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AATM_CHICK_23_423

Aspartate aminotransferase, mitochondrial [Class-I pyridoxal-phosphate-dependent aminotransferase family]

Composition of the binding site

Protein chains monomer
A1 (AATM_CHICK):37, 38, 57, 58, 126:128, 131, 155, 158, 203, 208, 236, 238, 239, 269, 271, 272, 280, 374, 40037, 38, 57, 58, 126:128, 131, 155, 158, 203, 208, 236, 238, 239, 269, 271, 272, 280, 374, 400

Full PDB list

1aka, 1akb, 1akc, 1ama, 1ivr, 1map, 1maq, 1oxo, 1oxp, 1tar, 1tas, 1tat, 7aat, 8aat, 9aat (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
3
7
L
3
8
V
5
7
G
5
8
S
1
2
6
G
1
2
7
T
1
2
8
L
1
3
1
W
1
5
5
H
1
5
8
H
2
0
3
N
2
0
8
D
2
3
6
A
2
3
8
Y
2
3
9
S
2
6
9
A
2
7
1
K
2
7
2
R
2
8
0
F
3
7
4
R
4
0
0
[1]1aka.a plp16 . . . . . . . . . . . . . . . . . H . . .
[1]1aka.b none . . . . . . . . . . . . . . . . . H . . .
[1]1akb.a ppd24 . . . . . . . . . . . . . . . . . H . . .
[1]1akc.a ppe25 . . . . . . . . . . . . . . . . . H . . .
[1]1ama.a pla25 . . . . . . . . . . . . . . . . . . . . .
[1]1ivr.a cba26 . . . . . . . . . . . . . . . . . . . . .
[1]1map.a ket24 . . . . . . . . . . . . . . . . . . . . .
[1]1maq.a pgu25 . . . . . . . . . . . . . . . . . . . . .
[1]1oxp.a ik221 . . . . . . . . . . . . . . . . . . . . .
[1]1tat.a plp15 . . . . . . . . . . . . . . . . . * . . .
[1]9aat.a pmp16 . . . . . . . . . . . . . . . . . . . . .

