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PYRC_AQUAE_1_422

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PYRC_AQUAE):R: Substrate binding (63, 65)
R: Substrate binding (322, 323)
95, 154, 181:184, 186, 277, 278, 307, 309
63, 65, 95, 154, 181:184, 186, 277, 278, 307, 309, 322, 323
Metals (Me):Zn

Full PDB list

1xrf, 1xrt, 3d6n, 4bjh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
6
3
R
6
5
N
9
5
G
1
5
4
V
2
7
7
N
2
7
8
A
3
0
7
H
3
0
9
P
3
2
2
G
3
2
3
[1]4bjh.a dor11 . . . . . . . . . . Zn
[2]1xrt.a none . . . . - - . . - . 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
3
R
6
5
N
9
5
G
1
5
4
C
1
8
1
E
1
8
2
D
1
8
3
D
1
8
4
L
1
8
6
V
2
7
7
N
2
7
8
A
3
0
7
H
3
0
9
P
3
2
2
G
3
2
3
[1]4bjh.a . . . . . . . . . . . . . . . Zn
[2]1xrt.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
4bjh.a:dor
1xrt.a is apo
[1] 4bjh.a
0
-
[2] 1xrt.a 4.7
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4bjh.a
1xrt.a
[1] 4bjh.a
0
.26
[2] 1xrt.a .26
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 4.4 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
4bjh.a
1xrt.a
[1] 4bjh.a
0
8.1
[2] 1xrt.a 8.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 4.1 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
4bjh.a
1xrt.a
[1] 4bjh.a
0
8.8
[2] 1xrt.a 8.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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