If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

AROG_ECOLI_1_350

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

Composition of the binding site

Protein chains monomer
A1 (AROG_ECOLI):61, 92, 94, 97:100, 143, 163:165, 186, 234, 268, 273, 300, 302, 32661, 92, 94, 97:100, 143, 163:165, 186, 234, 268, 273, 300, 302, 326
Metals (Me):Mn

Full PDB list

1gg1, 1kfl, 1n8f, 1qr7, 5cks (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
C
6
1
R
9
2
Y
9
4
K
9
7
P
9
8
R
9
9
T
1
0
0
E
1
4
3
G
1
6
3
A
1
6
4
R
1
6
5
K
1
8
6
R
2
3
4
H
2
6
8
M
3
0
0
E
3
0
2
D
3
2
6
[1]1gg1.b pga9 . . . . . . . . . . . . . . . . . Mn
[1]1kfl.a pep10 . . . . . . . . . . . . . . * . . Mn
[1]1n8f.a pep10 . . . . . . . . . . . . . . . . . Mn
[1]5cks.a none . . . . . . . . . . . . . . . . .
[1]5cks.b 52l19 . . . . . . . . . . . . . . . . .

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
C
6
1
R
9
2
Y
9
4
K
9
7
P
9
8
R
9
9
T
1
0
0
E
1
4
3
G
1
6
3
A
1
6
4
R
1
6
5
K
1
8
6
R
2
3
4
H
2
6
8
K
2
7
3
M
3
0
0
E
3
0
2
D
3
2
6
[1]1gg1.b . . . . . . . . . . . . . . . . . . Mn
[1]1kfl.a . . . * . . . . . . . . . . . * . . Mn
[1]1n8f.a . . . . . . . . . . . . . . . . . . Mn
[1]5cks.a . . . * . . . . . . . . . . . . . .
[1]5cks.b . . . . . . . . . . . . . . . . . .

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1gg1.b:pga
1kfl.a:pep
1n8f.a:pep
5cks.a is apo
5cks.b:52l
[1] 1gg1.b
0
0.5 0.1 - 0.1
[1] 1kfl.a 0.4
0
0.4 - 3.1
[1] 1n8f.a 0.1 0.5
0
- 0
[1] 5cks.a 0.5 0.2 0.6
-
2.5
[1] 5cks.b 0 0 0.1 -
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1gg1.b
1kfl.a
1n8f.a
5cks.a
5cks.b
[1] 1gg1.b
0
.22 .01 .19 .03
[1] 1kfl.a .22
0
.21 .16 .19
[1] 1n8f.a .01 .21
0
.19 .03
[1] 5cks.a .19 .16 .19
0
.17
[1] 5cks.b .03 .19 .03 .17
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
1gg1.b
1kfl.a
1n8f.a
5cks.a
5cks.b
[1] 1gg1.b
0
1.1 0.2 1.3 0.3
[1] 1kfl.a 1.1
0
1.1 0.9 1.1
[1] 1n8f.a 0.2 1.1
0
1.3 0.3
[1] 5cks.a 1.3 0.9 1.3
0
1.2
[1] 5cks.b 0.3 1.1 0.3 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1gg1.b
1kfl.a
1n8f.a
5cks.a
5cks.b
[1] 1gg1.b
0
1.9 0.7 2.0 0.8
[1] 1kfl.a 1.9
0
1.8 1.6 1.8
[1] 1n8f.a 0.7 1.8
0
2.0 0.7
[1] 5cks.a 2.0 1.6 2.0
0
1.9
[1] 5cks.b 0.8 1.8 0.7 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...