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DESV_STRVZ_1_379

dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase [DegT/dnrJ/eryC1 family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DESV_STRVZ):R: Pyridoxal phosphate binding (188, 190, 193)
66:68, 93, 95, 138, 164, 166, 167, 318
66:68, 93, 95, 138, 164, 166, 167, 188, 190, 193, 318
A2 (DESV_STRVZ):R: Pyridoxal phosphate binding (235, 237)
221, 226, 227
221, 226, 227, 235, 237
Metals (Me):Na

Full PDB list

2oga, 2oge

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
S
6
6
G
6
7
M
6
8
Y
9
3
A
9
5
V
1
3
8
D
1
6
4
A
1
6
6
Q
1
6
7
S
1
8
8
Y
1
9
0
K
1
9
3
Y
3
1
8
Y
2
2
1
K
2
2
6
Y
2
2
7
N
2
3
5
R
2
3
7
[1]2oga.b pgu25 . . . . . . . . . . . . . . . . . . Na
[1]2oge.a plp15 . . . . . . . . . . . * . . . . . . 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 A2 Me
S
6
6
G
6
7
M
6
8
Y
9
3
A
9
5
V
1
3
8
D
1
6
4
A
1
6
6
Q
1
6
7
S
1
8
8
Y
1
9
0
K
1
9
3
Y
3
1
8
Y
2
2
1
K
2
2
6
Y
2
2
7
N
2
3
5
R
2
3
7
[1]2oga.b . . . . . . . . . . . . . . . . . . Na
[1]2oge.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
2oga.b:pgu
2oge.a:plp
[1] 2oga.b
0.2
0.5
[1] 2oge.a 0.7
0.7
[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
2oga.b
2oge.a
[1] 2oga.b
0
.02
[1] 2oge.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2oga.b
2oge.a
[1] 2oga.b
0
0.6
[1] 2oge.a 0.6
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
2oga.b
2oge.a
[1] 2oga.b
0
1.3
[1] 2oge.a 1.3
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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