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6PGD_LACLM_1_472

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (6PGD_LACLM):R: Substrate binding (128:130)
R: Substrate binding (187, 188)
102, 184, 191, 192, 261, 262, 264, 289, 367
102, 128:130, 184, 187, 188, 191, 192, 261, 262, 264, 289, 367

Full PDB list

2iyo, 2iyp, 2iz0, 2iz1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
1
0
2
S
1
2
8
G
1
2
9
G
1
3
0
K
1
8
4
H
1
8
7
N
1
8
8
E
1
9
1
Y
1
9
2
N
2
6
1
K
2
6
2
R
2
8
9
I
3
6
7
[1]2iyo.a 6pg17 . . . . . . . . . . . . .
[1]2iyp.a 5rp14 . . . . . . . . . . . . .
[1]2iz1.a res14 . . . . . . . . . . . . .
[1]2iz1.b none . . . . . . . . . . . . .

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
N
1
0
2
S
1
2
8
G
1
2
9
G
1
3
0
K
1
8
4
H
1
8
7
N
1
8
8
E
1
9
1
Y
1
9
2
N
2
6
1
K
2
6
2
T
2
6
4
R
2
8
9
I
3
6
7
[1]2iyo.a . . . . . . . . . . . . . .
[1]2iyp.a . . . . . . . . . . . . . .
[1]2iz1.a . . . . . . . . . . . . . .
[1]2iz1.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
2iyo.a:6pg
2iyp.a:5rp
2iz1.a:res
2iz1.b is apo
[1] 2iyo.a
0.1
0.2 0.1 -
[1] 2iyp.a 0
0.1
0.1 -
[1] 2iz1.a 0.1 0.2
0.1
-
[1] 2iz1.b 0 0 0
-
[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
2iyo.a
2iyp.a
2iz1.a
2iz1.b
[1] 2iyo.a
0
0 .01 .01
[1] 2iyp.a 0
0
.01 .01
[1] 2iz1.a .01 .01
0
.02
[1] 2iz1.b .01 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2iyo.a
2iyp.a
2iz1.a
2iz1.b
[1] 2iyo.a
0
0.3 0.3 1.8
[1] 2iyp.a 0.3
0
0.2 1.7
[1] 2iz1.a 0.3 0.2
0
1.8
[1] 2iz1.b 1.8 1.7 1.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2iyo.a
2iyp.a
2iz1.a
2iz1.b
[1] 2iyo.a
0
0.6 0.6 2.9
[1] 2iyp.a 0.6
0
0.2 2.8
[1] 2iz1.a 0.6 0.2
0
2.8
[1] 2iz1.b 2.9 2.8 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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