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BIOF_ECOLI_1_384

8-amino-7-oxononanoate synthase [Class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (BIOF_ECOLI):R: Pyridoxal phosphate binding (108, 109)
20, 21, 47, 107, 112, 133, 135, 175, 179, 180, 204, 206, 207, 233, 236, 348, 352
20, 21, 47, 107:109, 112, 133, 135, 175, 179, 180, 204, 206, 207, 233, 236, 348, 352
A2 (BIOF_ECOLI):75, 76, 78, 79, 263:26675, 76, 78, 79, 263:266

Full PDB list

1bs0, 1dj9, 1dje, 2g6w

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
R
2
1
N
4
7
S
1
0
7
G
1
0
8
F
1
0
9
H
1
3
3
S
1
3
5
E
1
7
5
S
1
7
9
M
1
8
0
D
2
0
4
A
2
0
6
H
2
0
7
T
2
3
3
K
2
3
6
I
3
4
8
T
3
5
2
G
7
5
S
7
6
H
7
8
V
7
9
I
2
6
3
Y
2
6
4
S
2
6
5
T
2
6
6
[1]1bs0.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dj9.a kam,mg29 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dje.a plp15 . . . . . . . . . . . . . . * . . . . . . . . . .
[1]2g6w.a llf20 . . . . . . . . . . . . . . * . . . . . . . . . .

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
L
2
0
R
2
1
N
4
7
S
1
0
7
G
1
0
8
F
1
0
9
N
1
1
2
H
1
3
3
S
1
3
5
E
1
7
5
S
1
7
9
M
1
8
0
D
2
0
4
A
2
0
6
H
2
0
7
T
2
3
3
K
2
3
6
I
3
4
8
T
3
5
2
G
7
5
S
7
6
H
7
8
V
7
9
I
2
6
3
Y
2
6
4
S
2
6
5
T
2
6
6
[1]1bs0.a . . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1dj9.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dje.a . . . . . . . . . . . . . . . . * . . . . . . . . . .
[1]2g6w.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1bs0.a is apo
1dj9.a:kam,mg
1dje.a:plp
2g6w.a:llf
[1] 1bs0.a
-
2.3 2.3 2.0
[1] 1dj9.a -
0.2
0.7 0.5
[1] 1dje.a - 0.9
1.0
0.4
[1] 2g6w.a - 0.7 0.7
1.0
[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
1bs0.a
1dj9.a
1dje.a
2g6w.a
[1] 1bs0.a
0
.09 .12 .09
[1] 1dj9.a .09
0
.04 .03
[1] 1dje.a .12 .04
0
.04
[1] 2g6w.a .09 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
1bs0.a
1dj9.a
1dje.a
2g6w.a
[1] 1bs0.a
0
1.6 0.9 0.8
[1] 1dj9.a 1.6
0
1.2 1.2
[1] 1dje.a 0.9 1.2
0
0.4
[1] 2g6w.a 0.8 1.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1bs0.a
1dj9.a
1dje.a
2g6w.a
[1] 1bs0.a
0
2.6 2.3 2.3
[1] 1dj9.a 2.6
0
1.5 1.6
[1] 1dje.a 2.3 1.5
0
0.9
[1] 2g6w.a 2.3 1.6 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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