If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

DMGO_ARTGO_2_830

Dimethylglycine oxidase [GcvT family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DMGO_ARTGO):R: Tetrahydrofolate binding (658, 660)
505, 508, 539, 552, 554, 566:568, 631, 632, 649:651, 699, 719, 825, 829
505, 508, 539, 552, 554, 566:568, 631, 632, 649:651, 658, 660, 699, 719, 825, 829

Full PDB list

1pj5, 1pj6, 1pj7, 3gsi

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
5
0
5
L
5
0
8
Y
5
3
9
D
5
5
2
T
5
5
4
G
5
6
6
A
5
6
7
N
5
6
8
Y
6
3
1
F
6
3
2
L
6
4
9
S
6
5
0
Y
6
5
1
E
6
5
8
Y
6
6
0
Y
6
9
9
F
7
1
9
[1]1pj5.a none . . . . . . . . . . . . . . . . .
[1]1pj6.a fol32 . . . . . . . . . . . . . . . . .
[1]1pj7.a ffo34 . . . . . . . . . . . . . . . . .
[1]3gsi.a thg32 . . . A . . . . . . . . . . . . .

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
M
5
0
5
L
5
0
8
Y
5
3
9
D
5
5
2
T
5
5
4
G
5
6
6
A
5
6
7
N
5
6
8
Y
6
3
1
F
6
3
2
L
6
4
9
S
6
5
0
Y
6
5
1
E
6
5
8
Y
6
6
0
Y
6
9
9
F
7
1
9
M
8
2
5
R
8
2
9
[1]1pj5.a . . . . . . . . . . . . * . . . . . .
[1]1pj6.a . . . . . . . . . . . . * . . . . . .
[1]1pj7.a . . . . . . . . . . . . . . . . . . .
[1]3gsi.a . . . 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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1pj5.a is apo
1pj6.a:fol
1pj7.a:ffo
3gsi.a:thg
[1] 1pj5.a
-
1.3 2.9 3.1
[1] 1pj6.a -
0
1.3 1.1
[1] 1pj7.a - 0.1
0
0.1
[1] 3gsi.a - 0.2 0.1
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1pj5.a
1pj6.a
1pj7.a
3gsi.a
[1] 1pj5.a
0
.11 .16 .17
[1] 1pj6.a .11
0
.08 .08
[1] 1pj7.a .16 .08
0
.01
[1] 3gsi.a .17 .08 .01
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

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
1pj5.a
1pj6.a
1pj7.a
3gsi.a
[1] 1pj5.a
0
0.3 0.4 0.4
[1] 1pj6.a 0.3
0
0.2 0.3
[1] 1pj7.a 0.4 0.2
0
0.3
[1] 3gsi.a 0.4 0.3 0.3
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
1pj5.a
1pj6.a
1pj7.a
3gsi.a
[1] 1pj5.a
0
1.8 1.9 2.0
[1] 1pj6.a 1.8
0
0.6 0.7
[1] 1pj7.a 1.9 0.6
0
0.5
[1] 3gsi.a 2.0 0.7 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...