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AROB_STAAR_1_354

3-dehydroquinate synthase [Sugar phosphate cyclases superfamily. Dehydroquinate synthase family]

Composition of the binding site

Protein chains homodimer
A1 (AROB_STAAR):130, 136, 146, 178, 181, 221, 231, 235, 238, 239, 242, 246, 256, 314130, 136, 146, 178, 181, 221, 231, 235, 238, 239, 242, 246, 256, 314
A2 (AROB_STAAR):115115
Cofactors (cF):nad
Metals (Me):Zn

Full PDB list

1xag, 1xah, 1xai, 1xaj, 1xal (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 cF Me
D
1
3
0
K
1
3
6
N
1
4
6
E
1
7
8
K
1
8
1
K
2
2
1
R
2
3
5
L
2
3
8
N
2
3
9
H
2
4
2
H
2
4
6
H
2
5
6
K
3
1
4
R
1
1
5
[1]1xah.a none . . . . . . . . . . . . - . nad Zn
[1]1xai.a crb17 . . . . . . . . . . . . . . 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 A2 cF Me
D
1
3
0
K
1
3
6
N
1
4
6
E
1
7
8
K
1
8
1
K
2
2
1
E
2
3
1
R
2
3
5
L
2
3
8
N
2
3
9
H
2
4
2
H
2
4
6
H
2
5
6
K
3
1
4
R
1
1
5
[1]1xah.a . . . . . . . . . . . . . - . nad Zn
[1]1xai.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
1xah.a is apo
1xai.a:crb
[1] 1xah.a
-
0.6
[1] 1xai.a -
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
1xah.a
1xai.a
[1] 1xah.a
0
.03
[1] 1xai.a .03
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
1xah.a
1xai.a
[1] 1xah.a
0
0.4
[1] 1xai.a 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1xah.a
1xai.a
[1] 1xah.a
0
0.6
[1] 1xai.a 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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