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PYRC_BACAN_1_428

Dihydroorotase [Metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PYRC_BACAN):R: Substrate binding (61, 63)
R: Substrate binding (322, 323)
93, 152, 178, 276, 277, 304, 306, 308
61, 63, 93, 152, 178, 276, 277, 304, 306, 308, 322, 323
Metals (Me):Zn

Full PDB list

3mpg, 4yiw

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
6
1
R
6
3
N
9
3
M
2
7
6
N
2
7
7
D
3
0
4
A
3
0
6
H
3
0
8
F
3
2
2
G
3
2
3
[1]3mpg.a none . . . . . . . . . . Zn
[1]4yiw.a ncd12 . . . . . . . . . . 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
1
R
6
3
N
9
3
G
1
5
2
H
1
7
8
M
2
7
6
N
2
7
7
D
3
0
4
A
3
0
6
H
3
0
8
F
3
2
2
G
3
2
3
[1]3mpg.a . . . . . . . . . . . . Zn
[1]4yiw.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
3mpg.a is apo
4yiw.a:ncd
[1] 3mpg.a
-
0.1
[1] 4yiw.a -
0.1
[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
3mpg.a
4yiw.a
[1] 3mpg.a
0
0
[1] 4yiw.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3mpg.a
4yiw.a
[1] 3mpg.a
0
0.2
[1] 4yiw.a 0.2
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
3mpg.a
4yiw.a
[1] 3mpg.a
0
0.4
[1] 4yiw.a 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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