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BIOA_ECOLI_1_429

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

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (BIOA_ECOLI):R: Pyridoxal phosphate binding (112, 113)
17, 52, 53, 111, 144:147, 211, 217, 245, 247, 248, 274, 376, 391, 393, 398
17, 52, 53, 111:113, 144:147, 211, 217, 245, 247, 248, 274, 376, 391, 393, 398
A2 (BIOA_ECOLI):R: Pyridoxal phosphate binding (308, 309)
307
307:309

Full PDB list

1dty, 1mgv, 1mly, 1mlz, 1qj3, 1qj5, 1s06, 1s07, 1s08, 1s09, 1s0a (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
Y
1
7
W
5
2
W
5
3
G
1
1
2
S
1
1
3
Y
1
4
4
H
1
4
5
G
1
4
6
D
1
4
7
E
2
1
1
A
2
1
7
D
2
4
5
I
2
4
7
A
2
4
8
K
2
7
4
R
3
9
1
F
3
9
3
G
3
0
7
P
3
0
8
T
3
0
9
[1]1mgv.a plp15 . . . . . . . . . . . . . . * A . . . .
[1]1mly.a acz.plp29 . . . . . . . . . . . . . . . . . . . .
[1]1mlz.a plp.tza29 . . . . . . . . . . . . . . . . . . . .
[1]1mlz.b plp,tza29 . . . . . . . . . . . . . . . . . . . .
[1]1qj3.a kap,plp28 . . . . . . . . . . . . . . * . . . . .
[1]1s07.a plp16 . . . . . . . . . . . . . . . . . . . .
[1]1s08.a plp15 . . . . . . . . N . . . . . * . . . . .
[1]1s09.a plp15 . . . . . F . . . . . . . . * . . . . .
[1]1s0a.b plp15 F . . . . . . . . . . . . . * . . . . .

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
Y
1
7
W
5
2
W
5
3
S
1
1
1
G
1
1
2
S
1
1
3
Y
1
4
4
H
1
4
5
G
1
4
6
D
1
4
7
E
2
1
1
A
2
1
7
D
2
4
5
I
2
4
7
A
2
4
8
K
2
7
4
M
3
7
6
R
3
9
1
F
3
9
3
Y
3
9
8
G
3
0
7
P
3
0
8
T
3
0
9
[1]1mgv.a . . . . . . . . . . . . . . . * . A . . . . .
[1]1mly.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1mlz.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1mlz.b . . . . . . . . . . . . . . . . . . . . . . .
[1]1qj3.a . . . . . . . . . . . . . . . * . . . . . . .
[1]1s07.a . . . . . . . . . . . . . . . * . . . . . . .
[1]1s08.a . . . . . . . . . N . . . . . * . . * . . . .
[1]1s09.a . . . . . . F . . . . . . . . * . . . . . . .
[1]1s0a.b F . . . . . . . . . . . . . . * . . . . . . .

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
1mgv.a:plp
1mly.a:acz.plp
1mlz.a:plp.tza
1mlz.b:plp,tza
1qj3.a:kap,plp
1s07.a:plp
1s08.a:plp
1s09.a:plp
1s0a.b:plp
[1] 1mgv.a
0.6
0.4 0.4 0.8 1.1 0.6 0.6 0.8 0.8
[1] 1mly.a 0.2
0
0 0.2 0.3 0.1 0.2 0.2 0.2
[1] 1mlz.a 0.2 0
0
0.3 0.2 0.2 0.2 0.2 0.3
[1] 1mlz.b 0.5 0.1 0.1
0.1
0.6 0.2 0.5 0.5 0.5
[1] 1qj3.a 0.6 0.6 0.6 1.1
0.9
0.6 0.6 0.6 0.6
[1] 1s07.a 0.4 0.4 0.2 0.5 0.7
0.2
0.4 0.4 0.4
[1] 1s08.a 0.8 3.8 3.2 3.9 3.9 0.6
0.8
0.8 0.8
[1] 1s09.a 0.6 0.2 0.1 1.0 0.9 0.4 0.6
0.6
0.6
[1] 1s0a.b 0.6 0.4 0.4 0.5 1.0 0.6 0.6 0.8
0.6
[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
1mgv.a
1mly.a
1mlz.a
1mlz.b
1qj3.a
1s07.a
1s08.a
1s09.a
1s0a.b
[1] 1mgv.a
0
.06 .06 .05 .04 .05 .17 .02 .03
[1] 1mly.a .06
0
0 .02 .06 .04 .20 .05 .04
[1] 1mlz.a .06 0
0
.03 .07 .04 .20 .05 .04
[1] 1mlz.b .05 .02 .03
0
.06 .04 .20 .05 .03
[1] 1qj3.a .04 .06 .07 .06
0
.05 .20 .03 .05
[1] 1s07.a .05 .04 .04 .04 .05
0
.20 .04 .03
[1] 1s08.a .17 .20 .20 .20 .20 .20
0
.19 .17
[1] 1s09.a .02 .05 .05 .05 .03 .04 .19
0
.03
[1] 1s0a.b .03 .04 .04 .03 .05 .03 .17 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1mgv.a
1mly.a
1mlz.a
1mlz.b
1qj3.a
1s07.a
1s08.a
1s09.a
1s0a.b
[1] 1mgv.a
0
0.3 0.3 0.3 0.3 1.0 0.3 0.2 0.2
[1] 1mly.a 0.3
0
0.1 0.4 0.3 1.0 0.5 0.4 0.4
[1] 1mlz.a 0.3 0.1
0
0.4 0.3 1.0 0.5 0.4 0.4
[1] 1mlz.b 0.3 0.4 0.4
0
0.5 1.0 0.4 0.3 0.2
[1] 1qj3.a 0.3 0.3 0.3 0.5
0
1.0 0.5 0.4 0.5
[1] 1s07.a 1.0 1.0 1.0 1.0 1.0
0
1.0 1.0 1.0
[1] 1s08.a 0.3 0.5 0.5 0.4 0.5 1.0
0
0.3 0.3
[1] 1s09.a 0.2 0.4 0.4 0.3 0.4 1.0 0.3
0
0.2
[1] 1s0a.b 0.2 0.4 0.4 0.2 0.5 1.0 0.3 0.2
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
1mgv.a
1mly.a
1mlz.a
1mlz.b
1qj3.a
1s07.a
1s08.a
1s09.a
1s0a.b
[1] 1mgv.a
0
0.9 0.8 1.1 1.0 2.4 1.5 1.1 1.1
[1] 1mly.a 0.9
0
0.3 1.0 0.8 2.4 1.6 1.1 1.1
[1] 1mlz.a 0.8 0.3
0
1.1 0.7 2.4 1.6 1.1 1.1
[1] 1mlz.b 1.1 1.0 1.1
0
1.1 2.5 1.4 0.7 0.5
[1] 1qj3.a 1.0 0.8 0.7 1.1
0
2.4 1.5 1.2 1.2
[1] 1s07.a 2.4 2.4 2.4 2.5 2.4
0
2.7 2.5 2.5
[1] 1s08.a 1.5 1.6 1.6 1.4 1.5 2.7
0
1.2 1.3
[1] 1s09.a 1.1 1.1 1.1 0.7 1.2 2.5 1.2
0
0.5
[1] 1s0a.b 1.1 1.1 1.1 0.5 1.2 2.5 1.3 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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