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BIOK_BACSU_1_448

L-Lysine--8-amino-7-oxononanoate transaminase [Class-III pyridoxal-phosphate-dependent aminotransferase family. BioA subfamily]

Composition of the binding site

Protein chains homodimer
A1 (BIOK_BACSU):17, 53, 54, 146, 149, 162, 223, 280, 410, 41217, 53, 54, 146, 149, 162, 223, 280, 410, 412
A2 (BIOK_BACSU):82, 313, 315:31782, 313, 315:317

Full PDB list

3dod, 3drd, 3du4

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
F
1
7
V
5
3
Y
1
4
6
D
1
4
9
A
2
2
3
K
2
8
0
R
4
1
0
L
4
1
2
L
8
2
G
3
1
5
H
3
1
6
S
3
1
7
[1]3dod.a none . . - - . . . . . . . .
[1]3drd.b none . . - - . . . . . . . .
[1]3du4.b kap13 . . . . . . . . . . . .

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
F
1
7
V
5
3
W
5
4
Y
1
4
6
D
1
4
9
F
1
6
2
A
2
2
3
K
2
8
0
R
4
1
0
L
4
1
2
L
8
2
F
3
1
3
G
3
1
5
H
3
1
6
S
3
1
7
[1]3dod.a . . . - - - . . * . . . . . .
[1]3drd.b . . . - - - . . * . . . . . .
[1]3du4.b . . . . . . . . . . . . . . .

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
3dod.a is apo
3drd.b is apo
3du4.b:kap
[1] 3dod.a
-
- 1.8
[1] 3drd.b -
-
1.8
[1] 3du4.b - -
0.2
[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
3dod.a
3drd.b
3du4.b
[1] 3dod.a
0
.01 .12
[1] 3drd.b .01
0
.12
[1] 3du4.b .12 .12
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
3dod.a
3drd.b
3du4.b
[1] 3dod.a
0
0.4 0.5
[1] 3drd.b 0.4
0
0.5
[1] 3du4.b 0.5 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
3dod.a
3drd.b
3du4.b
[1] 3dod.a
0
1.1 1.1
[1] 3drd.b 1.1
0
0.7
[1] 3du4.b 1.1 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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