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PYRC_ECOLI_2_348

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PYRC_ECOLI):R: Substrate binding (19, 21)
45, 103, 110, 111, 140, 178, 222, 223, 251, 253, 255, 267, 268
19, 21, 45, 103, 110, 111, 140, 178, 222, 223, 251, 253, 255, 267, 268
Metals (Me):Zn

Full PDB list

1j79, 1xge, 2e25, 2eg6, 2eg7, 2eg8, 2z24, 2z25, 2z26, 2z27, 2z28, 2z29, 2z2a, 2z2b, 3mjm (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
9
R
2
1
N
4
5
K
1
0
3
T
1
1
0
T
1
1
1
H
1
4
0
H
1
7
8
C
2
2
2
L
2
2
3
D
2
5
1
A
2
5
3
H
2
5
5
A
2
6
7
G
2
6
8
[1]1j79.a oro11 . . . * . . . . . . . . . . . Zn
[1]2e25.a fot12 . . . * S . . . . . . . . . . Zn
[1]2eg6.a none . . . * . . . . . . . . . . . Zn
[1]2eg7.b otd13 . . . * . . . . . . . . . . . Zn
[1]2eg8.a fot12 . . . * . . . . . . . . . . . Zn
[1]2z24.a dor11 . . . * . S . . . . . . . . . Zn
[1]2z25.a dor11 . . . * . V . . . . . . . . . Zn
[1]2z25.b ncd12 . . . * . V . . . . . . . . . Zn
[1]2z26.a dor11 . . . * . A . . . . . . . . . Zn
[1]2z26.b dor,ncd23 . . . * - - . . . . . . . . . Zn
[1]2z27.a dor11 . . . * S . . . . . . . . . . Zn
[1]2z28.a dor11 . . . * V . . . . . . . . . . Zn
[1]2z29.a dor11 . . . * A . . . . . . . . . . Zn
[1]2z2a.a dor11 . . . * G . . . . . . . . . . Zn
[1]3mjm.a dor11 . . . * . . . . . . . . . . . Zn
[1]3mjm.b 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
1
9
R
2
1
N
4
5
K
1
0
3
T
1
1
0
T
1
1
1
H
1
4
0
H
1
7
8
C
2
2
2
L
2
2
3
D
2
5
1
A
2
5
3
H
2
5
5
A
2
6
7
G
2
6
8
[1]1j79.a . . . * . . . . . . . . . . . Zn
[1]2e25.a . . . * S . . . . . . . . . . Zn
[1]2eg6.a . . . * . . . . . . . . . . . Zn
[1]2eg7.b . . . * . . . . . . . . . . . Zn
[1]2eg8.a . . . * . . . . . . . . . . . Zn
[1]2z24.a . . . * . S . . . . . . . . . Zn
[1]2z25.a . . . * . V . . . . . . . . . Zn
[1]2z25.b . . . * . V . . . . . . . . . Zn
[1]2z26.a . . . * . A . . . . . . . . . Zn
[1]2z26.b . . . * - - . . . . . . . . . Zn
[1]2z27.a . . . * S . . . . . . . . . . Zn
[1]2z28.a . . . * V . . . . . . . . . . Zn
[1]2z29.a . . . * A . . . . . . . . . . Zn
[1]2z2a.a . . . * G . . . . . . . . . . Zn
[1]3mjm.a . . . * . . . . . . . . . . . Zn
[1]3mjm.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
1j79.a:oro
2e25.a:fot
2eg6.a is apo
2eg7.b:otd
2eg8.a:fot
2z24.a:dor
2z25.a:dor
2z25.b:ncd
2z26.a:dor
2z26.b:dor,ncd
2z27.a:dor
2z28.a:dor
2z29.a:dor
2z2a.a:dor
3mjm.a:dor
3mjm.b:ncd
[1] 1j79.a
0
0 - 0.1 0 0 0 0.2 0 0 0 0 0 0 0 0.1
