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ARO1_EMENI_1_393

Pentafunctional AROM polypeptide

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ARO1_EMENI):R: 3-dehydroquinate synthase (146, 152, 162, 194, 197, 250, 264, 267, 268, 271, 275, 287, 356)
R: Substrate binding 2 (194, 197)
R: Substrate binding 2 (264, 267, 268)
146, 152, 162, 194, 197, 250, 264, 267, 268, 271, 275, 287, 356
Cofactors (cF):nad
Metals (Me):Zn

Full PDB list

1dqs, 1nr5, 1nrx, 1nua, 1nva, 1nvb, 1nvd, 1nve, 1nvf, 1sg6 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
D
1
4
6
K
1
5
2
N
1
6
2
E
1
9
4
K
1
9
7
K
2
5
0
R
2
6
4
L
2
6
7
N
2
6
8
H
2
7
1
H
2
7
5
H
2
8
7
K
3
5
6
[1]1dqs.a crb17 . . . . . . . . . . . . . nad Zn
[1]1nrx.b none . . . . . . . . . . . . - nad 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

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PDB.ch
A1 cF Me
D
1
4
6
K
1
5
2
N
1
6
2
E
1
9
4
K
1
9
7
K
2
5
0
R
2
6
4
L
2
6
7
N
2
6
8
H
2
7
1
H
2
7
5
H
2
8
7
K
3
5
6
[1]1dqs.a . . . . . . . . . . . . . nad Zn
[1]1nrx.b . . . . . . . . . . . . - nad 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
1dqs.a:crb
1nrx.b is apo
[1] 1dqs.a
0.1
-
[1] 1nrx.b 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
1dqs.a
1nrx.b
[1] 1dqs.a
0
.02
[1] 1nrx.b .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1dqs.a
1nrx.b
[1] 1dqs.a
0
1.6
[1] 1nrx.b 1.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1dqs.a
1nrx.b
[1] 1dqs.a
0
1.6
[1] 1nrx.b 1.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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