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ATDA_VIBCH_1_173_allosteric

Spermidine N(1)-acetyltransferase [Acetyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ATDA_VIBCH):D: N-acetyltransferase (22, 28:31, 33:37, 41)22, 28:31, 33:37, 41

Full PDB list

4jjx, 4jly, 4mhd, 4mi4, 4mj8, 4ncz, 4r57, 4r87, 4ygo, 5cnp, 5ug4 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
N
2
2
E
3
3
E
3
4
P
3
5
Y
3
6
E
3
7
E
4
1
[1]4ncz.a none . . . . . . .
[1]4ygo.d ca1 . . . . . . .
[1]5ug4.a none . . . . . . .
[2]4mhd.a spd10 . . . . . . .
[2]4mi4.a spm14 . . . . . . .

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

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PDB.ch
A1
N
2
2
M
2
8
S
2
9
Y
3
0
W
3
1
E
3
3
E
3
4
P
3
5
Y
3
6
E
3
7
E
4
1
[1]4ncz.a . mse * . . . . . * . .
[1]4ygo.d . * * . . . . . * . .
[1]5ug4.a . * * . . . . . * . .
[2]4mhd.a . . . . . . . . . . .
[2]4mi4.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
4ncz.a is apo
4ygo.d:ca
5ug4.a is apo
4mhd.a:spd
4mi4.a:spm
[1] 4ncz.a
-
0.2 - 3.1 5.6
[1] 4ygo.d -
0.3
- 2.9 5.5
[1] 5ug4.a - 0.5
-
3.1 6.0
[2] 4mhd.a - 0.1 -
0
0
[2] 4mi4.a - 0.1 - 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4ncz.a
4ygo.d
5ug4.a
4mhd.a
4mi4.a
[1] 4ncz.a
0
.15 .11 .54 .54
[1] 4ygo.d .15
0
.20 .55 .55
[1] 5ug4.a .11 .20
0
.61 .61
[2] 4mhd.a .54 .55 .61
0
0
[2] 4mi4.a .54 .55 .61 0
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
4ncz.a
4ygo.d
5ug4.a
4mhd.a
4mi4.a
[1] 4ncz.a
0
0.4 0.4 8.6 8.9
[1] 4ygo.d 0.4
0
0.2 8.4 8.8
[1] 5ug4.a 0.4 0.2
0
8.5 8.8
[2] 4mhd.a 8.6 8.4 8.5
0
0.5
[2] 4mi4.a 8.9 8.8 8.8 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
4ncz.a
4ygo.d
5ug4.a
4mhd.a
4mi4.a
[1] 4ncz.a
0
1.0 1.2 9.9 10
[1] 4ygo.d 1.0
0
0.9 9.6 9.9
[1] 5ug4.a 1.2 0.9
0
9.6 9.9
[2] 4mhd.a 9.9 9.6 9.6
0
0.7
[2] 4mi4.a 10 9.9 9.9 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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