.7 1.8
[1] 1ra0.a 1.8 0.2 1.8 1.8 1.9
0
0.1 0.1 0.3 0.2 0.3 0.4
[1] 1ra5.a 1.8 0.1 1.8 1.8 1.9 0.1
0
0.1 0.3 0.2 0.2 0.3
[1] 1rak.a 1.8 0.1 1.8 1.8 1.9 0.1 0.1
0
0.3 0.2 0.2 0.3
[1] 3g77.a 1.7 0.2 1.8 1.8 1.8 0.3 0.3 0.3
0
0.2 0.2 0.3
[1] 3o7u.a 1.7 0.1 1.8 1.8 1.8 0.2 0.2 0.2 0.2
0
0.1 0.3
[1] 3r0d.a 1.7 0.2 1.7 1.7 1.7 0.3 0.2 0.2 0.2 0.1
0
0.2
[1] 3rn6.a 1.7 0.3 1.7 1.7 1.8 0.4 0.3 0.3 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
1k6w.a
1k70.a
1r9x.a
1r9y.a
1r9z.a
1ra0.a
1ra5.a
1rak.a
3g77.a
3o7u.a
3r0d.a
3rn6.a
[1] 1k6w.a
0
1.8 0.5 0.6 0.3 1.9 1.8 1.9 1.9 1.8 1.7 1.7
[1] 1k70.a 1.8
0
2.0 1.9 1.9 0.2 0.3 0.4 0.6 0.2 0.2 0.4
[1] 1r9x.a 0.5 2.0
0
0.3 0.5 2.0 2.0 2.0 2.0 1.9 1.9 1.9
[1] 1r9y.a 0.6 1.9 0.3
0
0.5 2.0 1.9 1.9 2.0 1.9 1.9 1.9
[1] 1r9z.a 0.3 1.9 0.5 0.5
0
1.9 1.9 2.0 2.0 1.9 1.8 1.8
[1] 1ra0.a 1.9 0.2 2.0 2.0 1.9
0
0.3 0.4 0.4 0.2 0.3 0.4
[1] 1ra5.a 1.8 0.3 2.0 1.9 1.9 0.3
0
0.3 0.5 0.4 0.4 0.5
[1] 1rak.a 1.9 0.4 2.0 1.9 2.0 0.4 0.3
0
0.6 0.4 0.5 0.6
[1] 3g77.a 1.9 0.6 2.0 2.0 2.0 0.4 0.5 0.6
0
0.7 0.6 0.7
[1] 3o7u.a 1.8 0.2 1.9 1.9 1.9 0.2 0.4 0.4 0.7
0
0.1 0.3
[1] 3r0d.a 1.7 0.2 1.9 1.9 1.8 0.3 0.4 0.5 0.6 0.1
0
0.3
[1] 3rn6.a 1.7 0.4 1.9 1.9 1.8 0.4 0.5 0.6 0.7 0.3 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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