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6PGD_ECOLI_1_468

6-phosphogluconate dehydrogenase, decarboxylating [6-phosphogluconate dehydrogenase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (6PGD_ECOLI):R: Substrate binding (128:130)
R: Substrate binding (186, 187)
102, 183, 190, 191, 259, 260, 287, 365
102, 128:130, 183, 186, 187, 190, 191, 259, 260, 287, 365
A2 (6PGD_ECOLI):445, 448, 451445, 448, 451

Full PDB list

2zya, 2zyd, 2zyg, 3fwn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
N
1
0
2
S
1
2
8
G
1
2
9
G
1
3
0
K
1
8
3
H
1
8
6
N
1
8
7
E
1
9
0
Y
1
9
1
N
2
5
9
K
2
6
0
R
2
8
7
I
3
6
5
R
4
4
5
F
4
4
8
H
4
5
1
[1]2zyd.b glo12 . . . . . . . . . . . . . . . .
[1]2zyg.a none . . . . . . . . . . . . . . . .
[1]3fwn.b 6pg17 . . . . . . . . . . . . . . . .

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 A2
N
1
0
2
S
1
2
8
G
1
2
9
G
1
3
0
K
1
8
3
H
1
8
6
N
1
8
7
E
1
9
0
Y
1
9
1
N
2
5
9
K
2
6
0
R
2
8
7
I
3
6
5
R
4
4
5
F
4
4
8
H
4
5
1
[1]2zyd.b . . . . . . . . . . . . . . . .
[1]2zyg.a . . . . . . . . . . . . . . . .
[1]3fwn.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2zyd.b:glo
2zyg.a is apo
3fwn.b:6pg
[1] 2zyd.b
0.3
- 0.1
[1] 2zyg.a 0.3
-
0
[1] 3fwn.b 0.3 -
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
2zyd.b
2zyg.a
3fwn.b
[1] 2zyd.b
0
.01 .02
[1] 2zyg.a .01
0
.01
[1] 3fwn.b .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
2zyd.b
2zyg.a
3fwn.b
[1] 2zyd.b
0
0.4 0.2
[1] 2zyg.a 0.4
0
0.5
[1] 3fwn.b 0.2 0.5
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

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
2zyd.b
2zyg.a
3fwn.b
[1] 2zyd.b
0
0.9 0.3
[1] 2zyg.a 0.9
0
0.9
[1] 3fwn.b 0.3 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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