[1] 2e25.a 0
0
- 0.2 0 0 0 0.3 0 0.1 0 0 0 0 0.1 0.1
[1] 2eg6.a 0.1 0.1
-
0.1 0 0 0 0.2 0 0.1 0 0 0 0 0 0
[1] 2eg7.b 0.3 0.8 -
0
0.6 0.5 0.5 0.4 0.5 0.5 0.3 0.2 0.3 0.5 0.5 0.2
[1] 2eg8.a 0 0 - 0.1
0
0 0 0.2 0 0.1 0 0 0 0 0 0.1
[1] 2z24.a 0 0 - 0.2 0
0
0 0.2 0 0 0 0 0 0 0 0.1
[1] 2z25.a 0 0 - 0.1 0 0
0
0.2 0 0 0 0 0 0 0 0.1
[1] 2z25.b 0.2 0.4 - 0.1 0.3 0.1 0.1
0
0.1 0.3 0.1 0.1 0.1 0.1 0.1 0
[1] 2z26.a 0 0 - 0.3 0 0 0 0.1
0
0.1 0 0 0 0 0 0.1
[1] 2z26.b 0 0 - 0.3 0 0 0 0.1 0
0
0 0 0 0 0 0.1
[1] 2z27.a 0 0 - 0.3 0 0 0 0.1 0 0
0
0 0 0 0 0.1
[1] 2z28.a 0 0 - 0.2 0 0 0 0.1 0 0 0
0
0 0 0 0.1
[1] 2z29.a 0 0 - 0.2 0 0 0 0.2 0 0 0 0
0
0 0 0.1
[1] 2z2a.a 0 0 - 0.3 0 0 0 0 0 0 0 0 0
0
0 0.1
[1] 3mjm.a 0 0 - 0.2 0 0 0 0.1 0 0 0 0 0 0
0
0.1
[1] 3mjm.b 0.3 0.5 - 0.4 0.4 0.1 0.2 0.1 0.3 0.4 0.1 0.1 0.1 0.1 0.3
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
1j79.a
2e25.a
2eg6.a
2eg7.b
2eg8.a
2z24.a
2z25.a
2z25.b
2z26.a
2z26.b
2z27.a
2z28.a
2z29.a
2z2a.a
3mjm.a
3mjm.b
[1] 1j79.a
0
.01 .02 .06 0 .02 0 .07 .02 .02 .02 .01 .01 .02 .01 .08
[1] 2e25.a .01
0
.01 .07 .01 .01 .01 .08 .03 .03 .03 .02 .01 .03 .01 .09
[1] 2eg6.a .02 .01
0
.08 .02 .01 .02 .07 .03 .03 .03 .02 .03 .03 .01 .07
[1] 2eg7.b .06 .07 .08
0
.06 .08 .06 .04 .08 .08 .08 .07 .07 .08 .07 .05
[1] 2eg8.a 0 .01 .02 .06
0
.02 0 .07 .02 .02 .02 .01 .01 .02 .01 .08
[1] 2z24.a .02 .01 .01 .08 .02
0
.02 .07 .01 .01 .01 .01 .01 .01 .01 .07
[1] 2z25.a 0 .01 .02 .06 0 .02
0
.07 .02 .02 .02 .01 .01 .02 .01 .08
[1] 2z25.b .07 .08 .07 .04 .07 .07 .07
0
.07 .07 .07 .06 .07 .07 .07 .01
[1] 2z26.a .02 .03 .03 .08 .02 .01 .02 .07
0
0 0 .01 .01 0 .02 .06
[1] 2z26.b .02 .03 .03 .08 .02 .01 .02 .07 0
0
0 .01 .01 0 .02 .06
[1] 2z27.a .02 .03 .03 .08 .02 .01 .02 .07 0 0
0
.01 .01 0 .02 .06
[1] 2z28.a .01 .02 .02 .07 .01 .01 .01 .06 .01 .01 .01
0
.01 .01 .01 .07
[1] 2z29.a .01 .01 .03 .07 .01 .01 .01 .07 .01 .01 .01 .01
0
.01 .02 .07
[1] 2z2a.a .02 .03 .03 .08 .02 .01 .02 .07 0 0 0 .01 .01
0
.02 .06
[1] 3mjm.a .01 .01 .01 .07 .01 .01 .01 .07 .02 .02 .02 .01 .02 .02
0
.08
[1] 3mjm.b .08 .09 .07 .05 .08 .07 .08 .01 .06 .06 .06 .07 .07 .06 .08
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
1j79.a
2e25.a
2eg6.a
2eg7.b
2eg8.a
2z24.a
2z25.a
2z25.b
2z26.a
2z26.b
2z27.a
2z28.a
2z29.a
2z2a.a
3mjm.a
3mjm.b
[1] 1j79.a
0
0.4 0.2 4.8 0.2 0.2 0.2 4.7 0.2 0.1 0.2 0.2 0.2 0.2 0.2 4.8
[1] 2e25.a 0.4
0
0.2 5.0 0.2 0.3 0.3 4.9 0.3 0.2 0.2 0.3 0.3 0.3 0.2 4.9
[1] 2eg6.a 0.2 0.2