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
I
3
7
L
3
8
V
5
7
G
5
8
S
1
2
6
G
1
2
7
T
1
2
8
L
1
3
1
W
1
5
5
H
1
5
8
H
2
0
3
N
2
0
8
D
2
3
6
A
2
3
8
Y
2
3
9
S
2
6
9
A
2
7
1
K
2
7
2
R
2
8
0
F
3
7
4
R
4
0
0
[1]1aka.a . . . . . . . . . . . . . . . . . H . . .
[1]1aka.b . . . . . . . . . . . . . . . . . H . . .
[1]1akb.a . . . . . . . . . . . . . . . . . H . . .
[1]1akc.a . . . . . . . . . . . . . . . . . H . . .
[1]1ama.a . . . . . . . . . . . . . . . . . * . . .
[1]1ivr.a . . . . . . . . . . . . . . . . . . . . .
[1]1map.a . . . . . . . . . . . . . . . . . * . . .
[1]1maq.a . . . . . . . . . . . . . . . . . . . . .
[1]1oxp.a . . . . . . . . . . . . . . . . . * . . .
[1]1tat.a . . . . . . . . . . . . . . . . . * . . .
[1]9aat.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
1aka.a:plp
1aka.b is apo
1akb.a:ppd
1akc.a:ppe
1ama.a:pla
1ivr.a:cba
1map.a:ket
1maq.a:pgu
1oxp.a:ik2
1tat.a:plp
9aat.a:pmp
[1] 1aka.a
0.4
- 0.3 0.3 0.3 0.5 0.4 0.5 0.3 0.5 0.5
[1] 1aka.b 0.4
-
0.4 0.3 0.4 0.6 0.3 0.2 0.3 0.6 0.6
[1] 1akb.a 0.1 -
0
0.1 0.1 0.2 0.2 0.1 0.2 0.3 0.5
[1] 1akc.a 0.1 - 0.3
0.3
0.3 0.5 0.3 0.3 0.2 0.5 0.6
[1] 1ama.a 0.7 - 0.3 0.3
0.2
0.4 0.3 0.3 0.1 0.7 0.9
[1] 1ivr.a 0.4 - 0.2 0.3 0.3
0.2
0.2 0.1 0.1 0.3 0.5
[1] 1map.a 0.3 - 0.1 0.2 0.5 0.3
0.1
0.1 0.1 0.2 0.7
[1] 1maq.a 0.2 - 0.1 0.1 0.3 0.1 0.1
0.2
0.1 0.1 0.5
[1] 1oxp.a 0.6 - 0.2 0.4 0.3 0.4 0.5 0.2
0.1
0.4 0.7
[1] 1tat.a 0.9 - 0.3 0.4 0.5 0.4 0.5 0.4 0.3
0.9
1.5
[1] 9aat.a 0.3 - 0.2 0.3 0.8 0.6 0.4 0.3 0.2 0.4
0.4
[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
1aka.a
1aka.b
1akb.a
1akc.a
1ama.a
1ivr.a
1map.a
1maq.a
1oxp.a
1tat.a
9aat.a
[1] 1aka.a
0
0 .03 .03 .05 .04 .06 .04 .05 .09 .04
[1] 1aka.b 0
0
.03 .02 .05 .04 .06 .04 .05 .09 .03
[1] 1akb.a .03 .03
0
.01 .04 .02 .04 .02 .03 .07 .02
[1] 1akc.a .03 .02 .01
0
.03 .02 .05 .01 .03 .08 .02
[1] 1ama.a .05 .05 .04 .03
0
.03 .03 .04 .02 .05 .02
[1] 1ivr.a .04 .04 .02 .02 .03
0
.04 .03 .01 .07 .02
[1] 1map.a .06 .06 .04 .05 .03 .04
0
.04 .03 .05 .04
[1] 1maq.a .04 .04 .02 .01 .04 .03 .04
0
.04 .07 .03
[1] 1oxp.a .05 .05 .03 .03 .02 .01 .03 .04
0
.06 .01
[1] 1tat.a .09 .09 .07 .08 .05 .07 .05 .07 .06
0
.06
[1] 9aat.a .04 .03 .02 .02 .02 .02 .04 .03 .01 .06
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
1aka.a
1aka.b
1akb.a
1akc.a
1ama.a
1ivr.a
1map.a
1maq.a
1oxp.a
1tat.a
9aat.a
[1] 1aka.a
0
0.3 1.8 1.9 1.8 1.8 1.8 1.8 1.8 1.8 0.2
[1] 1aka.b 0.3
0
1.6 1.7 1.6 1.6 1.6 1.6 1.6 1.7 0.4
[1] 1akb.a 1.8 1.6
0
0.2 0.2 0.2 0.1 0.2 0.3 0.3 1.8
[1] 1akc.a 1.9 1.7 0.2
0
0.2 0.2 0.2 0.2 0.3 0.3 1.9
[1] 1ama.a 1.8 1.6 0.2 0.2
0
0.2 0.2 0.2 0.2 0.3 1.9
[1] 1ivr.a 1.8 1.6 0.2 0.2 0.2
0
0.2 0.2 0.2 0.3 1.9
[1] 1map.a 1.8 1.6 0.1 0.2 0.2 0.2
0
0.2 0.3 0.3 1.9
[1] 1maq.a 1.8 1.6 0.2 0.2 0.2 0.2 0.2
0
0.3 0.3 1.9
[1] 1oxp.a 1.8 1.6 0.3 0.3 0.2 0.2 0.3 0.3
0
0.3 1.9
[1] 1tat.a 1.8 1.7 0.3 0.3 0.3 0.3 0.3 0.3 0.3
0
1.9
[1] 9aat.a 0.2 0.4 1.8 1.9 1.9 1.9 1.9 1.9 1.9 1.9
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

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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
1aka.a
1aka.b
1akb.a
1akc.a
1ama.a
1ivr.a
1map.a
1maq.a
1oxp.a
1tat.a
9aat.a
[1] 1aka.a
0
0.5 2.2 2.3 2.3 2.2 2.2 2.2 2.2 2.2 0.5
[1] 1aka.b 0.5
0
2.0 2.1 2.1 2.0 2.1 2.1 2.0 2.1 0.6
[1] 1akb.a 2.2 2.0
0
0.2 0.4 0.2 0.4 0.4 0.3 0.7 2.1
[1] 1akc.a 2.3 2.1 0.2
0
0.4 0.3 0.5 0.4 0.3 0.7 2.2
[1] 1ama.a 2.3 2.1 0.4 0.4
0
0.5 0.3 0.3 0.5 0.7 2.2
[1] 1ivr.a 2.2 2.0 0.2 0.3 0.5
0
0.5 0.5 0.3 0.7 2.1
[1] 1map.a 2.2 2.1 0.4 0.5 0.3 0.5
0
0.2 0.5 0.8 2.1
[1] 1maq.a 2.2 2.1 0.4 0.4 0.3 0.5 0.2
0
0.5 0.8 2.1
[1] 1oxp.a 2.2 2.0 0.3 0.3 0.5 0.3 0.5 0.5
0
0.7 2.1
[1] 1tat.a 2.2 2.1 0.7 0.7 0.7 0.7 0.8 0.8 0.7
0
2.2
[1] 9aat.a 0.5 0.6 2.1 2.2 2.2 2.1 2.1 2.1 2.1 2.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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