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DMDA_PELUB_1_369

Dimethylsulfonioproprionate demethylase DmdA [GcvT family. DmdA subfamily]

Composition of the binding site

Protein chains monomer
A1 (DMDA_PELUB):32, 63, 95, 108, 110, 122:124, 177, 178, 196, 197, 199, 204, 206, 244, 26532, 63, 95, 108, 110, 122:124, 177, 178, 196, 197, 199, 204, 206, 244, 265
Metals (Me):Na

Full PDB list

3tfh, 3tfi, 3tfj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Y
3
2
E
6
3
Y
9
5
D
1
0
8
V
1
1
0
S
1
2
2
I
1
2
3
A
1
2
4
F
1
7
7
F
1
7
8
G
1
9
6
W
1
9
7
K
1
9
9
E
2
0
4
Y
2
0
6
L
2
4
4
Y
2
6
5
[1]3tfi.a none . . . . . . . . . . . . . . . . . Na
[1]3tfj.a thg32 . . . . . . . . . . . . . . . . . Na

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
Y
3
2
E
6
3
Y
9
5
D
1
0
8
V
1
1
0
S
1
2
2
I
1
2
3
A
1
2
4
F
1
7
7
F
1
7
8
G
1
9
6
W
1
9
7
K
1
9
9
E
2
0
4
Y
2
0
6
L
2
4
4
Y
2
6
5
[1]3tfi.a . * . . . . . . . . . . . . . . . Na
[1]3tfj.a . . . . . . . . . . . . . . . . . Na

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
3tfi.a is apo
3tfj.a:thg
[1] 3tfi.a
-
0.6
[1] 3tfj.a -
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
3tfi.a
3tfj.a
[1] 3tfi.a
0
.04
[1] 3tfj.a .04
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
3tfi.a
3tfj.a
[1] 3tfi.a
0
0.1
[1] 3tfj.a 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.0 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
3tfi.a
3tfj.a
[1] 3tfi.a
0
0.4
[1] 3tfj.a 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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