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DMGD_CHRSD_1_403

D-galactonate dehydratase family member ManD [Mandelate racemase/muconate lactonizing enzyme family. GalD subfamily]

Composition of the binding site

Protein chains homodimer
A1 (DMGD_CHRSD):37, 122, 147, 159, 211, 213, 237, 263, 284, 313, 315, 317, 340, 390, 40337, 122, 147, 159, 211, 213, 237, 263, 284, 313, 315, 317, 340, 390, 403
A2 (DMGD_CHRSD):75, 7675, 76
Metals (Me):Co/Mg

Full PDB list

3bsm, 3ow1, 3p93, 3pk7, 3qke, 3rgt, 4f4r, 4k2s, 4kpl, 4kt2, 4kws (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
N
3
7
H
1
2
2
R
1
4
7
Y
1
5
9
D
2
1
1
H
2
1
3
E
2
3
7
E
2
6
3
R
2
8
4
H
3
1
3
P
3
1
5
D
3
1
7
E
3
4
0
L
3
9
0
W
4
0
3
Y
7
5
W
7
6
[1]3p93.a cs213 . . . - . . . . . . . . . . . . . Mg
[1]3p93.c kdg12 . . . - . . . . . . . . . . . . . Mg
[1]3pk7.a none . . . . . . . . . . . . . . . . . Mg
[1]3qke.a gco13 . . . . . . . . . . . . . . . . . Mg
[1]3rgt.b ez412 . . . . . . . . . . . . . . . . . Co
[1]4k2s.a gco13 . . . . . . . . . . A . . . . . . Mg

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 Me
N
3
7
H
1
2
2
R
1
4
7
Y
1
5
9
D
2
1
1
H
2
1
3
E
2
3
7
E
2
6
3
R
2
8
4
H
3
1
3
P
3
1
5
D
3
1
7
E
3
4
0
L
3
9
0
W
4
0
3
Y
7
5
W
7
6
[1]3p93.a . . . - . . . . . . . . . . . . . Mg
[1]3p93.c . . . - . . . . . . . . . . . . . Mg
[1]3pk7.a . . . . . . . . . . . . . . . . . Mg
[1]3qke.a . . . . . . . . . . . . . . . . . Mg
[1]3rgt.b . . . . . . . . . . . . . . . . . Co
[1]4k2s.a . . . . . . . . . . A . . . . . . Mg

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
3p93.a:cs2
3p93.c:kdg
3pk7.a is apo
3qke.a:gco
3rgt.b:ez4
4k2s.a:gco
[1] 3p93.a
0
0 - 0 0 0
[1] 3p93.c 0
0
- 0 0 0
[1] 3pk7.a 0.2 0
-
0.3 0.1 0.2
[1] 3qke.a 0.1 0 -
0.2
0.1 0.2
[1] 3rgt.b 0.1 0 - 0.1
0
0.2
[1] 4k2s.a 0 0 - 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
3p93.a
3p93.c
3pk7.a
3qke.a
3rgt.b
4k2s.a
[1] 3p93.a
0
0 .02 .01 .02 0
[1] 3p93.c 0
0
.02 .01 .02 0
[1] 3pk7.a .02 .02
0
.01 0 .02
[1] 3qke.a .01 .01 .01
0
.01 .01
[1] 3rgt.b .02 .02 0 .01
0
.02
[1] 4k2s.a 0 0 .02 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3p93.a
3p93.c
3pk7.a
3qke.a
3rgt.b
4k2s.a
[1] 3p93.a
0
0.1 0.1 0.1 0.2 0.2
[1] 3p93.c 0.1
0
0.2 0.2 0.1 0.2
[1] 3pk7.a 0.1 0.2
0
0.1 0.2 0.2
[1] 3qke.a 0.1 0.2 0.1
0
0.2 0.1
[1] 3rgt.b 0.2 0.1 0.2 0.2
0
0.2
[1] 4k2s.a 0.2 0.2 0.2 0.1 0.2
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
3p93.a
3p93.c
3pk7.a
3qke.a
3rgt.b
4k2s.a
[1] 3p93.a
0
0.1 0.2 0.2 0.2 0.2
[1] 3p93.c 0.1
0
0.2 0.2 0.2 0.2
[1] 3pk7.a 0.2 0.2
0
0.1 0.2 0.2
[1] 3qke.a 0.2 0.2 0.1
0
0.2 0.2
[1] 3rgt.b 0.2 0.2 0.2 0.2
0
0.2
[1] 4k2s.a 0.2 0.2 0.2 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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