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AATC_HUMAN_4_413

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

Composition of the binding site

Protein chains homodimer
A1 (AATC_HUMAN):18, 19, 38, 39, 108:110, 113, 141, 142, 144, 190, 195, 223, 225, 226, 256, 258, 259, 267, 361, 38718, 19, 38, 39, 108:110, 113, 141, 142, 144, 190, 195, 223, 225, 226, 256, 258, 259, 267, 361, 387
A2 (AATC_HUMAN):71, 29371, 293

Full PDB list

1ajr, 1ajs, 3ii0, 3wzf, 5ton, 5toq, 5tor, 5tot (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
V
1
8
F
1
9
V
3
8
G
3
9
G
1
0
8
G
1
0
9
T
1
1
0
L
1
1
3
W
1
4
1
H
1
4
4
H
1
9
0
N
1
9
5
D
2
2
3
A
2
2
5
Y
2
2
6
S
2
5
6
S
2
5
8
K
2
5
9
R
2
6
7
F
3
6
1
R
3
8
7
Y
7
1
R
2
9
3
[1]1ajs.a pla25 . . . . . . . . . . . . . . . . . . . . . . .
[1]3ii0.a plp,tar26 . . . . . . . . . . . . . . . . . . . . . . .
[1]3wzf.a none . . . . . . . . . . . . . . . . . . . . . . .
[1]5ton.b plp15 - - . . . . . . . L . . . . . . . * . . . . .
[1]5toq.b plp15 - - . . . . . . . . . . . . . . . * . . . . .
[1]5tor.a plp15 . . . . . . . . . . . . T . . . . * . . . . .
[1]5tot.a plp15 . . . . . . . . . L L . . . . . . * . . . . .

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
V
1
8
F
1
9
V
3
8
G
3
9
G
1
0
8
G
1
0
9
T
1
1
0
L
1
1
3
W
1
4
1
E
1
4
2
H
1
4
4
H
1
9
0
N
1
9
5
D
2
2
3
A
2
2
5
Y
2
2
6
S
2
5
6
S
2
5
8
K
2
5
9
R
2
6
7
F
3
6
1
R
3
8
7
Y
7
1
R
2
9
3
[1]1ajs.a . . . . . . . . . . . . . . . . . . * . . . . .
[1]3ii0.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]3wzf.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ton.b - - . . . . . . . . L . . . . . . . * . . . . .
[1]5toq.b - - . . . . . . . . . . . . . . . . * . . . . .
[1]5tor.a . . . . . . . . . . . . . T . . . . * . . . . .
[1]5tot.a . . . . . . . . . . L L . . . . . . * . . . . .

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
1ajs.a:pla
3ii0.a:plp,tar
3wzf.a is apo
5ton.b:plp
5toq.b:plp
5tor.a:plp
5tot.a:plp
[1] 1ajs.a
0.2
1.0 - 0.8 0.8 1.0 0.8
[1] 3ii0.a 0.4
0.1
- 0.4 0.4 0.4 0.3
[1] 3wzf.a 1.2 0.9
-
1.4 1.4 1.2 1.2
[1] 5ton.b 0.2 1.4 -
0.6
0.6 0.7 0.9
[1] 5toq.b 0.3 1.0 - 0.6
0.6
0.8 0.7
[1] 5tor.a 0.8 1.3 - 0.6 0.5
0.8
0.5
[1] 5tot.a 0.5 1.3 - 0.7 0.7 0.7
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
1ajs.a
3ii0.a
3wzf.a
5ton.b
5toq.b
5tor.a
5tot.a
[1] 1ajs.a
0
.03 .06 .05 .03 .07 .05
[1] 3ii0.a .03
0
.05 .07 .05 .09 .07
[1] 3wzf.a .06 .05
0
.09 .08 .07 .08
[1] 5ton.b .05 .07 .09
0
.02 .05 .02
[1] 5toq.b .03 .05 .08 .02
0
.04 .02
[1] 5tor.a .07 .09 .07 .05 .04
0
.04
[1] 5tot.a .05 .07 .08 .02 .02 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1ajs.a
3ii0.a
3wzf.a
5ton.b
5toq.b
5tor.a
5tot.a
[1] 1ajs.a
0
0.3 1.4 0.8 0.8 1.4 1.5
[1] 3ii0.a 0.3
0
1.4 0.8 0.8 1.4 1.5
[1] 3wzf.a 1.4 1.4
0
0.5 0.6 0.6 0.6
[1] 5ton.b 0.8 0.8 0.5
0
0.3 0.4 0.3
[1] 5toq.b 0.8 0.8 0.6 0.3
0
0.3 0.5
[1] 5tor.a 1.4 1.4 0.6 0.4 0.3
0
0.6
[1] 5tot.a 1.5 1.5 0.6 0.3 0.5 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1ajs.a
3ii0.a
3wzf.a
5ton.b
5toq.b
5tor.a
5tot.a
[1] 1ajs.a
0
0.7 1.9 1.1 1.1 1.7 2.0
[1] 3ii0.a 0.7
0
1.9 1.0 1.2 1.8 2.0
[1] 3wzf.a 1.9 1.9
0
1.1 1.4 1.3 0.9
[1] 5ton.b 1.1 1.0 1.1
0
0.9 1.1 1.0
[1] 5toq.b 1.1 1.2 1.4 0.9
0
0.9 1.4
[1] 5tor.a 1.7 1.8 1.3 1.1 0.9
0
1.3
[1] 5tot.a 2.0 2.0 0.9 1.0 1.4 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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