0
4.9 0.1 0.1 0.1 4.8 0.1 0.1 0.1 0.1 0.1 0.1 0.1 4.9
[1] 2eg7.b 4.8 5.0 4.9
0
4.9 4.8 4.9 0.3 4.9 0.2 4.9 4.9 4.9 4.9 4.9 0.2
[1] 2eg8.a 0.2 0.2 0.1 4.9
0
0.1 0.1 4.8 0.1 0.1 0.1 0.1 0.1 0.1 0.1 4.9
[1] 2z24.a 0.2 0.3 0.1 4.8 0.1
0
0.1 4.8 0.1 0.1 0.1 0.1 0.1 0.1 0.1 4.8
[1] 2z25.a 0.2 0.3 0.1 4.9 0.1 0.1
0
4.8 0.1 0.1 0.1 0.1 0.1 0.1 0.1 4.8
[1] 2z25.b 4.7 4.9 4.8 0.3 4.8 4.8 4.8
0
4.8 0.1 4.8 4.8 4.8 4.8 4.8 0.1
[1] 2z26.a 0.2 0.3 0.1 4.9 0.1 0.1 0.1 4.8
0
0.1 0.1 0.1 0.1 0.1 0.1 4.8
[1] 2z26.b 0.1 0.2 0.1 0.2 0.1 0.1 0.1 0.1 0.1
0
0.1 0.1 0.1 0.1 0.1 0.1
[1] 2z27.a 0.2 0.2 0.1 4.9 0.1 0.1 0.1 4.8 0.1 0.1
0
0.1 0.1 0.1 0.1 4.8
[1] 2z28.a 0.2 0.3 0.1 4.9 0.1 0.1 0.1 4.8 0.1 0.1 0.1
0
0.1 0.1 0.1 4.8
[1] 2z29.a 0.2 0.3 0.1 4.9 0.1 0.1 0.1 4.8 0.1 0.1 0.1 0.1
0
0.1 0.1 4.8
[1] 2z2a.a 0.2 0.3 0.1 4.9 0.1 0.1 0.1 4.8 0.1 0.1 0.1 0.1 0.1
0
0.1 4.8
[1] 3mjm.a 0.2 0.2 0.1 4.9 0.1 0.1 0.1 4.8 0.1 0.1 0.1 0.1 0.1 0.1
0
4.8
[1] 3mjm.b 4.8 4.9 4.9 0.2 4.9 4.8 4.8 0.1 4.8 0.1 4.8 4.8 4.8 4.8 4.8
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
1j79.a
2e25.a
2eg6.a
2eg7.b
2eg8.a
2z24.a
2z25.a
2z25.b
2z26.a
2z26.b
2z27.a
2z28.a
2z29.a
2z2a.a
3mjm.a
3mjm.b
[1] 1j79.a
0
0.4 0.4 4.7 0.2 0.5 0.5 4.5 0.5 0.3 0.3 0.4 0.3 0.3 0.5 4.6
[1] 2e25.a 0.4
0
0.3 4.4 0.3 0.4 0.4 4.2 0.4 0.4 0.4 0.4 0.4 0.4 0.4 4.4
[1] 2eg6.a 0.4 0.3
0
4.8 0.4 0.3 0.3 4.6 0.3 0.3 0.3 0.4 0.3 0.3 0.3 4.7
[1] 2eg7.b 4.7 4.4 4.8
0
4.7 4.4 4.6 0.5 4.5 0.4 4.3 4.5 4.3 4.1 4.7 0.4
[1] 2eg8.a 0.2 0.3 0.4 4.7
0
0.5 0.5 4.5 0.5 0.3 0.3 0.3 0.3 0.3 0.5 4.7
[1] 2z24.a 0.5 0.4 0.3 4.4 0.5
0
0.1 4.3 0.1 0.1 0.1 0.2 0.1 0.1 0.1 4.4
[1] 2z25.a 0.5 0.4 0.3 4.6 0.5 0.1
0
4.7 0.1 0.1 0.1 0.2 0.1 0.1 0.1 4.5
[1] 2z25.b 4.5 4.2 4.6 0.5 4.5 4.3 4.7
0
4.3 0.1 4.1 4.3 4.1 3.9 4.5 0.2
[1] 2z26.a 0.5 0.4 0.3 4.5 0.5 0.1 0.1 4.3
0
0.1 0.1 0.2 0.1 0.1 0.1 4.4
[1] 2z26.b 0.3 0.4 0.3 0.4 0.3 0.1 0.1 0.1 0.1
0
0.1 0.1 0.1 0.1 0.1 0.1
[1] 2z27.a 0.3 0.4 0.3 4.3 0.3 0.1 0.1 4.1 0.1 0.1
0
0.1 0.1 0.1 0.1 4.3
[1] 2z28.a 0.4 0.4 0.4 4.5 0.3 0.2 0.2 4.3 0.2 0.1 0.1
0
0.1 0.1 0.2 4.5
[1] 2z29.a 0.3 0.4 0.3 4.3 0.3 0.1 0.1 4.1 0.1 0.1 0.1 0.1
0
0.1 0.1 4.3
[1] 2z2a.a 0.3 0.4 0.3 4.1 0.3 0.1 0.1 3.9 0.1 0.1 0.1 0.1 0.1
0
0.1 4.1
[1] 3mjm.a 0.5 0.4 0.3 4.7 0.5 0.1 0.1 4.5 0.1 0.1 0.1 0.2 0.1 0.1
0
4.7
[1] 3mjm.b 4.6 4.4 4.7 0.4 4.7 4.4 4.5 0.2 4.4 0.1 4.3 4.5 4.3 4.1 4.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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