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DAAA_BACYM_2_281

D-alanine aminotransferase [Class-IV pyridoxal-phosphate-dependent aminotransferase family]

Composition of the binding site

Protein chains homodimer
A1 (DAAA_BACYM):32, 34, 48, 51, 139, 146, 178:183, 202, 204:206, 240:24332, 34, 48, 51, 139, 146, 178:183, 202, 204:206, 240:243
A2 (DAAA_BACYM):99, 10199, 101

Full PDB list

1a0g, 1daa, 1g2w, 2daa, 2dab, 3daa, 3lqs, 4daa, 5daa (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
Y
3
2
V
3
4
H
4
8
R
5
1
R
1
3
9
K
1
4
6
E
1
7
8
G
1
7
9
S
1
8
0
S
1
8
1
S
1
8
2
N
1
8
3
L
2
0
2
G
2
0
4
I
2
0
5
T
2
0
6
S
2
4
1
T
2
4
2
T
2
4
3
R
9
9
H
1
0
1
[1]1a0g.a pmp16 . . . . . . . . . . . . A . . . . . . . .
[1]1g2w.a plp15 . . . . . * S . . . . . . . . . . . . . .
[1]2daa.a dcs22 . . . . . . . . . . . . . . . . . . . . .
[1]2dab.a plp15 . . . . . * . . . . . . A . . . . . . . .
[1]3daa.a pdd21 . . . . . . . . . . . . . . . . . . . . .
[1]3lqs.a psz24 . . . . . . . . . . . . . . . . . . . . .
[1]4daa.a plp15 . . . . . * . . . . . . . . . . . . . . .
[1]5daa.b plp15 . . . . . * K . . . . . . . . . . . . . .

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
3
2
V
3
4
H
4
8
R
5
1
R
1
3
9
K
1
4
6
E
1
7
8
G
1
7
9
S
1
8
0
S
1
8
1
S
1
8
2
N
1
8
3
L
2
0
2
G
2
0
4
I
2
0
5
T
2
0
6
T
2
4
0
S
2
4
1
T
2
4
2
T
2
4
3
R
9
9
H
1
0
1
[1]1a0g.a . . . . . . . . . . . . A . . . . . . . . .
[1]1g2w.a . . . . . * S . . . . . . . . . . . . . . .
[1]2daa.a . . . . . . . . . . . . . . . . . . . . . .
[1]2dab.a . . . . . * . . . . . . A . . . . . . . . .
[1]3daa.a . . . . . . . . . . . . . . . . . . . . . .
[1]3lqs.a . . . . . . . . . . . . . . . . . . . . . .
[1]4daa.a . . . . . * . . . . . . . . . . . . . . . .
[1]5daa.b . . . . . * K . . . . . . . . . . . . . . .

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
1a0g.a:pmp
1g2w.a:plp
2daa.a:dcs
2dab.a:plp
3daa.a:pdd
3lqs.a:psz
4daa.a:plp
5daa.b:plp
[1] 1a0g.a
0.1
0.4 0 0.1 0.1 0.2 0.3 0.5
[1] 1g2w.a 0.1
0.6
0 0.4 0.2 0.2 0.6 0.6
[1] 2daa.a 0.1 0.5
0
0.3 0 0.1 0.4 0.4
[1] 2dab.a 0.4 0.8 0.1
0.6
0.2 0.3 0.8 1.0
[1] 3daa.a 0.1 0.5 0 0.3
0.1
0.1 0.4 0.5
[1] 3lqs.a 0.2 0.5 0 0.1 0
0.1
0.4 0.5
[1] 4daa.a 0.1 0.9 0 0.4 0 0.2
0.6
0.9
[1] 5daa.b 0.2 0.8 0.1 0.4 0.1 0.2 0.6
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
1a0g.a
1g2w.a
2daa.a
2dab.a
3daa.a
3lqs.a
4daa.a
5daa.b
[1] 1a0g.a
0
.02 .02 .03 .02 .01 .04 .03
[1] 1g2w.a .02
0
.02 .03 .02 .04 .02 .02
[1] 2daa.a .02 .02
0
.04 0 .01 .02 .04
[1] 2dab.a .03 .03 .04
0
.04 .05 .02 .01
[1] 3daa.a .02 .02 0 .04
0
.01 .02 .04
[1] 3lqs.a .01 .04 .01 .05 .01
0
.03 .04
[1] 4daa.a .04 .02 .02 .02 .02 .03
0
.02
[1] 5daa.b .03 .02 .04 .01 .04 .04 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1a0g.a
1g2w.a
2daa.a
2dab.a
3daa.a
3lqs.a
4daa.a
5daa.b
[1] 1a0g.a
0
0.2 0.2 0.1 0.2 0.1 0.2 0.4
[1] 1g2w.a 0.2
0
0.3 0.2 0.2 0.2 0.2 0.3
[1] 2daa.a 0.2 0.3
0
0.2 0.2 0.2 0.2 0.3
[1] 2dab.a 0.1 0.2 0.2
0
0.2 0.2 0.2 0.4
[1] 3daa.a 0.2 0.2 0.2 0.2
0
0.2 0.2 0.3
[1] 3lqs.a 0.1 0.2 0.2 0.2 0.2
0
0.2 0.3
[1] 4daa.a 0.2 0.2 0.2 0.2 0.2 0.2
0
0.3
[1] 5daa.b 0.4 0.3 0.3 0.4 0.3 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1a0g.a
1g2w.a
2daa.a
2dab.a
3daa.a
3lqs.a
4daa.a
5daa.b
[1] 1a0g.a
0
0.3 0.4 0.2 0.3 0.3 0.3 0.8
[1] 1g2w.a 0.3
0
0.5 0.3 0.4 0.3 0.4 0.8
[1] 2daa.a 0.4 0.5
0
0.4 0.4 0.3 0.4 0.7
[1] 2dab.a 0.2 0.3 0.4
0
0.3 0.3 0.3 0.8
[1] 3daa.a 0.3 0.4 0.4 0.3
0
0.3 0.2 0.8
[1] 3lqs.a 0.3 0.3 0.3 0.3 0.3
0
0.4 0.8
[1] 4daa.a 0.3 0.4 0.4 0.3 0.2 0.4
0
0.8
[1] 5daa.b 0.8 0.8 0.7 0.8 0.8 0.8 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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