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AROF_THEMA_67_338

Phospho-2-dehydro-3-deoxyheptonate aldolase [Class-I DAHP synthase family]

Composition of the binding site

Protein chains monomer
A1 (AROF_THEMA):102, 126, 131, 132, 164, 182, 184:186, 207, 237, 272102, 126, 131, 132, 164, 182, 184:186, 207, 237, 272

Full PDB list

1rzm, 1vr6, 3pg8, 3pg9 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
R
1
2
6
K
1
3
1
P
1
3
2
Q
1
8
2
G
1
8
4
A
1
8
5
R
1
8
6
K
2
0
7
R
2
3
7
H
2
7
2
[1]1rzm.a pep10 . . . . . . . . . .
[1]1vr6.a none . . . . . . . . . .
[1]3pg8.a none . . . . . . . . . .

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

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PDB.ch
A1
C
1
0
2
R
1
2
6
K
1
3
1
P
1
3
2
E
1
6
4
Q
1
8
2
G
1
8
4
A
1
8
5
R
1
8
6
K
2
0
7
R
2
3
7
H
2
7
2
[1]1rzm.a . . . . . . . . . . . .
[1]1vr6.a . . . . . . . . . . . .
[1]3pg8.a * . . . . . . . . . . .

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
1rzm.a:pep
1vr6.a is apo
3pg8.a is apo
[1] 1rzm.a
0.1
- -
[1] 1vr6.a 0
-
-
[1] 3pg8.a 0 -
-
[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
1rzm.a
1vr6.a
3pg8.a
[1] 1rzm.a
0
.01 .01
[1] 1vr6.a .01
0
0
[1] 3pg8.a .01 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.2 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
1rzm.a
1vr6.a
3pg8.a
[1] 1rzm.a
0
1.7 3.7
[1] 1vr6.a 1.7
0
2.9
[1] 3pg8.a 3.7 2.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
1rzm.a
1vr6.a
3pg8.a
[1] 1rzm.a
0
2.2 3.5
[1] 1vr6.a 2.2
0
2.8
[1] 3pg8.a 3.5 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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