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6PGD_HUMAN_1_476

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (6PGD_HUMAN):R: Substrate binding (129:131)
R: Substrate binding (187, 188)
9:15, 33:35, 38, 74:77, 80, 84, 101:103, 128, 132, 184, 191, 192, 260:263, 288, 367
9:15, 33:35, 38, 74:77, 80, 84, 101:103, 128:132, 184, 187, 188, 191, 192, 260:263, 288, 367

Full PDB list

1pgn, 1pgo, 1pgp, 1pgq, 2jkv, 2pgd, 4gwg, 4gwk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
0
L
1
1
A
1
2
V
1
3
M
1
4
N
3
3
R
3
4
T
3
5
K
3
8
L
7
4
V
7
5
K
7
6
A
8
0
F
8
4
G
1
0
2
N
1
0
3
V
1
2
8
S
1
2
9
G
1
3
0
G
1
3
1
E
1
3
2
K
1
8
4
H
1
8
7
N
1
8
8
E
1
9
1
Y
1
9
2
K
2
6
1
G
2
6
2
T
2
6
3
R
2
8
8
I
3
6
7
[1]1pgn.a nbp49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pgo.a ndp48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pgp.a 6pg17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pgq.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gwg.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gwk.a 3pg11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2jkv.a nap48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
I
9
G
1
0
L
1
1
A
1
2
V
1
3
M
1
4
G
1
5
N
3
3
R
3
4
T
3
5
K
3
8
L
7
4
V
7
5
K
7
6
A
7
7
A
8
0
F
8
4
G
1
0
1
G
1
0
2
N
1
0
3
V
1
2
8
S
1
2
9
G
1
3
0
G
1
3
1
E
1
3
2
K
1
8
4
H
1
8
7
N
1
8
8
E
1
9
1
Y
1
9
2
Q
2
6
0
K
2
6
1
G
2
6
2
T
2
6
3
R
2
8
8
I
3
6
7
[1]1pgn.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . * . . . .
[1]1pgo.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]1pgp.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]1pgq.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . * . . . .
[1]4gwg.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]4gwk.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2jkv.a . * . . * * . * . . . . . . . . * . . . . . . . . . . . . . . * . . . .

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
1pgn.a:nbp
1pgo.a:ndp
1pgp.a:6pg
1pgq.a is apo
4gwg.a is apo
4gwk.a:3pg
2jkv.a:nap
[1] 1pgn.a
0.2
0.1 0.1 - - 3.2 1.3
[1] 1pgo.a 0.1
0
0.2 - - 3.4 0.7
[1] 1pgp.a 2.6 2.1
0
- - 2.8 0.7
[1] 1pgq.a 1.0 1.5 0.2
-
- 3.2 1.8
[1] 4gwg.a 0.6 0.2 0.1 -
-
0.2 0.8
[1] 4gwk.a 0.7 0.2 0 - -
0.2
0.6
[2] 2jkv.a 12 7.2 0.1 - - 2.7
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1pgn.a
1pgo.a
1pgp.a
1pgq.a
4gwg.a
4gwk.a
2jkv.a
[1] 1pgn.a
0
.03 .08 .04 .13 .13 .38
[1] 1pgo.a .03
0
.09 .06 .13 .13 .37
[1] 1pgp.a .08 .09
0
.10 .17 .16 .38
[1] 1pgq.a .04 .06 .10
0
.15 .15 .39
[1] 4gwg.a .13 .13 .17 .15
0
.01 .44
[1] 4gwk.a .13 .13 .16 .15 .01
0
.44
[2] 2jkv.a .38 .37 .38 .39 .44 .44
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.3 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
1pgn.a
1pgo.a
1pgp.a
1pgq.a
4gwg.a
4gwk.a
2jkv.a
[1] 1pgn.a
0
0.3 0.3 0.5 2.8 2.8 2.0
[1] 1pgo.a 0.3
0
0.3 0.5 2.8 2.8 2.0
[1] 1pgp.a 0.3 0.3
0
0.5 2.8 2.8 2.0
[1] 1pgq.a 0.5 0.5 0.5
0
2.8 2.8 2.1
[1] 4gwg.a 2.8 2.8 2.8 2.8
0
0.1 4.5
[1] 4gwk.a 2.8 2.8 2.8 2.8 0.1
0
4.5
[2] 2jkv.a 2.0 2.0 2.0 2.1 4.5 4.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.0 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
1pgn.a
1pgo.a
1pgp.a
1pgq.a
4gwg.a
4gwk.a
2jkv.a
[1] 1pgn.a
0
0.8 0.9 0.8 3.4 3.4 2.4
[1] 1pgo.a 0.8
0
0.9 1.0 3.3 3.3 2.3
[1] 1pgp.a 0.9 0.9
0
1.1 3.3 3.3 2.3
[1] 1pgq.a 0.8 1.0 1.1
0
3.4 3.4 2.5
[1] 4gwg.a 3.4 3.3 3.3 3.4
0
0.5 5.0
[1] 4gwk.a 3.4 3.3 3.3 3.4 0.5
0
5.1
[2] 2jkv.a 2.4 2.3 2.3 2.5 5.0 5.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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