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AROG_YEAST_1_370

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

Composition of the binding site

Protein chains monomer
A1 (AROG_YEAST):107, 109, 112, 113, 158, 178:180, 201, 249, 282, 314107, 109, 112, 113, 158, 178:180, 201, 249, 282, 314
Metals (Me):Co/Mn

Full PDB list

1hfb, 1oab, 1of6, 1of8, 1ofa, 1ofb, 1ofo, 1ofp, 1ofq, 1ofr, 1og0 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
R
1
0
7
Y
1
0
9
K
1
1
2
P
1
1
3
E
1
5
8
G
1
7
8
A
1
7
9
R
1
8
0
K
2
0
1
R
2
4
9
H
2
8
2
[1]1of8.a pep10 . . . . . . . . . . . Co
[1]1ofb.b none . . . . . . . . . . . Mn
[1]1ofo.a pga9 . . . . . . . . . . .

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 Me
R
1
0
7
Y
1
0
9
K
1
1
2
P
1
1
3
E
1
5
8
G
1
7
8
A
1
7
9
R
1
8
0
K
2
0
1
R
2
4
9
H
2
8
2
M
3
1
4
[1]1of8.a . . . . . . . . . . . . Co
[1]1ofb.b . . . . . . . . . . . . Mn
[1]1ofo.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
1of8.a:pep
1ofb.b is apo
1ofo.a:pga
[1] 1of8.a
0
- 0.2
[1] 1ofb.b 0.1
-
0.3
[1] 1ofo.a 0 -
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
1of8.a
1ofb.b
1ofo.a
[1] 1of8.a
0
.01 .01
[1] 1ofb.b .01
0
.02
[1] 1ofo.a .01 .02
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
1of8.a
1ofb.b
1ofo.a
[1] 1of8.a
0
0.1 0.2
[1] 1ofb.b 0.1
0
0.1
[1] 1ofo.a 0.2 0.1
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

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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
1of8.a
1ofb.b
1ofo.a
[1] 1of8.a
0
0.2 0.2
[1] 1ofb.b 0.2
0
0.2
[1] 1ofo.a 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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